1G6I

Crystal structure of the yeast alpha-1,2-mannosidase with bound 1-deoxymannojirimycin at 1.59 A resolution

Structural Biology Knowledgebase: 1G6I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.230

Literature

Macromolecules
Sequence Display for 1G6I

Classification: HYDROLASE

Total Structure Weight: 65203.50

Macromolecule Entities
Molecule Chains Length Organism Details
CLASS I ALPHA-1,2-MANNOSIDASE A 545 Saccharomyces cerevisiae EC#: 3.2.1.113 IUBMB
Mutation: H328Q, ΔL367, ΔS368, ΔL369, ΔE370, ΔR371
Gene Name(s): MNS1 Gene View YJR131W J2110
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDG
Query on NDG

A 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMJ
Query on DMJ

A 1-DEOXYMANNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-KVTDHHQDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.230
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 89.05 α = 90.00
b = 89.05 β = 90.00
c = 153.14 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-11-06
  • Released Date: 2003-06-24
  • Deposition author(s): Herscovics, A., Lipari, F., Sleno, B., Romera, P.A., Vallee, F., Yip, P., Howell, P.A

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4