8YUH | pdb_00008yuh

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with allosamidin

PDB DOI: https://doi.org/10.2210/pdb8YUH/pdb

Classification: HYDROLASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-27 Released: 2025-04-02
Deposition Author(s): Ebi, S., Sunagawa, N., Yamaguchi, S., Igarashi, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.170 (Depositor), 0.169 (DCC)
R-Value Work:
0.154 (Depositor), 0.153 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with allosamidin

Ebi, S., Igarashi, K.

To be published.

Macromolecule Content

Total Structure Weight: 124.58 kDa
Atom Count: 10,930
Modeled Residue Count: 998
Deposited Residue Count: 1,022
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase B	A, B	511	Serratia marcescens	Mutation(s): 0 Gene Names: chiB EC: 3.2.1.14
UniProt
Find proteins for P11797 (Serratia marcescens) Explore P11797 Go to UniProtKB: P11797
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11797
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose	C, D, E, F	2		N/A	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G77950XB GlyCosmos: G77950XB

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMI (Subject of Investigation/LOI) Query on AMI Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain JC [auth B] SDF format, chain LC [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain JC [auth B] MOL2 format, chain LC [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain JC [auth B] mmCIF format, chain LC [auth B]	EA [auth A], FA [auth A], JC [auth B], LC [auth B]	ALLOSAMIZOLINE C₉ H₁₆ N₂ O₄ MKJAYSJDHSEFRI-PVFLNQBWSA-N		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Focus chain JC [auth B] Focus chain LC [auth B] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth A] Focus chain JC [auth B] Focus chain LC [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain GB [auth A] SDF format, chain HB [auth A] SDF format, chain PC [auth B] SDF format, chain R [auth A] SDF format, chain U [auth A] SDF format, chain XB [auth B] MOL2 format, chain GB [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain PC [auth B] MOL2 format, chain R [auth A] MOL2 format, chain U [auth A] MOL2 format, chain XB [auth B] mmCIF format, chain GB [auth A] mmCIF format, chain HB [auth A] mmCIF format, chain PC [auth B] mmCIF format, chain R [auth A] mmCIF format, chain U [auth A] mmCIF format, chain XB [auth B]	GB [auth A] HB [auth A] PC [auth B] R [auth A] U [auth A] GB [auth A], HB [auth A], PC [auth B], R [auth A], U [auth A], XB [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GB [auth A] Focus chain HB [auth A] Focus chain PC [auth B] Focus chain R [auth A] Focus chain U [auth A] Focus chain XB [auth B] Interactions & Density Focus chain GB [auth A] Focus chain HB [auth A] Focus chain PC [auth B] Focus chain R [auth A] Focus chain U [auth A] Focus chain XB [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AC [auth B] SDF format, chain AD [auth B] SDF format, chain BC [auth B] SDF format, chain BD [auth B] SDF format, chain CC [auth B] SDF format, chain DC [auth B] SDF format, chain EC [auth B] SDF format, chain FB [auth A] SDF format, chain FC [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain IB [auth A] SDF format, chain ID [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain JD [auth B] SDF format, chain K [auth A] SDF format, chain KD [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MB [auth B] SDF format, chain N [auth A] SDF format, chain NB [auth B] SDF format, chain O [auth A] SDF format, chain OB [auth B] SDF format, chain OC [auth B] SDF format, chain P [auth A] SDF format, chain PB [auth B] SDF format, chain Q [auth A] SDF format, chain QB [auth B] SDF format, chain QC [auth B] SDF format, chain RB [auth B] SDF format, chain S [auth A] SDF format, chain SB [auth B] SDF format, chain SC [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth A] SDF format, chain TB [auth B] SDF format, chain UB [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth A] SDF format, chain VB [auth B] SDF format, chain W [auth A] SDF format, chain WB [auth B] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain YB [auth B] SDF format, chain Z [auth A] SDF format, chain ZB [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain AD [auth B] MOL2 format, chain BC [auth B] MOL2 format, chain BD [auth B] MOL2 format, chain CC [auth B] MOL2 format, chain DC [auth B] MOL2 format, chain EC [auth B] MOL2 format, chain FB [auth A] MOL2 format, chain FC [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain ID [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JD [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KD [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain OC [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain QC [auth B] MOL2 format, chain RB [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain SC [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth B] MOL2 format, chain UB [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WB [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZB [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AC [auth