9KQ7 | pdb_00009kq7

The structure of the YcfA from Erwinia amylovora bound with ATP

PDB DOI: https://doi.org/10.2210/pdb9KQ7/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: 2.84 Å
R-Value Free:
0.252 (Depositor), 0.254 (DCC)
R-Value Work:
0.210 (Depositor), 0.218 (DCC)
R-Value Observed:
0.212 (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

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: 373.03 kDa
Atom Count: 24,784
Modeled Residue Count: 3,064
Deposited Residue Count: 3,276
Unique protein chains: 1

Macromolecules

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(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 E] C [auth G] D [auth I] E [auth J] A [auth B], B [auth E], C [auth G], D [auth I], E [auth J], F [auth L], G [auth M], H [auth A], I [auth C], J [auth D], K [auth F], L [auth H], M [auth K], 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain AA [auth K] SDF format, chain BA [auth N] SDF format, chain O [auth B] SDF format, chain P [auth E] SDF format, chain Q [auth G] SDF format, chain R [auth I] SDF format, chain S [auth J] SDF format, chain T [auth L] SDF format, chain U [auth M] SDF format, chain V [auth A] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth F] SDF format, chain Z [auth H] MOL2 format, chain AA [auth K] MOL2 format, chain BA [auth N] MOL2 format, chain O [auth B] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth I] MOL2 format, chain S [auth J] MOL2 format, chain T [auth L] MOL2 format, chain U [auth M] MOL2 format, chain V [auth A] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth H] mmCIF format, chain AA [auth K] mmCIF format, chain BA [auth N] mmCIF format, chain O [auth B] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth I] mmCIF format, chain S [auth J] mmCIF format, chain T [auth L] mmCIF format, chain U [auth M] mmCIF format, chain V [auth A] mmCIF format, chain W [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth H]	AA [auth K] BA [auth N] O [auth B] P [auth E] Q [auth G] AA [auth K], BA [auth N], O [auth B], P [auth E], Q [auth G], R [auth I], S [auth J], T [auth L], U [auth M], V [auth A], W [auth C], X [auth D], Y [auth F], Z [auth H]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth N] Focus chain O [auth B] Focus chain P [auth E] Focus chain Q [auth G] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth L] Focus chain U [auth M] Focus chain V [auth A] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth F] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth N] Focus chain O [auth B] Focus chain P [auth E] Focus chain Q [auth G] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth L] Focus chain U [auth M] Focus chain V [auth A] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth F] Focus chain Z [auth H]