9KQD | pdb_00009kqd

YcfA-D19A-ATP-GTP complex

PDB DOI: https://doi.org/10.2210/pdb9KQD/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Erwinia amylovora ATCC 49946
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-25 Released: 2025-10-01
Deposition Author(s): Zhang, L., Dou, C., Zheng, Y.H., Zhu, X.F., Cheng, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.192 (Depositor), 0.201 (DCC)
R-Value Work:
0.166 (Depositor), 0.179 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: in silico
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

The Mechanism of Thioamide Formation by the YcfA-YcfC System in 6-Thioguanine Biosynthesis

Zhang, L., Dou, C., Zheng, Y.H., Zhu, X.F., Cheng, W.

(2025) Nat Commun

DOI: https://doi.org/10.1038/s41467-025-63937-7

Macromolecule Content

Total Structure Weight: 380.7 kDa
Atom Count: 27,628
Modeled Residue Count: 3,092
Deposited Residue Count: 3,276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asparagine synthetase domain-containing protein	A [auth B] B [auth D] C [auth G] D [auth I] E [auth J] A [auth B], B [auth D], C [auth G], D [auth I], E [auth J], F [auth K], G [auth M], H [auth A], I [auth C], J [auth E], K [auth F], L [auth H], M [auth L], N	234	Erwinia amylovora ATCC 49946	Mutation(s): 0 Gene Names: BN437_1047
UniProt
Find proteins for A0A831ERP2 (Erwinia amylovora NBRC 12687 = CFBP 1232) Explore A0A831ERP2 Go to UniProtKB: A0A831ERP2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A831ERP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain BA [auth J] SDF format, chain CB [auth N] SDF format, chain EA [auth K] SDF format, chain HA [auth M] SDF format, chain KA [auth A] SDF format, chain NA [auth C] SDF format, chain P [auth B] SDF format, chain QA [auth E] SDF format, chain S [auth D] SDF format, chain TA [auth F] SDF format, chain V [auth G] SDF format, chain WA [auth H] SDF format, chain Y [auth I] SDF format, chain ZA [auth L] MOL2 format, chain BA [auth J] MOL2 format, chain CB [auth N] MOL2 format, chain EA [auth K] MOL2 format, chain HA [auth M] MOL2 format, chain KA [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain S [auth D] MOL2 format, chain TA [auth F] MOL2 format, chain V [auth G] MOL2 format, chain WA [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain ZA [auth L] mmCIF format, chain BA [auth J] mmCIF format, chain CB [auth N] mmCIF format, chain EA [auth K] mmCIF format, chain HA [auth M] mmCIF format, chain KA [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain S [auth D] mmCIF format, chain TA [auth F] mmCIF format, chain V [auth G] mmCIF format, chain WA [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain ZA [auth L]	BA [auth J] CB [auth N] EA [auth K] HA [auth M] KA [auth A] BA [auth J], CB [auth N], EA [auth K], HA [auth M], KA [auth A], NA [auth C], P [auth B], QA [auth E], S [auth D], TA [auth F], V [auth G], WA [auth H], Y [auth I], ZA [auth L]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain BA [auth J] Focus chain CB [auth N] Focus chain EA [auth K] Focus chain HA [auth M] Focus chain KA [auth A] Focus chain NA [auth C] Focus chain P [auth B] Focus chain QA [auth E] Focus chain S [auth D] Focus chain TA [auth F] Focus chain V [auth G] Focus chain WA [auth H] Focus chain Y [auth I] Focus chain ZA [auth L] Interactions & Density Focus chain BA [auth J] Focus chain CB [auth N] Focus chain EA [auth K] Focus chain HA [auth M] Focus chain KA [auth A] Focus chain NA [auth C] Focus chain P [auth B] Focus chain QA [auth E] Focus chain S [auth D] Focus chain TA [auth F] Focus chain V [auth G] Focus chain WA [auth H] Focus chain Y [auth I] Focus chain ZA [auth L]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BB [auth N] SDF format, chain DA [auth K] SDF format, chain GA [auth M] SDF format, chain JA [auth A] SDF format, chain MA [auth C] SDF format, chain O [auth B] SDF format, chain PA [auth E] SDF format, chain R [auth D] SDF format, chain SA [auth F] SDF format, chain U [auth