6GPJ

Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-Man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-Man

Pfeiffer, M.Krojer, T.Johansson, C.Bushell, S.Mathea, S.Pike, A.von Delft, F.Bountra, C.Arrowsmith, C.H.Edwards, A.Nidetzky, B.Oppermann, U.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GDP-mannose 4,6 dehydratase
A, D, C, B
352Homo sapiensMutation(s): 0 
Gene Names: GMDS
EC: 4.2.1.47
Find proteins for O60547 (Homo sapiens)
Go to Gene View: GMDS
Go to UniProtKB:  O60547
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

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Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

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A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
G4F
Query on G4F

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A, B, C, D
[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate
C16 H24 F N5 O15 P2
LDMYSLGOFVDHNN-YVXBHLEUSA-N
 Ligand Interaction
EDO
Query on EDO

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B, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.080α = 90.00
b = 114.438β = 90.00
c = 140.536γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PHASERphasing
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release