8ZN9 | pdb_00008zn9

A vast marine sulfonate-based carbon cycle fueled by novel sulfoquinovosidases

PDB DOI: https://doi.org/10.2210/pdb8ZN9/pdb

Classification: PROTEIN BINDING
Organism(s): Roseobacter denitrificans OCh 114
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-26 Released: 2025-08-27
Deposition Author(s): Tang, K., Ma, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.238 (Depositor), 0.236 (DCC)
R-Value Work:
0.219 (Depositor), 0.218 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A vast marine sulfonate-based carbon cycle fueled by novel sulfoquinovosidases

Ma, X., Tang, K.

To be published.

Macromolecule Content

Total Structure Weight: 272.57 kDa
Atom Count: 19,937
Modeled Residue Count: 2,203
Deposited Residue Count: 2,400
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, putative	A, B, C, D, E A, B, C, D, E, F	400	Roseobacter denitrificans OCh 114	Mutation(s): 0 Gene Names: RD1_2308
UniProt
Find proteins for Q167F5 (Roseobacter denitrificans (strain ATCC 33942 / OCh 114)) Explore Q167F5 Go to UniProtKB: Q167F5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q167F5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain VA [auth D] SDF format, chain TB [auth F] SDF format, chain T [auth B] SDF format, chain JA [auth C] SDF format, chain IB [auth E] SDF format, chain G [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain TB [auth F] MOL2 format, chain T [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain G [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain TB [auth F] mmCIF format, chain T [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain IB [auth E] mmCIF format, chain G [auth A]	G [auth A] IB [auth E] JA [auth C] T [auth B] TB [auth F] G [auth A], IB [auth E], JA [auth C], T [auth B], TB [auth F], VA [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain IB [auth E] Focus chain JA [auth C] Focus chain T [auth B] Focus chain TB [auth F] Focus chain VA [auth D] Interactions & Density Focus chain G [auth A] Focus chain IB [auth E] Focus chain JA [auth C] Focus chain T [auth B] Focus chain TB [auth F] Focus chain VA [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain ZB [auth F] SDF format, chain ZA [auth D] SDF format, chain Z [auth B] SDF format, chain YB [auth F] SDF format, chain YA [auth D] SDF format, chain Y [auth B] SDF format, chain XB [auth F] SDF format, chain XA [auth D] SDF format, chain X [auth B] SDF format, chain WB [auth F] SDF format, chain WA [auth D] SDF format, chain W [auth B] SDF format, chain VB [auth F] SDF format, chain V [auth B] SDF format, chain UB [auth F] SDF format, chain UA [auth C] SDF format, chain U [auth B] SDF format, chain TA [auth C] SDF format, chain SB [auth E] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RB [auth E] SDF format, chain RA [auth C] SDF format, chain R [auth A] SDF format, chain QB [auth E] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PB [auth E] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OB [auth E] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NB [auth E] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain MB [auth E] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain LB [auth E] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain KB [auth E] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JB [auth E] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HB [auth D] SDF format, chain HA [auth B] SDF format, chain H [auth A] SDF format, chain GB [auth D] SDF format, chain GA [auth B] SDF format, chain FB [auth D] SDF format, chain FA [auth B] SDF format, chain EC [auth F] SDF format, chain EB [auth D] SDF format, chain EA [auth B] SDF format, chain DC [auth F] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CC [auth F] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BC [auth F] SDF format, chain BB [auth D] SDF format, chain BA [auth B] SDF format, chain AC [auth F] SDF format, chain AB [auth D] SDF format, chain AA [auth B] MOL2 format, chain ZB [auth F] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain YB [auth F] MOL2 format, chain YA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain XB [auth F] MOL2 format, chain XA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain WB [auth F] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain VB [auth F] MOL2 format, chain V [auth B] MOL2 format, chain UB [auth F] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain SB [auth E] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RB [auth E] MOL2 format, chain RA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QB [auth E] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PB [auth E] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth E] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth E] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth E] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth E] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth E] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain EC [auth F] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain DC [auth F] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CC [auth F] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BC [auth F] MOL2 format, chain BB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain AC [auth F] MOL2 format, chain AB [auth D] MOL2 format, chain AA [auth B] mmCIF format, chain ZB [auth F] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain YB [auth F] mmCIF format, chain YA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain XB [auth F] mmCIF format, chain XA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain WB [auth F] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain VB [auth F] mmCIF format, chain V [auth B] mmCIF format, chain UB [auth F] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain SB [auth E] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RB [auth E] mmCIF format, chain RA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QB [auth E] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PB [auth E] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth E] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth E] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth E] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth E] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth E] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth E] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain EC [auth F] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain DC [auth F] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CC [auth F] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BC [auth F] mmCIF format, chain BB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain AC [auth F] mmCIF format, chain AB [auth D] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth D] AC [auth F] BA [auth B] BB [auth D] AA [auth B], AB [auth D], AC [auth F], BA [auth B], BB [auth D], BC [auth F], CA [auth B], CB [auth D], CC [auth F], DA [auth B], DB [auth D], DC [auth F], EA [auth B], EB [auth D], EC [auth F], FA [auth B], FB [auth D], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth D], I [auth A], IA [auth B], J [auth A], JB [auth E], K [auth A], KA [auth C], KB [auth E], L [auth A], LA [auth C], LB [auth E], M [auth A], MA [auth C], MB [auth E], N [auth A], NA [auth C], NB [auth E], O [auth A], OA [auth C], OB [auth E], P [auth A], PA [auth C], PB [auth E], Q [auth A], QA [auth C], QB [auth E], R [auth A], RA [auth C], RB [auth E], S [auth A], SA [auth C], SB [auth E], TA [auth C], U [auth B], UA [auth C], UB [auth F], V [auth B], VB [auth F], W [auth B], WA [auth D], WB [auth F], X [auth B], XA [auth D], XB [auth F], Y [auth B], YA [auth D], YB [auth F], Z [auth B], ZA [auth D], ZB [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain AC [auth F] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain BC [auth F] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain EC [auth F] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JB [auth E] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain UB [auth F] Focus chain V [auth B] Focus chain VB [auth F] Focus chain W [auth B] Focus chain WA [auth D] Focus chain WB [auth F] Focus chain X [auth B] Focus chain XA [auth D] Focus chain XB [auth F] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain Z [auth B] Focus chain ZA [auth D] Focus chain ZB [auth F] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain AC [auth F] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain BC [auth F] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain EC [auth F] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JB [auth E] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain UB [auth F] Focus chain V [auth B] Focus chain VB [auth F] Focus chain W [auth B] Focus chain WA [auth D] Focus chain WB [auth F] Focus chain X [auth B] Focus chain XA [auth D] Focus chain XB [auth F] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain Z [auth B] Focus chain ZA [auth D] Focus chain ZB [auth F]