1PJ4

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, ATP, Mn++, and allosteric activator fumarate.

Structural Biology Knowledgebase: 1PJ4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 1PJ4

Classification: OXIDOREDUCTASE

Total Structure Weight: 260849.16

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent malic enzyme, mitochondrial A, B, C, D 564 Homo sapiens EC#: 1.1.1.38 IUBMB
Mutation: M29M, M38M, M47M, M75M, M86M, M108M, M177M, M219M, M239M, M325M, M327M, M343M, M407M, M539M
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)
MLT
Query on MLT

A, B, C, D D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY- SUCCINIC ACID (Synonym)
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-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)
MN
Query on MN

A, B, C, D MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.211
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 226.05 α = 90.00
b = 117.35 β = 109.00
c = 111.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-31
  • Released Date: 2003-09-30
  • Deposition author(s): Tao, X., Yang, Z., Tong, L.

Revision History

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