4D6Q

crystal structure of human JMJD2D in complex with 2,4-PDCA

PDB DOI: https://doi.org/10.2210/pdb4D6Q/pdb

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

Deposited: 2014-11-14 Released: 2014-12-24
Deposition Author(s): Krojer, T., Vollmar, M., Bradley, A., Crawley, L., Szykowska, A., Burgess-Brown, N., Gileadi, C., Johansson, C., Oppermann, U., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.161
R-Value Work: 0.135
R-Value Observed: 0.136

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Human Jmjd2D in Complex with 2,4-Pdca

Krojer, T., Vollmar, M., Bradley, A., Crawley, L., Szykowska, A., Burgess-Brown, N., Gileadi, C., Johansson, C., Oppermann, U., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 40.28 kDa
Atom Count: 3,300
Modelled Residue Count: 330
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4D	A	343	Homo sapiens	Mutation(s): 0 EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B0I6 (Homo sapiens) Explore Q6B0I6 Go to UniProtKB: Q6B0I6
PHAROS: Q6B0I6 GTEx: ENSG00000186280
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B0I6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PD2 Query on PD2 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]	PYRIDINE-2,4-DICARBOXYLIC ACID C₇ H₅ N O₄ MJIVRKPEXXHNJT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
PD2	BindingDB: 4D6Q	IC50: 2400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.161
R-Value Work: 0.135
R-Value Observed: 0.136
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.91	α = 90
b = 71.91	β = 90
c = 151.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-24
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other