9KPV | pdb_00009kpv

Crystal structure of enzyme

• PDB DOI: https://doi.org/10.2210/pdb9KPV/pdb

• Classification: LIGASE/ANTIBIOTIC
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-24 Released: 2025-12-24 
• Deposition Author(s): Li, L., Lin, L.Y., Liu, C., Hao, Z.Y., Zhang, J., Xiang, W.S., Yuchi, Z.G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.274 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of enzyme

Li, H., Li, L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 236.74 kDa 
• Atom Count: 15,041 
• Modeled Residue Count: 1,945 
• Deposited Residue Count: 2,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP synthase [glutamine-hydrolyzing]	A, B, C, D	525	Escherichia coli K-12	Mutation(s): 0  Gene Names: guaA, BWG_2271 EC: 6.3.5.2
UniProt
Find proteins for C4ZX82 (Escherichia coli (strain K12 / MC4100 / BW2952)) Explore C4ZX82  Go to UniProtKB:  C4ZX82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XMP	E [auth A], F [auth B], G [auth C], I [auth D]	XANTHOSINE-5'-MONOPHOSPHATE C10 H14 N4 O9 P DCTLYFZHFGENCW-UUOKFMHZSA-O
A1L67 (Subject of Investigation/LOI)	H [auth C]	(2~{R},3~{R},4~{R})-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylidene-oxolane-3,4-diol C11 H13 N5 O4 UZSSGAOAYPICBZ-VAOFZXAKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.274 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.343	α = 90
b = 78.803	β = 123.68
c = 167.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Li, L., Lin, L.Y., Liu, C., Hao, Z.Y., Zhang, J., Xiang, W.S., Yuchi, Z.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release
  
• Version 1.1: 2026-01-21
  Changes: Database references, Structure summary