4QU1 | pdb_00004qu1

Crystal structure of human JMJD5 jmj-c domain

PDB DOI: https://doi.org/10.2210/pdb4QU1/pdb

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

Deposited: 2014-07-10 Released: 2015-07-15
Deposition Author(s): Liu, H.L., Wang, C., Zhang, G.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.174 (Depositor), 0.179 (DCC)
R-Value Work:
0.149 (Depositor), 0.153 (DCC)
R-Value Observed:
0.150 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4QU1

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

Literature

The Histone Arginine Demethylase JMJD5

Liu, H.L., Wang, C., Dege, C., Ning, F.K., Weisz, J., Hansen, K., Zang, J.Y., Pan, C.H., Marrack, P., Kappler, J., Hagmen, J., Zhang, G.Y.

To be published.

Macromolecule Content

Total Structure Weight: 27.62 kDa
Atom Count: 2,240
Modeled Residue Count: 236
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 8	A	236	Homo sapiens	Mutation(s): 0 Gene Names: KDM8, JMJD5 EC: 1.14.11.27 (PDB Primary Data), 3.4 (UniProt), 1.14.11.73 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N371 (Homo sapiens) Explore Q8N371 Go to UniProtKB: Q8N371
PHAROS: Q8N371 GTEx: ENSG00000155666
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N371
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG Query on AKG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 1.57 Å
R-Value Free: 0.174 (Depositor), 0.179 (DCC)
R-Value Work: 0.149 (Depositor), 0.153 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.627	α = 90
b = 65.03	β = 90
c = 77.782	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-15
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.