4AYR

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

Structural Biology Knowledgebase: 4AYR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.102
  • R-Value Work: 0.083

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AYR

Classification: HYDROLASE

Total Structure Weight: 52744.86

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

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PE4
Query on PE4

A 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]- ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000 (Synonym)
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IFL
Query on IFL

A (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN- 2-ONE
ISOFAGOMINE LACTAM (Synonym)
C6 H11 N O4
ARBXEMIAJIJEQI-WDCZJNDASA-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 %)
IFL N/A in BindingDB
Kd: 99 nM  BindingMOAD
Kd: 99 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.102
  • R-Value Work: 0.083
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 143.92 α = 90.00
b = 143.92 β = 90.00
c = 50.19 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