G] SDF format, chain VA [auth H] SDF format, chain X [auth I] SDF format, chain YA [auth L] MOL2 format, chain AA [auth J] MOL2 format, chain BB [auth N] MOL2 format, chain DA [auth K] MOL2 format, chain GA [auth M] MOL2 format, chain JA [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain R [auth D] MOL2 format, chain SA [auth F] MOL2 format, chain U [auth G] MOL2 format, chain VA [auth H] MOL2 format, chain X [auth I] MOL2 format, chain YA [auth L] mmCIF format, chain AA [auth J] mmCIF format, chain BB [auth N] mmCIF format, chain DA [auth K] mmCIF format, chain GA [auth M] mmCIF format, chain JA [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain O [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain R [auth D] mmCIF format, chain SA [auth F] mmCIF format, chain U [auth G] mmCIF format, chain VA [auth H] mmCIF format, chain X [auth I] mmCIF format, chain YA [auth L]	AA [auth J] BB [auth N] DA [auth K] GA [auth M] JA [auth A] AA [auth J], BB [auth N], DA [auth K], GA [auth M], JA [auth A], MA [auth C], O [auth B], PA [auth E], R [auth D], SA [auth F], U [auth G], VA [auth H], X [auth I], YA [auth L]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth J] Focus chain BB [auth N] Focus chain DA [auth K] Focus chain GA [auth M] Focus chain JA [auth A] Focus chain MA [auth C] Focus chain O [auth B] Focus chain PA [auth E] Focus chain R [auth D] Focus chain SA [auth F] Focus chain U [auth G] Focus chain VA [auth H] Focus chain X [auth I] Focus chain YA [auth L] Interactions & Density Focus chain AA [auth J] Focus chain BB [auth N] Focus chain DA [auth K] Focus chain GA [auth M] Focus chain JA [auth A] Focus chain MA [auth C] Focus chain O [auth B] Focus chain PA [auth E] Focus chain R [auth D] Focus chain SA [auth F] Focus chain U [auth G] Focus chain VA [auth H] Focus chain X [auth I] Focus chain YA [auth L]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain CA [auth J] SDF format, chain DB [auth N] SDF format, chain FA [auth K] SDF format, chain IA [auth M] SDF format, chain LA [auth A] SDF format, chain OA [auth C] SDF format, chain Q [auth B] SDF format, chain RA [auth E] SDF format, chain T [auth D] SDF format, chain UA [auth F] SDF format, chain W [auth G] SDF format, chain XA [auth H] SDF format, chain Z [auth I] MOL2 format, chain AB [auth L] MOL2 format, chain CA [auth J] MOL2 format, chain DB [auth N] MOL2 format, chain FA [auth K] MOL2 format, chain IA [auth M] MOL2 format, chain LA [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain T [auth D] MOL2 format, chain UA [auth F] MOL2 format, chain W [auth G] MOL2 format, chain XA [auth H] MOL2 format, chain Z [auth I] mmCIF format, chain AB [auth L] mmCIF format, chain CA [auth J] mmCIF format, chain DB [auth N] mmCIF format, chain FA [auth K] mmCIF format, chain IA [auth M] mmCIF format, chain LA [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain T [auth D] mmCIF format, chain UA [auth F] mmCIF format, chain W [auth G] mmCIF format, chain XA [auth H] mmCIF format, chain Z [auth I]	AB [auth L] CA [auth J] DB [auth N] FA [auth K] IA [auth M] AB [auth L], CA [auth J], DB [auth N], FA [auth K], IA [auth M], LA [auth A], OA [auth C], Q [auth B], RA [auth E], T [auth D], UA [auth F], W [auth G], XA [auth H], Z [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth L] Focus chain CA [auth J] Focus chain DB [auth N] Focus chain FA [auth K] Focus chain IA [auth M] Focus chain LA [auth A] Focus chain OA [auth C] Focus chain Q [auth B] Focus chain RA [auth E] Focus chain T [auth D] Focus chain UA [auth F] Focus chain W [auth G] Focus chain XA [auth H] Focus chain Z [auth I] Interactions & Density Focus chain AB [auth L] Focus chain CA [auth J] Focus chain DB [auth N] Focus chain FA [auth K] Focus chain IA [auth M] Focus chain LA [auth A] Focus chain OA [auth C] Focus chain Q [auth B] Focus chain RA [auth E] Focus chain T [auth D] Focus chain UA [auth F] Focus chain W [auth G] Focus chain XA [auth H] Focus chain Z [auth I]