1N86 Blood Clotting date Nov 19, 2002
title Crystal Structure Of Human D-Dimer From Cross-Linked Fibrin With Gpr And Ghrpldk Peptide Ligands.
authors Z.Yang, L.Pandi, R.F.Doolittle
compound source
Molecule: Fibrin Alphaalpha-E Chain
Chain: A, D
Fragment: Double-D Alpha Chain
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Fibrinogen From Blood Bank Plasma

Molecule: Fibrin Beta Chain
Chain: B, E
Fragment: Double-D Beta Chain
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Fibrinogen From Blood Bank Plasma

Molecule: Fibrin Gamma Chain
Chain: C, F
Fragment: Double-D Gamma Chain
Synonym: Pro2061
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Fibrinogen From Blood Bank Plasma

Molecule: Fibrin Alpha Chain Peptide Ligand Fragment Gly-Pr
Chain: G, H
Fragment: Sequence Database Residues 36-38
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Peptide Matching Portion Of Human Alpha Chain;

Molecule: Fibrin Beta Chain Peptide Ligand Fragment Gly-His Leu-Asp-Lys;
Chain: I, J
Fragment: Sequence Database Residues 45-51
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Peptide Matching Portion Of Human Beta Chain
symmetry Space Group: P 21 21 21
R_factor 0.226 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.328 130.093 298.313 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand CA, MAN, NDG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


F, C


Primary referenceThe crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface., Yang Z, Pandi L, Doolittle RF, Biochemistry 2002 Dec 31;41(52):15610-7. PMID:12501189
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (229 Kb) [Save to disk]
  • Biological Unit Coordinates (1n86.pdb1.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 1N86
  • CSU: Contacts of Structural Units for 1N86
  • Likely Quarternary Molecular Structure file(s) for 1N86
  • Retrieve 1N86 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N86 from S2C, [Save to disk]
    • View 1N86 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1N86
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1N86, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n86a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1n86b2, region B:151-199 [Jmol] [rasmolscript] [script source]
        - Domain d1n86b1, region B:200-457 [Jmol] [rasmolscript] [script source]
        - Domain d1n86c1, region C:142-391 [Jmol] [rasmolscript] [script source]
        - Domain d1n86c2, region C:97-141 [Jmol] [rasmolscript] [script source]
        - Domain d1n86d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1n86e2, region E:151-199 [Jmol] [rasmolscript] [script source]
        - Domain d1n86e1, region E:200-457 [Jmol] [rasmolscript] [script source]
        - Domain d1n86f1, region F:142-391 [Jmol] [rasmolscript] [script source]
        - Domain d1n86f2, region F:97-141 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1n86_C] [1n86_D] [1n86_E] [1n86_G] [1n86_B] [1n86] [1n86_F] [1n86_J] [1n86_A] [1n86_H] [1n86_I]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 1N86: [FBG ] by SMART
    • Other resources with information on 1N86
  • Community annotation for 1N86 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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