1JMJ

Crystal Structure of Native Heparin Cofactor II

Structural Biology Knowledgebase: 1JMJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1JMJ

Classification: BLOOD CLOTTING

Total Structure Weight: 110902.63

Macromolecule Entities
Molecule Chains Length Organism Details
HEPARIN COFACTOR II A, B 480 Homo sapiens Gene Name(s): SERPIND1 Gene View HCF2

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

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.208
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 74.73 α = 90.00
b = 80.00 β = 102.04
c = 92.24 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-07-18
  • Released Date: 2002-08-30
  • Deposition author(s): Baglin, T.P., Carrell, R.W., Church, F.C., Huntington, J.A.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4