1OFL

CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE

Structural Biology Knowledgebase: 1OFL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.133

Literature

Macromolecules
Sequence Display for 1OFL

Classification: LYASE

Total Structure Weight: 56740.04

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

Small Molecules
Ligands 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NGK
Query on NGK

A 2-(ACETYLAMINO)-2-DEOXY-4-O-SULFO-ALPHA-D- GALACTOPYRANOSE
C8 H15 N O9 S
WHCJUIFHMJFEFZ-YQXRAVKXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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)
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)
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)
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)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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: 1.7 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.133
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.57 α = 90.00
b = 73.99 β = 93.93
c = 59.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-15
  • Released Date: 2004-06-10
  • Deposition author(s): Michel, G., Cygler, M.

Revision History

  • 2013-01-23
    Type: Linkage | Details: CONECT,LINK
  • 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: FORMUL,REMARK 620,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: REMARK 2,SCALE1,SCALE3,TER,SCALE2,REMARK 525,REMARK 290
  • 2013-01-23
    Type: Atom nomenclature | Details: HETATM
  • 2013-01-23
    Type: Biological assembly | Details: REMARK 300,REMARK 350