B] mmCIF format, chain AD [auth B] mmCIF format, chain BC [auth B] mmCIF format, chain BD [auth B] mmCIF format, chain CC [auth B] mmCIF format, chain DC [auth B] mmCIF format, chain EC [auth B] mmCIF format, chain FB [auth A] mmCIF format, chain FC [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth A] mmCIF format, chain ID [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain JD [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KD [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth B] mmCIF format, chain OC [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth B] mmCIF format, chain QC [auth B] mmCIF format, chain RB [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SB [auth B] mmCIF format, chain SC [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth B] mmCIF format, chain UB [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain VB [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WB [auth B] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZB [auth B]	AA [auth A] AC [auth B] AD [auth B] BC [auth B] BD [auth B] AA [auth A], AC [auth B], AD [auth B], BC [auth B], BD [auth B], CC [auth B], DC [auth B], EC [auth B], FB [auth A], FC [auth B], G [auth A], H [auth A], I [auth A], IA [auth A], IB [auth A], ID [auth B], J [auth A], JA [auth A], JD [auth B], K [auth A], KD [auth B], L [auth A], M [auth A], MB [auth B], N [auth A], NB [auth B], O [auth A], OB [auth B], OC [auth B], P [auth A], PB [auth B], Q [auth A], QB [auth B], QC [auth B], RB [auth B], S [auth A], SB [auth B], SC [auth B], T [auth A], TA [auth A], TB [auth B], UB [auth B], V [auth A], VA [auth A], VB [auth B], W [auth A], WB [auth B], X [auth A], Y [auth A], YB [auth B], Z [auth A], ZB [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AC [auth B] Focus chain AD [auth B] Focus chain BC [auth B] Focus chain BD [auth B] Focus chain CC [auth B] Focus chain DC [auth B] Focus chain EC [auth B] Focus chain FB [auth A] Focus chain FC [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth A] Focus chain ID [auth B] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JD [auth B] Focus chain K [auth A] Focus chain KD [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OB [auth B] Focus chain OC [auth B] Focus chain P [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QB [auth B] Focus chain QC [auth B] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SB [auth B] Focus chain SC [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WB [auth B] Focus chain X [auth A] Focus chain Y [auth A] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZB [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AC [auth B] Focus chain AD [auth B] Focus chain BC [auth B] Focus chain BD [auth B] Focus chain CC [auth B] Focus chain DC [auth B] Focus chain EC [auth B] Focus chain FB [auth A] Focus chain FC [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth A] Focus chain ID [auth B] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JD [auth B] Focus chain K [auth A] Focus chain KD [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OB [auth B] Focus chain OC [auth B] Focus chain P [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QB [auth B] Focus chain QC [auth B] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SB [auth B] Focus chain SC [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WB [auth B] Focus chain X [auth A] Focus chain Y [auth A] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZB [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain BA [auth A] SDF format, chain BB [auth A] SDF format, chain CA [auth A] SDF format, chain CB [auth A] SDF format, chain CD [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth A] SDF format, chain DD [auth B] SDF format, chain EB [auth A] SDF format, chain ED [auth B] SDF format, chain FD [auth B] SDF format, chain GA [auth A] SDF format, chain GC [auth B] SDF format, chain GD [auth B] SDF format, chain HA [auth A] SDF format, chain HC [auth B] SDF format, chain HD [auth B] SDF format, chain IC [auth B] SDF format, chain JB [auth A] SDF format, chain KA [auth A] SDF format, chain KB [auth A] SDF format, chain KC [auth B] SDF format, chain LA [auth A] SDF format, chain LB [auth A] SDF format, chain LD [auth B] SDF format, chain MA [auth A] SDF format, chain MC [auth B] SDF format, chain NA [auth A] SDF format, chain NC [auth B] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain RC [auth B] SDF format, chain SA [auth A] SDF format, chain TC [auth B] SDF format, chain UA [auth A] SDF format, chain UC [auth B] SDF format, chain VC [auth B] SDF format, chain WA [auth A] SDF format, chain WC [auth B] SDF format, chain XA [auth A] SDF format, chain XC [auth B] SDF format, chain YA [auth A] SDF format, chain YC [auth B] SDF format, chain ZA [auth A] SDF format, chain ZC [auth B] MOL2 format, chain AB [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain CD [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain DD [auth B] MOL2 format, chain EB [auth A] MOL2 format, chain ED [auth B] MOL2 format, chain FD [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GC [auth B] MOL2 format, chain