5RAL | pdb_00005ral

PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS039332c

PDB DOI: https://doi.org/10.2210/pdb5RAL/pdb
Deposition Group: G_1002146 (changed state) | Explore G_1002146

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

Deposited: 2020-03-16 Released: 2020-04-22
Deposition Author(s): Snee, M., Nowak, R., Johansson, C., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.221 (Depositor), 0.251 (DCC)
R-Value Work:
0.189 (Depositor), 0.221 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library

Snee, M., Nowak, R., Johansson, C., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 86.62 kDa
Atom Count: 6,251
Modeled Residue Count: 684
Deposited Residue Count: 744
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 3B	A, B	372	Homo sapiens	Mutation(s): 0 Gene Names: KDM3B, C5orf7, JHDM2B, JMJD1B, KIAA1082 EC: 1.14.11 (PDB Primary Data), 1.14.11.65 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7LBC6 (Homo sapiens) Explore Q7LBC6 Go to UniProtKB: Q7LBC6
PHAROS: Q7LBC6 GTEx: ENSG00000120733
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7LBC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SNQ (Subject of Investigation/LOI) Query on SNQ Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	5-azanyl-2-pyrrol-1-yl-benzenecarbonitrile C₁₁ H₉ N₃ VDMUMLCWGQEGDZ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]