5Y2I | pdb_00005y2i

Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor PGMI-004A

• PDB DOI: https://doi.org/10.2210/pdb5Y2I/pdb

• Classification: ISOMERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2017-07-26 Released: 2018-08-08 
• Deposition Author(s): Jiang, L., Zhou, L.
• Funding Organization(s): NSFC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor PGMI-004A

Jiang, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.53 kDa 
• Atom Count: 4,082 
• Modeled Residue Count: 467 
• 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
8KX (Subject of Investigation/LOI)	C [auth B]	3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)-~{N}-[4-(trifluoromethyl)phenyl]anthracene-2-sulfonamide C21 H12 F3 N O6 S XKVNBCMGEUDKNP-UHFFFAOYSA-N
MES	E [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CL	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
8KX	BindingDB:  5Y2I	Ki: 3910 (nM) from 1 assay(s)
		Kd: 7200 (nM) from 1 assay(s)
		IC50: min: 1.13e+4, max: 2.00e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.762	α = 90
b = 85.036	β = 90
c = 102.48	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Jiang, L., Zhou, L.

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Funding Organization	Location	Grant Number
NSFC	China	21472026

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description