1N73 Blood Clotting date Nov 12, 2002
title Fibrin D-Dimer, Lamprey Complexed With The Peptide Ligand: G Arg-Pro-Amide
authors Z.Yang, L.Pandi, R.F.Doolittle
compound source
Molecule: Fibrin Alpha-1 Chain
Chain: A, D
Organism_scientific: Petromyzon Marinus
Organism_common: Sea Lamprey
Organism_taxid: 7757
Tissue: Blood

Molecule: Fibrin Beta Chain
Chain: B, E

Organism_scientific: Petromyzon Marinus
Organism_common: Sea Lamprey
Organism_taxid: 7757
Tissue: Blood

Molecule: Fibrin Gamma Chain
Chain: C, F

Organism_scientific: Petromyzon Marinus
Organism_common: Sea Lamprey
Organism_taxid: 7757
Tissue: Blood

Molecule: Peptide Ligand: Gly-His-Arg-Pro-Amide
Chain: G, H, I, J
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide That Occurs Naturally In H
symmetry Space Group: P 1
R_factor 0.258 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.732 99.302 120.732 99.58 101.46 92.36
method X-Ray Diffractionresolution 2.90 Å
ligand CA, NAG enzyme
related structures by homologous chain: 1LWU
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] (245 Kb) [Save to disk]
  • Biological Unit Coordinates (1n73.pdb1.gz) 239 Kb
  • LPC: Ligand-Protein Contacts for 1N73
  • CSU: Contacts of Structural Units for 1N73
  • Likely Quarternary Molecular Structure file(s) for 1N73
  • Retrieve 1N73 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N73 from S2C, [Save to disk]
  • View 1N73 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 1N73
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1N73, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n73a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1n73b2, region B:163-218 [Jmol] [rasmolscript] [script source]
        - Domain d1n73b1, region B:219-477 [Jmol] [rasmolscript] [script source]
        - Domain d1n73c1, region C:138-404 [Jmol] [rasmolscript] [script source]
        - Domain d1n73c2, region C:83-137 [Jmol] [rasmolscript] [script source]
        - Domain d1n73d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1n73e2, region E:163-218 [Jmol] [rasmolscript] [script source]
        - Domain d1n73e1, region E:219-477 [Jmol] [rasmolscript] [script source]
        - Domain d1n73f1, region F:138-404 [Jmol] [rasmolscript] [script source]
        - Domain d1n73f2, region F:83-137 [Jmol] [rasmolscript] [script source]
  • Fold representative 1n73 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1n73_H] [1n73_C] [1n73_A] [1n73_B] [1n73] [1n73_I] [1n73_F] [1n73_E] [1n73_D] [1n73_J] [1n73_G]
  • SWISS-PROT database: [P02674] [P02678] [P04115]
  • Domain organization of [FIBA1_PETMA] [FIBB_PETMA] [FIBG_PETMA] by SWISSPFAM
  • Domain found in 1N73: [FBG ] by SMART
  • Other resources with information on 1N73
  • Community annotation for 1N73 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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