5EC3 | pdb_00005ec3

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.150 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Yang, W.C., Yang, G.F.

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32754
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.150 (DCC)
R-Value Observed: 0.156 (Depositor)

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.