1MV8

1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from Psuedomonas aeruginosa

Structural Biology Knowledgebase: 1MV8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.174

Literature

Macromolecules
Sequence Display for 1MV8

Classification: OXIDOREDUCTASE

Total Structure Weight: 196681.56

Macromolecule Entities
Molecule Chains Length Organism Details
GDP-mannose 6-dehydrogenase A, B, C, D 436 Pseudomonas aeruginosa EC#: 1.1.1.132 IUBMB
Gene Name(s): algD PA3540
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, C, D NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GDX
Query on GDX

A, D GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'- D-MANNOPYRANOSYL ESTER
C16 H23 N5 O17 P2
DNBSDUDYNPJVCN-ZXTXFPBHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

B, D SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

C (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

C ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.174
  • Space Group: P 43
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.47 α = 90.00
b = 82.47 β = 90.00
c = 309.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-09-24
  • Released Date: 2003-05-06
  • Deposition author(s): Snook, C.F., Tipton, P.A., Beamer, L.J.

Revision History

  • 2014-11-12
    Type: Function and keywords | Details: --
  • 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