4B9Z

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with Acarbose

Structural Biology Knowledgebase: 4B9Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.161

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4B9Z

Classification: HYDROLASE

Total Structure Weight: 94763.33

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B A 817 Cellvibrio japonicus EC#: 2.4.1.161 IUBMB
Gene Name(s): agd31B CJA_3248
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ACR
Query on ACR

A ALPHA-ACARBOSE
1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX- 5,6-ENYL)AMINO)FRUCTOSE (Synonym)
C25 H43 N O18
XUFXOAAUWZOOIT-WVJZLWNXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXL
Query on OXL

A OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ACR N/A in BindingDB
Ki: 81400 nM  BindingMOAD
Ki: 81400 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.161
  • Space Group: P 6 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 196.88 α = 90.00
b = 196.88 β = 90.00
c = 102.76 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-09
  • Released Date: 2012-11-14
  • Deposition author(s): Larsbrink, J., Izumi, A., Hemsworth, G.R., Davies, G.J., Brumer, H.

Revision History

  • 2013-01-16
    Type: Citation | Details: JRNL
  • 2012-11-21
    Type: Citation | Details: JRNL