9FDN | pdb_00009fdn

Human phosphoglycerate kinase in complex with ATP and 3PG formed by cross-soaking a TSA crystal

• PDB DOI: https://doi.org/10.2210/pdb9FDN/pdb

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


• Deposited: 2024-05-17 Released: 2025-05-28 
• Deposition Author(s): Cliff, M.J., Waltho, J.P., Bowler, M.W., Baxter, N.J., Bisson, C., Blackburn, G.M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.204 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

The role of magnesium in catalysis by phosphoglycerate kinase

Cliff, M.J., Serimbetov, Z., Bisson, C., Baxter, N.J., Blackburn, G.M., Hay, S., Bowler, M.W., Waltho, J.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: NMR relaxation study

Macromolecule Content 

• Total Structure Weight: 45.58 kDa 
• Atom Count: 3,603 
• Modeled Residue Count: 416 
• Deposited Residue Count: 417 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase 1	A	417	Homo sapiens	Mutation(s): 0  Gene Names: PGK1, PGKA, MIG10, OK/SW-cl.110 EC: 2.7.2.3 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00558 (Homo sapiens) Explore P00558  Go to UniProtKB:  P00558
PHAROS:  P00558 GTEx:  ENSG00000102144

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
3PG (Subject of Investigation/LOI)	D [auth A]	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.204 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.04	α = 90
b = 91.1	β = 90
c = 108.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
DIALS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Cliff, M.J., Waltho, J.P., Bowler, M.W., Baxter, N.J., Bisson, C., Blackburn, G.M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M021637/1

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release