6GVD

Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.

Ren, W.Pengelly, R.Farren-Dai, M.Shamsi Kazem Abadi, S.Oehler, V.Akintola, O.Draper, J.Meanwell, M.Chakladar, S.Swiderek, K.Moliner, V.Britton, R.Gloster, T.M.Bennet, A.J.

(2018) Nat Commun 9: 3243-3243


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-galactosidase
A
575Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: galA
EC: 3.2.1.22
Find proteins for G4FEF4 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  G4FEF4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FDK
Query on FDK

Download SDF File 
Download CCD File 
A
(1~{S},2~{S},3~{S},4~{S})-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol
C7 H12 O5
PJPGMULJEYSZBS-AXMZGBSTSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.957α = 90.00
b = 96.135β = 90.00
c = 97.900γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
REFMACrefinement
MOLREPphasing
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release