GD [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HC [auth B] MOL2 format, chain HD [auth B] MOL2 format, chain IC [auth B] MOL2 format, chain JB [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain KC [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth A] MOL2 format, chain LD [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain MC [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain NC [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain RC [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain TC [auth B] MOL2 format, chain UA [auth A] MOL2 format, chain UC [auth B] MOL2 format, chain VC [auth B] MOL2 format, chain WA [auth A] MOL2 format, chain WC [auth B] MOL2 format, chain XA [auth A] MOL2 format, chain XC [auth B] MOL2 format, chain YA [auth A] MOL2 format, chain YC [auth B] MOL2 format, chain ZA [auth A] MOL2 format, chain ZC [auth B] mmCIF format, chain AB [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth A] mmCIF format, chain CD [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth A] mmCIF format, chain DD [auth B] mmCIF format, chain EB [auth A] mmCIF format, chain ED [auth B] mmCIF format, chain FD [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain GC [auth B] mmCIF format, chain GD [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain HC [auth B] mmCIF format, chain HD [auth B] mmCIF format, chain IC [auth B] mmCIF format, chain JB [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth A] mmCIF format, chain KC [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth A] mmCIF format, chain LD [auth B] mmCIF format, chain MA [auth A] mmCIF format, chain MC [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain NC [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain RC [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain TC [auth B] mmCIF format, chain UA [auth A] mmCIF format, chain UC [auth B] mmCIF format, chain VC [auth B] mmCIF format, chain WA [auth A] mmCIF format, chain WC [auth B] mmCIF format, chain XA [auth A] mmCIF format, chain XC [auth B] mmCIF format, chain YA [auth A] mmCIF format, chain YC [auth B] mmCIF format, chain ZA [auth A] mmCIF format, chain ZC [auth B]	AB [auth A] BA [auth A] BB [auth A] CA [auth A] CB [auth A] AB [auth A], BA [auth A], BB [auth A], CA [auth A], CB [auth A], CD [auth B], DA [auth A], DB [auth A], DD [auth B], EB [auth A], ED [auth B], FD [auth B], GA [auth A], GC [auth B], GD [auth B], HA [auth A], HC [auth B], HD [auth B], IC [auth B], JB [auth A], KA [auth A], KB [auth A], KC [auth B], LA [auth A], LB [auth A], LD [auth B], MA [auth A], MC [auth B], NA [auth A], NC [auth B], OA [auth A], PA [auth A], QA [auth A], RA [auth A], RC [auth B], SA [auth A], TC [auth B], UA [auth A], UC [auth B], VC [auth B], WA [auth A], WC [auth B], XA [auth A], XC [auth B], YA [auth A], YC [auth B], ZA [auth A], ZC [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AB [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain CD [auth B] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain DD [auth B] Focus chain EB [auth A] Focus chain ED [auth B] Focus chain FD [auth B] Focus chain GA [auth A] Focus chain GC [auth B] Focus chain GD [auth B] Focus chain HA [auth A] Focus chain HC [auth B] Focus chain HD [auth B] Focus chain IC [auth B] Focus chain JB [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain KC [auth B] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LD [auth B] Focus chain MA [auth A] Focus chain MC [auth B] Focus chain NA [auth A] Focus chain NC [auth B] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain RC [auth B] Focus chain SA [auth A] Focus chain TC [auth B] Focus chain UA [auth A] Focus chain UC [auth B] Focus chain VC [auth B] Focus chain WA [auth A] Focus chain WC [auth B] Focus chain XA [auth A] Focus chain XC [auth B] Focus chain YA [auth A] Focus chain YC [auth B] Focus chain ZA [auth A] Focus chain ZC [auth B] Interactions & Density Focus chain AB [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain CD [auth B] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain DD [auth B] Focus chain EB [auth A] Focus chain ED [auth B] Focus chain FD [auth B] Focus chain GA [auth A] Focus chain GC [auth B] Focus chain GD [auth B] Focus chain HA [auth A] Focus chain HC [auth B] Focus chain HD [auth B] Focus chain IC [auth B] Focus chain JB [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain KC [auth B] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LD [auth B] Focus chain MA [auth A] Focus chain MC [auth B] Focus chain NA [auth A] Focus chain NC [auth B] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain RC [auth B] Focus chain SA [auth A] Focus chain TC [auth B] Focus chain UA [auth A] Focus chain UC [auth B] Focus chain VC [auth B] Focus chain WA [auth A] Focus chain WC [auth B] Focus chain XA [auth A] Focus chain XC [auth B] Focus chain YA [auth A] Focus chain YC [auth B] Focus chain ZA [auth A] Focus chain ZC [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000468 Query on PRD_000468	C, D, E, F	Allosamidin	Oligosaccharide / Inhibitor		Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F