1T2A

Crystal structure of human GDP-D-mannose 4,6-dehydratase

Structural Biology Knowledgebase: 1T2A SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1T2A

Classification: STRUCTURAL GENOMICS LYASE

Total Structure Weight: 175553.31

Macromolecule Entities
Molecule Chains Length Organism Details
GDP-mannose 4,6 dehydratase A, B, C, D 375 Homo sapiens EC#: 4.2.1.47 IUBMB
Gene Name(s): GMDS Gene View

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

A, B, C, D NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GDP
Query on GDP

A, B, C, D GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.173
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.60 α = 90.00
b = 122.06 β = 90.00
c = 139.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-04-20
  • Released Date: 2004-05-10
  • Deposition author(s): Walker, J.R., Vedadi, M., Sharma, S., Houston, S., Wasney, G., Loppnau, P., Sundstrom, M., Arrowsmith, C., Edwards, A., Oppermann, U.

Revision History

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