5Y64 | pdb_00005y64

Phosphoglycerate mutase 1 H11 phosphorylated form complexed with KH1

• PDB DOI: https://doi.org/10.2210/pdb5Y64/pdb

• Classification: ISOMERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-10 Released: 2018-12-05 
• Deposition Author(s): Zhou, L., Jiang, L.L.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Phosphoglycerate mutase 1 H11 phosphorylated form complexed with KH1

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.55 kDa 
• Atom Count: 3,957 
• Modeled Residue Count: 467 
• Deposited Residue Count: 524 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase 1	A [auth B]	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase 1	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
8LF (Subject of Investigation/LOI)	E [auth C]	~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-methyl-benzenesulfonamide C21 H15 N O6 S VUFVNHBHOYPKGQ-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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP	B [auth C]	L-PEPTIDE LINKING	C6 H10 N3 O5 P		HIS

Binding Affinity Annotations
ID	Source	Binding Affinity
8LF	BindingDB:  5Y64	IC50: 360 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.527	α = 90
b = 82.736	β = 90
c = 104.361	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Zhou, L., Jiang, L.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21472026

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Refinement description, Structure summary