4D6R | pdb_00004d6r

crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound o-toluenesulfonamide

PDB DOI: https://doi.org/10.2210/pdb4D6R/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: 1.40 Å
R-Value Free:
0.172 (Depositor), 0.174 (DCC)
R-Value Work:
0.145 (Depositor), 0.147 (DCC)
R-Value Observed:
0.146 (Depositor)

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 N-Oxalylglycine and Bound O-Toluenesulfonamide

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: 40.61 kDa
Atom Count: 3,267
Modeled Residue Count: 323
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B0I6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IEJ Query on IEJ Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	I [auth A], J [auth A], K [auth A]	O-TOLUENESULFONAMIDE C₇ H₉ N O₂ S YCMLQMDWSXFTIF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
OGA Query on OGA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	N-OXALYLGLYCINE C₄ H₅ N O₅ BIMZLRFONYSTPT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [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 D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.172 (Depositor), 0.174 (DCC)
R-Value Work: 0.145 (Depositor), 0.147 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.514	α = 90
b = 71.514	β = 90
c = 150.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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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