6ETE

Crystal structure of KDM4D with tetrazolhydrazide compound 5

PDB DOI: https://doi.org/10.2210/pdb6ETE/pdb

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

Deposited: 2017-10-26 Released: 2019-02-20
Deposition Author(s): Malecki, P.H., Weiss, M.S., Heinemann, U., Link, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.153
R-Value Work: 0.128
R-Value Observed: 0.128

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of KDM4D with tetrazolylhydrazide ligand NR128

Malecki, P.H., Link, A., Weiss, M.S., Heinemann, U.

To be published.

Macromolecule Content

Total Structure Weight: 40.46 kDa
Atom Count: 3,329
Modelled Residue Count: 330
Deposited Residue Count: 342
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	342	Homo sapiens	Mutation(s): 0 Gene Names: KDM4D, JHDM3D, JMJD2D EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B0I6 (Homo sapiens) Explore Q6B0I6 Go to UniProtKB: Q6B0I6
PHAROS: Q6B0I6
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
BWK Query on BWK Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A]	N [auth A]	[2-(1-methyl-1,2,3,4-tetrazol-4-ium-5-yl)ethanoylamino]azanium C₄ H₁₀ N₆ O MVCFGOJWEMLOIP-UHFFFAOYSA-P		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	L [auth A], M [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 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] SDF format, chain J [auth A] SDF format, chain K [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] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [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] Focus chain J [auth A] Focus chain K [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] Focus chain J [auth A] Focus chain K [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]