6RBJ

Crystal structure of KDM3B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol

PDB DOI: https://doi.org/10.2210/pdb6RBJ/pdb

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

Deposited: 2019-04-10 Released: 2020-05-13
Deposition Author(s): Johansson, C., Newman, J.A., Kawamura, A., Schofield, C.J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.210
R-Value Work: 0.189
R-Value Observed: 0.190

Starting Model: experimental
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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 KDM3B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol

Johansson, C., Newman, J.A., Kawamura, A., Schofield, C.J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.

To be published.

Macromolecule Content

Total Structure Weight: 81.93 kDa
Atom Count: 5,561
Modelled Residue Count: 676
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 3B	A, B	351	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7LBC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JX8 (Subject of Investigation/LOI) Query on JX8 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol C₁₀ H₇ N₅ O COSOIVLLWHGBPW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A], D [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.210
R-Value Work: 0.189
R-Value Observed: 0.190
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.929	α = 90
b = 93.754	β = 107.29
c = 90.494	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description