1T2A | pdb_00001t2a

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

• PDB DOI: https://doi.org/10.2210/pdb1T2A/pdb

• Classification: STRUCTURAL GENOMICS,LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-04-20 Released: 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure and Biophysical Characterization of Human GDP-D-mannose 4,6-dehydratase

Vedadi, M., Walker, J.R., Sharma, S., Houston, S., Wasney, G., Loppnau, P., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 175.55 kDa 
• Atom Count: 12,166 
• Modeled Residue Count: 1,351 
• Deposited Residue Count: 1,500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose 4,6 dehydratase	A, B, C, D	375	Homo sapiens	Mutation(s): 0  Gene Names: GMDS EC: 4.2.1.47
UniProt & NIH Common Fund Data Resources
Find proteins for O60547 (Homo sapiens) Explore O60547  Go to UniProtKB:  O60547
PHAROS:  O60547 GTEx:  ENSG00000112699

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], G [auth B], I [auth C], K [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
GDP	F [auth A], H [auth B], J [auth C], L [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.595	α = 90
b = 122.064	β = 90
c = 139.403	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• 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  

• Version 1.0: 2004-05-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description