2YDE

FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH S-2-HYDROXYGLUTARATE

Structural Biology Knowledgebase: 2YDE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.235

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YDE

Classification: OXIDOREDUCTASE

Total Structure Weight: 41531.50

Macromolecule Entities
Molecule Chains Length Organism Details
HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR A 352 Homo sapiens EC#: 1.14.11.30 IUBMB 1.14.11.n4 IUBMB
Gene Name(s): HIF1AN Gene View FIH1

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

A FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
S2G
Query on S2G

A (2S)-2-HYDROXYPENTANEDIOIC ACID
C5 H8 O5
HWXBTNAVRSUOJR-VKHMYHEASA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
S2G N/A in BindingDB
IC50: 189000 nM  BindingMOAD
IC50: 189000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.235
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 86.73 α = 90.00
b = 86.73 β = 90.00
c = 146.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-18
  • Released Date: 2011-03-30
  • Deposition author(s): Chowdhury, R., Clifton, I.J., Schofield, C.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4