3ISQ

Crystal structure of human 4-Hydroxyphenylpyruvate dioxygenase

• PDB DOI: https://doi.org/10.2210/pdb3ISQ/pdb

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


• Deposited: 2009-08-27 Released: 2009-09-15 
• Deposition Author(s): Pilka, E.S., Shafqat, N., Cocking, R., Bray, J.E., Krojer, T., Pike, A.C.W., von Delft, F., Yue, W.W., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U., Kavanagh, K.L., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.174 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Literature

Crystal structure of human 4-Hydroxyphenylpyruvate dioxygenase

Pilka, E.S., Shafqat, N., Cocking, R., Bray, J.E., Krojer, T., Pike, A.C.W., von Delft, F., Yue, W.W., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U., Kavanagh, K.L.

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 45.4 kDa 
• Atom Count: 3,601 
• 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 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.174 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.206	α = 90
b = 99.206	β = 90
c = 87.726	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Pilka, E.S., Shafqat, N., Cocking, R., Bray, J.E., Krojer, T., Pike, A.C.W., von Delft, F., Yue, W.W., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U., Kavanagh, K.L., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description