8ITB | pdb_00008itb

Phosphoglycerate mutase 1 complexed with a compound

• PDB DOI: https://doi.org/10.2210/pdb8ITB/pdb

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


• Deposited: 2023-03-22 Released: 2024-03-27 
• Deposition Author(s): Zhou, L., Jiang, L.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Phosphoglycerate mutase 1 complexed with a compound

Zhou, L., Jiang, L.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: 61.06 kDa 
• Atom Count: 4,002 
• Modeled Residue Count: 470 
• 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, CDABP0006 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q9R (Subject of Investigation/LOI)	E [auth C], F [auth C]	5-(3-chloranyl-4-fluoranyl-phenyl)-2-oxidanyl-3-[(4-phenylphenyl)sulfonylamino]benzoic acid C25 H17 Cl F N O5 S RNWNKFVHTIUWBB-UHFFFAOYSA-N
MES	D [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CL	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.956	α = 90
b = 89.336	β = 90
c = 93.048	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Zhou, L., Jiang, L.L.

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

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release