1MC5

Ternary complex of Human glutathione-dependent formaldehyde dehydrogenase with S-(hydroxymethyl)glutathione and NADH

Structural Biology Knowledgebase: 1MC5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 1MC5

Classification: OXIDOREDUCTASE

Total Structure Weight: 81794.70

Macromolecule Entities
Molecule Chains Length Organism Details
Alcohol dehydrogenase class III chi chain A, B 374 Homo sapiens EC#: 1.1.1.1 IUBMB
Gene Name(s): ADH5 Gene View ADHX FDH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAD
Query on NAD

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AHE
Query on AHE

A 2-AMINO-4-[1-CARBOXYMETHYL-CARBAMOYL)-2-HYDROXYMETHYLSULFANYL- ETHYLCARBAMOYL]-BUTYRIC ACID
S-HYDROXYMETHYL GLUTATHIONE (Synonym)
C11 H19 N3 O7 S
PIUSLWSYOYFRFR-BQBZGAKWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.197
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 78.66 α = 90.00
b = 78.66 β = 90.00
c = 311.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-08-05
  • Released Date: 2003-03-04
  • Deposition author(s): Sanghani, P.C., Bosron, W.F., Hurley, T.D.

Revision History

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