2I3Y | pdb_00002i3y

Crystal structure of human glutathione peroxidase 5

PDB DOI: https://doi.org/10.2210/pdb2I3Y/pdb

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

Deposited: 2006-08-21 Released: 2006-09-12
Deposition Author(s): Kavanagh, K.L., Johansson, C., Rojkova, A., Umeano, C., Bunkoczi, G., Gileadi, O., von Delft, F., Weigelt, J., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of human glutathione peroxidase 5

Kavanagh, K.L., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 24.65 kDa
Atom Count: 1,580
Modeled Residue Count: 188
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epididymal secretory glutathione peroxidase	A	215	Homo sapiens	Mutation(s): 0 Gene Names: GPX5 EC: 1.11.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for O75715 (Homo sapiens) Explore O75715 Go to UniProtKB: O75715
PHAROS: O75715 GTEx: ENSG00000224586
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75715
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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: 2.00 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.544	α = 90
b = 104.544	β = 90
c = 71.663	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-09-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-09-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-31
Changes: Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description