5EC3

Structural insight into the catalyitc mechanism of human 4-Hydroxyphenylpyruvate dioxygenase

• PDB DOI: https://doi.org/10.2210/pdb5EC3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-10-20 Released: 2015-11-18 
• Deposition Author(s): Yang, W.C., Yang, G.F.
• Funding Organization(s): National Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.192 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

Structural insight into the catalyitc mechanism of human 4-Hydroxyphenylpyruvate dioxygenase

Yang, W.C., Yang, G.F.

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: 45.06 kDa 
• Atom Count: 3,354 
• Modelled Residue Count: 376 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A	393	Homo sapiens	Mutation(s): 0  Gene Names: HPD, PPD EC: 1.13.11.27
UniProt & NIH Common Fund Data Resources
Find proteins for P32754 (Homo sapiens) Explore P32754  Go to UniProtKB:  P32754
PHAROS:  P32754 GTEx:  ENSG00000158104

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.192 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.54	α = 90
b = 98.54	β = 90
c = 87.27	γ = 120

Software Package:

Software Name	Purpose
REFMAC	data scaling
REFMAC	phasing
REFMAC	data reduction
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Yang, W.C., Yang, G.F.

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Funding Organization	Location	Grant Number
National Science Foundation of China	China	21332004

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations