2X15 | pdb_00002x15

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP and 1,3- bisphosphoglycerate

• PDB DOI: https://doi.org/10.2210/pdb2X15/pdb

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


• Deposited: 2009-12-21 Released: 2011-02-09 
• Deposition Author(s): Bowler, M.W., Cliff, M.J., Marston, J.P.M., Baxter, N.J., Hounslow, A.M.H., Varga, A.V., Szabo, J., Vas, M., Blackburn, G.M., Waltho, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

The Structure of Human Phosphoglycerate Kinase in its Fully Active Conformation in Complex with Ground State Analoges

Bowler, M.W., Cliff, M.J., Marston, J.P.M., Baxter, N.J., Hounslow, A.M.H., Varga, A.V., Szabo, J., Vas, M., Blackburn, G.M., 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)

Macromolecule Content 

• Total Structure Weight: 45.95 kDa 
• Atom Count: 3,228 
• Modeled Residue Count: 408 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOGLYCERATE KINASE 1	A	416	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
ATP	F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
X15	D [auth A]	1,3-BISPHOSPHOGLYCERIC ACID C3 H8 O10 P2 LJQLQCAXBUHEAZ-UWTATZPHSA-N
3PG	E [auth A]	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3PG	BindingDB:  2X15	Kd: min: 9.40e+4, max: 1.21e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.73	α = 90
b = 91.75	β = 90
c = 108.31	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: 2011-02-09 
Deposition Author(s): Bowler, M.W., Cliff, M.J., Marston, J.P.M., Baxter, N.J., Hounslow, A.M.H., Varga, A.V., Szabo, J., Vas, M., Blackburn, G.M., Waltho, J.P.

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description