1N86

Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and GHRPLDK peptide ligands.

Structural Biology Knowledgebase: 1N86 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.226

Literature

Macromolecules
Sequence Display for 1N86

Classification: BLOOD CLOTTING

Total Structure Weight: 172796.72

Macromolecule Entities
Molecule Chains Length Organism Details
Fibrin alpha/alpha-E chain A, D 87 Homo sapiens Fragment: DOUBLE-D ALPHA CHAIN
Gene Name(s): FGA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fibrin beta chain B, E 328 Homo sapiens Fragment: DOUBLE-D BETA CHAIN
Gene Name(s): FGB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fibrin gamma chain C, F 324 Homo sapiens Fragment: DOUBLE-D GAMMA CHAIN
Gene Name(s): FGG Gene View PRO2061
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
fibrin alpha chain peptide ligand fragment Gly-Pro-Arg G, H 3 Homo sapiens Fragment: sequence database residues 36-38
Gene Name(s): FGA Gene View
fibrin beta chain peptide ligand fragment Gly-His-Arg-Pro-Leu-Asp-Lys I, J 7 Homo sapiens Fragment: sequence database residues 45-51
Gene Name(s): FGB Gene View

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

B, E, I, J 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

B, C, E, F CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.226
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 52.33 α = 90.00
b = 130.09 β = 90.00
c = 298.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-11-19
  • Released Date: 2003-01-07
  • Deposition author(s): Yang, Z., Pandi, L., Doolittle, R.F.

Revision History

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