5FYI | pdb_00005fyi

Crystal structure of human JMJD2A in complex with pyruvate

PDB DOI: https://doi.org/10.2210/pdb5FYI/pdb

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

Deposited: 2016-03-07 Released: 2016-03-16
Deposition Author(s): Nowak, R., Kopec, J., Johansson, C., Szykowska, A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.236 (Depositor), 0.240 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Human Jmjd2A in Complex with Pyruvate

Nowak, R., Kopec, J., Johansson, C., Szykowska, A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 90.57 kDa
Atom Count: 6,036
Modeled Residue Count: 695
Deposited Residue Count: 762
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4A	A, B	381	Homo sapiens	Mutation(s): 0 EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens) Explore O75164 Go to UniProtKB: O75164
PHAROS: O75164 GTEx: ENSG00000066135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75164
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1KA Query on 1KA Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain DA [auth B]	DA [auth B]	(2-hydroxyethoxy)acetaldehyde C₄ H₈ O₃ DSGGHBUAHUMMHN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Interactions & Density Focus chain DA [auth B]
PYR Query on PYR Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth A], S [auth B], T [auth B]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B] Focus chain T [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain U [auth B]	F [auth A], U [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain U [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain O [auth A]	O [auth A], R [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain R [auth B] Interactions & Density Focus chain O [auth A] Focus chain R [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] G [auth A] H [auth A] AA [auth B], BA [auth B], CA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] 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] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] 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] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain Q [auth B]	C [auth A], Q [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.236 (Depositor), 0.240 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.45	α = 90
b = 148.83	β = 90
c = 57.06	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-16
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