2CFT | pdb_00002cft

Crystal structure of human pyridoxal 5'-phosphate phosphatase with its substrate

• PDB DOI: https://doi.org/10.2210/pdb2CFT/pdb

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


• Deposited: 2006-02-23 Released: 2007-02-27 
• Deposition Author(s): Kang, B.S., Cho, H.J., Kim, K.J., Kwon, O.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal Structure of Human Pyridoxal 5-Phosphate Phosphatase

Kang, B.S., Cho, H.J., Kim, K.J., Kwon, O.S.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 32.19 kDa 
• Atom Count: 2,472 
• Modeled Residue Count: 293 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRIDOXAL PHOSPHATE PHOSPHATASE	A	298	Homo sapiens	Mutation(s): 0  EC: 3.1.3.74 (PDB Primary Data), 3.1.3.16 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96GD0 (Homo sapiens) Explore Q96GD0  Go to UniProtKB:  Q96GD0
PHAROS:  Q96GD0 GTEx:  ENSG00000241360

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.303	α = 90
b = 54.303	β = 90
c = 210.19	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Kang, B.S., Cho, H.J., Kim, K.J., Kwon, O.S.

Revision History  

• Version 1.0: 2007-02-27
  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: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary