1OD8

XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH XYLOBIO-ISOFAGOMINE LACTAM

Structural Biology Knowledgebase: 1OD8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.126
  • R-Value Work: 0.103

Literature

Macromolecules
Sequence Display for 1OD8

Classification: HYDROLASE / LECTIN

Total Structure Weight: 34890.39

Macromolecule Entities
Molecule Chains Length Organism Details
ENDO-1,4-BETA-XYLANASE A A 313 Streptomyces lividans EC#: 3.2.1.8 IUBMB
Fragment: CATALYTIC MODULE, RESIDUES 42-354
Gene Name(s): xlnA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
XDL
Query on XDL

A XYLOSE-DERIVED ISOFAGOMINE LACTAM
(3S)-3-HYDROXYPIPERIDIN-2-ONE (Synonym)
C5 H9 N O2
RYKLZUPYJFFNRR-BYPYZUCNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.126
  • R-Value Work: 0.103
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 65.81 α = 90.00
b = 45.88 β = 90.00
c = 85.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-14
  • Released Date: 2003-04-08
  • Deposition author(s): Gloster, T.M., Roberts, S., Davies, G.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4