3ZLI

Crystal structure of JmjC domain of human histone demethylase UTY

Structural Biology Knowledgebase: 3ZLI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZLI

Classification: OXIDOREDUCTASE

Total Structure Weight: 111417.60

Macromolecule Entities
Molecule Chains Length Organism Details
HISTONE DEMETHYLASE UTY A, B 478 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: JMJC DOMAIN, RESIDUES 878-1347
Gene Name(s): UTY Gene View KDM6C

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AKG
Query on AKG

A, B 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A, B FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.176
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 90.58 α = 90.00
b = 110.25 β = 90.00
c = 118.24 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-31
  • Released Date: 2013-02-27
  • Deposition author(s): Vollmar, M., Gileadi, C., Shrestha, L., Goubin, S., Johansson, C., Krojer, T., Raynor, J.W., Bradley, A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Revision History

  • 2015-05-20
    Type: Citation | Details: JRNL
  • 2015-05-20
    Type: Other | Details: REMARK 900
  • 2014-01-29
    Type: Binding sites and description | Details: REMARK 800, SITE
  • 2014-01-29
    Type: Linkage | Details: LINK
  • 2014-01-29
    Type: Atom nomenclature | Details: HETATM
  • 2014-01-29
    Type: Non-polymer description | Details: HET, REMARK 620, FORMUL, HETNAM