1GZ3

MOLECULAR MECHANISM FOR THE REGULATION OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME BY ATP AND FUMARATE

Structural Biology Knowledgebase: 1GZ3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 1GZ3

Classification: OXIDOREDUCTASE

Total Structure Weight: 251708.98

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-DEPENDENT MALIC ENZYME A, B, C, D 554 Homo sapiens EC#: 1.1.1.38 IUBMB
Fragment: RESIDUES 20-573
Mutation: R197Q, R542V, R556Q
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)
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)
OXL
Query on OXL

A, B, C, D OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.194
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 71.82 α = 90.00
b = 192.65 β = 89.77
c = 110.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-14
  • Released Date: 2003-05-22
  • Deposition author(s): Yang, Z., Lanks, C.W., Tong, L.

Revision History

  • 2011-11-23
    Type: Polymer description | Details: REMARK 400
  • 2011-11-23
    Type: Entry authorship | Details: AUTHOR
  • 2011-11-23
    Type: Sequence database correspondence | Details: SEQADV
  • 2011-11-23
    Type: Entry title | Details: TITLE
  • 2011-11-23
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2011-11-23
    Type: Version format compliance | Details: REMARK 4
  • 2011-11-23
    Type: Function and keywords | Details: KEYWDS
  • 2011-11-23
    Type: Refinement description | Details: REMARK 3
  • 2011-11-23
    Type: Other | Details: REMARK 525,REMARK 280
  • 2011-11-23
    Type: Non-polymer description | Details: FORMUL
  • 2011-11-23
    Type: Geometry validation | Details: REMARK 500