3CYN

The structure of human GPX8

PDB DOI: https://doi.org/10.2210/pdb3CYN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-04-25 Released: 2008-08-12
Deposition Author(s): Kavanagh, K.L., Johansson, C., Yue, W.W., Kochan, G., Pike, A.C.W., Murray, J., Roos, A.K., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.199
R-Value Work: 0.171
R-Value Observed: 0.172

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The structure of human GPX8

Kavanagh, K.L., Johansson, C., Yue, W.W., Kochan, G., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 66.51 kDa
Atom Count: 4,506
Modelled Residue Count: 523
Deposited Residue Count: 567
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable glutathione peroxidase 8	A, B, C	189	Homo sapiens	Mutation(s): 0 Gene Names: LOC493869 EC: 1.11.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TED1 (Homo sapiens) Explore Q8TED1 Go to UniProtKB: Q8TED1
PHAROS: Q8TED1 GTEx: ENSG00000164294
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TED1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	D [auth A] F [auth B] G [auth B] H [auth B] I [auth B] D [auth A], F [auth B], G [auth B], H [auth B], I [auth B], K [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C]	E [auth A], J [auth B], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.199
R-Value Work: 0.171
R-Value Observed: 0.172
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.688	α = 90
b = 120.854	β = 119.38
c = 75.603	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-08-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description, Source and taxonomy
Version 1.3: 2018-01-31
Changes: Structure summary
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description