4L03

Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate

Structural Biology Knowledgebase: 4L03 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4L03

Classification: OXIDOREDUCTASE

Total Structure Weight: 147490.58

Macromolecule Entities
Molecule Chains Length Organism Details
Isocitrate dehydrogenase [NADP] cytoplasmic A, B, C 425 Homo sapiens EC#: 1.1.1.42 IUBMB
Mutation: G97D
Gene Name(s): IDH1 Gene View PICD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AKG
Query on AKG

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

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

A, B, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NAP N/A in BindingDB
Kd: 13 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.189
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 96.19 α = 90.00
b = 275.38 β = 90.00
c = 116.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-30
  • Released Date: 2013-07-17
  • Deposition author(s): Concha, N.O., Smallwood, A.M.

Revision History

No revisions since initial release