7XB7

Phosphoglycerate mutase 1 complexed with a covalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7XB7/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-21 Released: 2023-09-27 
• Deposition Author(s): Jiang, L.L., Zhou, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Literature

Phosphoglycerate mutase 1 complexed with a covalent inhibitor

Jiang, L.L., Zhou, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 60.74 kDa 
• Atom Count: 4,268 
• Modelled Residue Count: 482 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase 1	A [auth B], B [auth C]	262	Homo sapiens	Mutation(s): 0  Gene Names: PGAM1, PGAMA EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P18669 (Homo sapiens) Explore P18669  Go to UniProtKB:  P18669
PHAROS:  P18669 GTEx:  ENSG00000171314

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CKF (Subject of Investigation/LOI)	D [auth B], E [auth C]	3-[[5-(cyclopenten-1-yl)-2-(methylcarbamoyl)phenyl]sulfamoyl]benzenesulfonic acid C19 H20 N2 O6 S2 SVYGDMRPUQQJMH-UHFFFAOYSA-N
CL	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.276	α = 90
b = 72.959	β = 90
c = 167.956	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Jiang, L.L., Zhou, L.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22077019

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary