5LWB | pdb_00005lwb

Crystal structure of human JARID1B in complex with S40650a

PDB DOI: https://doi.org/10.2210/pdb5LWB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-09-15 Released: 2016-10-26
Deposition Author(s): Srikannathasan, V., Le Bihan, Y.V., Szykowska, A., Johansson, C., Gileadi, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Oppermann, U., Huber, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.218 (Depositor), 0.212 (DCC)
R-Value Work:
0.182 (Depositor)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human JARID1B in complex with S40650a

Srikannathasan, V.

To be published.

Macromolecule Content

Total Structure Weight: 56.67 kDa
Atom Count: 3,894
Modeled Residue Count: 452
Deposited Residue Count: 481
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B,Lysine-specific demethylase 5B	A	481	Homo sapiens	Mutation(s): 0 Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGL1 (Homo sapiens) Explore Q9UGL1 Go to UniProtKB: Q9UGL1
PHAROS: Q9UGL1 GTEx: ENSG00000117139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UGL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
79H Query on 79H Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	5-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile C₁₇ H₂₁ N₇ O IHWTUDNGWXTJCT-CQSZACIVSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [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 G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [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]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain C [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain C [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain C [auth A]	C [auth A], M [auth A], N [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain C [auth A] Focus chain M [auth A] Focus chain N [auth A]