4AYP

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with thiomannobioside

Structural Biology Knowledgebase: 4AYP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.106
  • R-Value Work: 0.096

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AYP

Classification: HYDROLASE

Total Structure Weight: 51022.79

Macromolecule Entities
Molecule Chains Length Organism Details
MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE A 447 Caulobacter sp. k31 EC#: 3.2.1.113 IUBMB
Gene Name(s): Caul_4035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO- ALPHA-D-MANNOPYRANOSIDE
C13 H24 O10 S
WAYOKHSZGNFKSX-ZEEOCKJESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

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

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SMD N/A in BindingDB
Kd: 755 nM  BindingMOAD
Kd: 755 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.106
  • R-Value Work: 0.096
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 144.13 α = 90.00
b = 144.13 β = 90.00
c = 50.30 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-06-21
  • Released Date: 2013-01-30
  • Deposition author(s): Thompson, A.J., Dabin, J., Iglesias-Fernandez, J., Iglesias-Fernandez, A., Dinev, Z., Williams, S.J., Siriwardena, A., Moreland, C., Hu, T.C., Smith, D.K., Gilbert, H.J., Rovira, C., Davies, G.J.

Revision History

No revisions since initial release