1GZ4

molecular mechanism of the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 1GZ4

Classification: OXIDOREDUCTASE

Total Structure Weight: 255424.30

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-DEPENDENT MALIC ENZYME A, B, C, D 551 Homo sapiens EC#: 1.1.1.38 IUBMB
Gene Name(s): ME2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TTN
Query on TTN

A, B, C, D TARTRONATE
C3 H2 O5
ROBFUDYVXSDBQM-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUM
Query on FUM

A, B, C, D FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B, C, D MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ATP N/A in BindingDB
Ki: 200000 nM  BindingMOAD
Ki: 200000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.209
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 224.94 α = 90.00
b = 117.45 β = 109.33
c = 111.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-15
  • Released Date: 2002-07-25
  • Deposition author(s): Yang, Z., Lanks, C.W., Tong, L.

Revision History

  • 2011-11-23
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance