1DBG

CRYSTAL STRUCTURE OF CHONDROITINASE B

Structural Biology Knowledgebase: 1DBG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 1DBG

Classification: LYASE

Total Structure Weight: 57495.89

Macromolecule Entities
Molecule Chains Length Organism Details
CHONDROITINASE B A 506 Pedobacter heparinus EC#: 4.2.2.19 IUBMB
Gene Name(s): cslB Phep_0789
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GCU
Query on GCU

A D-GLUCURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-WAXACMCWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

A BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MXY
Query on MXY

A 2-O-METHYL FUCOSE
C7 H14 O5
YLAMTMNJXPWCQN-XUVCUMPTSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RAM
Query on RAM

A ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
G4D
Query on G4D

A 4-DEOXY-ALPHA-D-GLUCOSE
C6 H12 O5
HDEMQQHXNOJATE-AZGQCCRYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
XYP
Query on XYP

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.180
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.60 α = 90.00
b = 74.40 β = 92.90
c = 58.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-11-02
  • Released Date: 2000-01-12
  • Deposition author(s): Huang, W., Matte, A., Li, Y., Kim, Y.S., Linhardt, R.J., Su, H., Cygler, M.

Revision History

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