5FY4

Crystal structure of the catalytic domain of human JARID1B in complex with succinate

PDB DOI: https://doi.org/10.2210/pdb5FY4/pdb

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

Deposited: 2016-03-04 Released: 2017-03-22
Deposition Author(s): Nowak, R., Srikannathasan, V., Johansson, C., Gileadi, C., Kupinska, K., Strain-Damerell, C., Szykowska, A., von Delft, F., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.193
R-Value Work: 0.193
R-Value Observed: 0.194

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Succinate

Nowak, R., Srikannathasan, V., Johansson, C., Gileadi, C., Kupinska, K., Strain-Damerell, C., Szykowska, A., von Delft, F., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 56.1 kDa
Atom Count: 3,996
Modelled Residue Count: 454
Deposited Residue Count: 479
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 5B	A	479	Homo sapiens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UGL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUM Query on FUM 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]	FUMARIC ACID C₄ H₄ O₄ VZCYOOQTPOCHFL-OWOJBTEDSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [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 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] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF 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]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	C [auth A], D [auth A], L [auth A], M [auth A], N [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.193
R-Value Work: 0.193
R-Value Observed: 0.194
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.14	α = 90
b = 142.14	β = 90
c = 152.1	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Structure summary
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Other
Version 2.1: 2024-01-10
Changes: Refinement description
Version 2.2: 2024-10-16
Changes: Structure summary