6GPL

Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4k6d-Man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.

Johansson, C.Krojer, T.Kavanagh, K.L.Oppermann, U.Nidetzky, B.Pfeiffer, M.

(2019) Acs Catalysis 9: 2962-2968


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GDP-mannose 4,6 dehydratase
B, C, D, E
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
F7E
Query on F7E

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B, C, D, E
[[(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},6~{R})-6-methyl-3,4-bis(oxidanyl)-5-oxidanylidene-oxan-2-yl] hydrogen phosphate
C16 H23 N5 O15 P2
PNHLMHWWFOPQLK-BKUUWRAGSA-N
 Ligand Interaction
NAP
Query on NAP

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

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B
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.260α = 90.00
b = 122.770β = 90.00
c = 139.500γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
xia2data 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
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references