1OFM

CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4-SULFATE TETRASACCHARIDE

Structural Biology Knowledgebase: 1OFM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.142

Literature

Macromolecules
Sequence Display for 1OFM

Classification: LYASE

Total Structure Weight: 55781.20

Macromolecule Entities
Molecule Chains Length Organism Details
CHONDROITINASE B A 481 Pedobacter heparinus EC#: 4.2.2.19 IUBMB
Details: HYDROXY-PROLINE AT N-TERMINUS GLYCOSYLATION AT SER234
Gene Name(s): cslB Phep_0789
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 10 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ASG
Query on ASG

A 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE
C8 H15 N O9 S
WHCJUIFHMJFEFZ-UIAUGNHASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BDP
Query on BDP

A BETA-D-GLUCOPYRANURONIC ACID
D-GLUCURONIC ACID (Synonym)
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GCU
Query on GCU

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

A ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-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)
BGC
Query on BGC

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

A 6-DEOXY-2-O-METHYL-ALPHA-L-GALACTOPYRANOSE
C7 H14 O5
YLAMTMNJXPWCQN-CXNFULCWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GCD
Query on GCD

A 4,5-DEHYDRO-D-GLUCURONIC ACID
C6 H8 O6
IAKKJSVSFCTLRY-YKKSOZKNSA-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)
XYP
Query on XYP

A BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
A L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.142
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.54 α = 90.00
b = 74.07 β = 93.76
c = 58.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-15
  • Released Date: 2004-04-19
  • Deposition author(s): Michel, G., Cygler, M.

Revision History

  • 2013-01-23
    Type: Refinement description | Details: REMARK 3
  • 2013-01-23
    Type: Binding sites and description | Details: REMARK 800,SITE
  • 2013-01-23
    Type: Non-polymer description | Details: HETSYN,FORMUL,HETNAM,HET
  • 2013-01-23
    Type: Geometry validation | Details: REMARK 500
  • 2013-01-23
    Type: Version format compliance | Details: REMARK 4
  • 2013-01-23
    Type: Polymer description | Details: COMPND
  • 2013-01-23
    Type: Other | Details: SCALE1,SCALE3,TER,SCALE2,REMARK 290
  • 2013-01-23
    Type: Atom nomenclature | Details: HETATM
  • 2013-01-23
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2013-01-23
    Type: Linkage | Details: CONECT,LINK