2YPD | pdb_00002ypd

Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein

PDB DOI: https://doi.org/10.2210/pdb2YPD/pdb

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

Deposited: 2012-10-30 Released: 2012-12-12
Deposition Author(s): Vollmar, M., Johansson, C., Krojer, T., Berridge, G., Burgess-Brown, N., Strain-Damerell, C., Froese, S., Williams, E., Goubin, S., Coutandin, D., 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:
0.240 (Depositor), 0.243 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein

Vollmar, M., Johansson, C., Krojer, T., Strain-Damerell, C., Froese, S., Williams, E., Coutandin, D., von Delft, F., Weigelt, J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 94.64 kDa
Atom Count: 5,434
Modeled Residue Count: 653
Deposited Residue Count: 784
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C	A, B	392	Homo sapiens	Mutation(s): 0 EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q15652 (Homo sapiens) Explore Q15652 Go to UniProtKB: Q15652
PHAROS: Q15652 GTEx: ENSG00000171988
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15652
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EMT Query on EMT Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [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] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [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] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	2-(ETHYLMERCURI-THIO)-BENZOIC ACID C₉ H₁₀ Hg O₂ S HXQVQGWHFRNKMS-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 G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [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 G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A]	I [auth A], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.240 (Depositor), 0.243 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.718	α = 90
b = 112.206	β = 90
c = 165.173	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2014-09-17
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy
Version 1.2: 2018-01-24
Changes: Advisory, Database references
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other