5YL6

Crystal structure of Ofd2 in complex with 2OG from Schizosaccharomyces pombe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of Ofd2 in complex with 2OG from Schizosaccharomyces pombe

Wang, J.Gao, Y.X.Guo, G.R.Zhu, Z.L.Niu, L.W.Teng, M.K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein P8A3.02cA184Schizosaccharomyces pombe 972h-Mutation(s): 2 
Gene Names: SPAP8A3.02c
UniProt
Find proteins for Q9UT12 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UT12 
Go to UniProtKB:  Q9UT12
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download Ideal Coordinates CCD File 
C [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.114α = 90
b = 80.312β = 90
c = 82.607γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Ministry of Science and TechnologyChina2012CB917200
Chinese Ministry of Science and TechnologyChina2011CBA00800
Chinese National Natural Science FoundationChina31130018
Chinese National Natural Science FoundationChina31170726

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release