3ZOZ | pdb_00003zoz

The structure of human phosphoglycerate kinase with bound bromide, a stimulating anion.

• PDB DOI: https://doi.org/10.2210/pdb3ZOZ/pdb

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


• Deposited: 2013-02-26 Released: 2014-03-12 
• Deposition Author(s): Bowler, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Identification of the Activating Anion Binding Site in Human Phosphoglycerate Kinase

Bowler, M.W.

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)

Macromolecule Content 

• Total Structure Weight: 45.47 kDa 
• Atom Count: 3,515 
• Modeled Residue Count: 405 
• 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  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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	F [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
3PG	E [auth A]	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
MGF	D [auth A]	TRIFLUOROMAGNESATE F3 Mg GJOMWUHGUQLOAC-UHFFFAOYSA-K
BR	C [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3PG	BindingDB:  3ZOZ	Kd: 1.09e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.98	α = 90
b = 91.81	β = 90
c = 108.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Bowler, M.W.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description