3EXE

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex

Structural Biology Knowledgebase: 3EXE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.158

Literature

Macromolecules
Sequence Display for 3EXE

Classification: OXIDOREDUCTASE

Total Structure Weight: 316551.63

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial A, C, E, G 382 Homo sapiens EC#: 1.2.4.1 IUBMB
Fragment: E1p-alpha
Details: wild type with bound Mn-ThDP
Gene Name(s): PDHA1 Gene View PHE1A
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Pyruvate dehydrogenase E1 component subunit beta, mitochondrial B, D, F, H 329 Homo sapiens EC#: 1.2.4.1 IUBMB
Fragment: E1p-beta
Gene Name(s): PDHB Gene View PHE1B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, C, E, G THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, C, E, G GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, C, E, G MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

B, D, F, H POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TPP N/A in BindingDB
N/A in BindingMoad
Kd: 110 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.158
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.57 α = 90.00
b = 129.62 β = 92.48
c = 124.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-10-16
  • Released Date: 2008-11-25
  • Deposition author(s): Kato, M., Wynn, R.M., Chuang, J.L., Tso, S.-C., Machius, M., Li, J., Chuang, D.T.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor