8ITD

Phosphoglycerate mutase 1 complexed with a compound

• PDB DOI: https://doi.org/10.2210/pdb8ITD/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: 1.90 Å
• R-Value Free: 0.197 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

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: 60.54 kDa 
• Atom Count: 4,367 
• Modelled Residue Count: 475 
• 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
QA3 (Subject of Investigation/LOI)	E [auth C]	4-(4-chloranyl-2-oxidanyl-phenyl)-2-[(4-phenylphenyl)sulfonylamino]benzoic acid C25 H18 Cl N O5 S FXWQMXHEUOMIKE-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: 1.90 Å
• R-Value Free: 0.197 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.544	α = 90
b = 85.99	β = 90
c = 101.383	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