4AYQ

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

Structural Biology Knowledgebase: 4AYQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.105
  • R-Value Work: 0.088

Literature

Macromolecules
Sequence Display for 4AYQ

Classification: HYDROLASE

Total Structure Weight: 51381.20

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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MVL
Query on MVL

A (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2- A]PYRIDINE-6,7,8-TRIOL
Mannoimidazole (Synonym)
C8 H12 N2 O4
RZRDQZQPTISYKY-JWXFUTCRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-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)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MVL N/A in BindingDB
Kd: 47 nM  BindingMOAD
Kd: 47 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.105
  • R-Value Work: 0.088
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 143.61 α = 90.00
b = 143.61 β = 90.00
c = 50.03 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

  • 2015-03-25
    Type: Citation | Details: JRNL