1RF1 Blood Clotting date Nov 07, 2003
title Crystal Structure Of Fragment D Of Gammae132a Fibrinogen Wit Peptide Ligand Gly-His-Arg-Pro-Amide
authors M.S.Kostelansky, O.V.Gorkun, S.T.Lord
compound source
Molecule: Fibrinogen Alphaalpha-E Chain
Chain: A, D
Fragment: Fibrinogen Alphaalpha-E Chain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fga
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho
Expression_system_organ: Ovary
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P767

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Fibrinogen Bbeta Chain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fgb
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho
Expression_system_organ: Ovary
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P767

Molecule: Fibrinogen Gamma Chain
Chain: C, F
Fragment: Fibrinogen Gamma Chain
Synonym: Pro2061
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fgg
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho
Expression_system_organ: Ovary
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P767

Molecule: Ghrp Peptide
Chain: G, H, I, J
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.714 94.683 228.198 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.53 Å
ligand CA, FUC, NAG enzyme
related structures by homologous chain: 1FZG, 1RE4
Primary referenceCalcium-binding site beta2, adjacent to the "b" polymerization site, modulates lateral aggregation of protofibrils during fibrin polymerization., Kostelansky MS, Lounes KC, Ping LF, Dickerson SK, Gorkun OV, Lord ST, Biochemistry 2004 Mar 9;43(9):2475-83. PMID:14992585
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (229 Kb) [Save to disk]
  • Biological Unit Coordinates (1rf1.pdb1.gz) 114 Kb
  • Biological Unit Coordinates (1rf1.pdb2.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 1RF1
  • CSU: Contacts of Structural Units for 1RF1
  • Likely Quarternary Molecular Structure file(s) for 1RF1
  • Structure Factors (735 Kb)
  • Retrieve 1RF1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RF1 from S2C, [Save to disk]
  • Re-refined 1rf1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RF1 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 1RF1
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1RF1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rf1a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rf1b2, region B:161-199 [Jmol] [rasmolscript] [script source]
        - Domain d1rf1b1, region B:200-459 [Jmol] [rasmolscript] [script source]
        - Domain d1rf1c1, region C:142-393 [Jmol] [rasmolscript] [script source]
        - Domain d1rf1c2, region C:96-141 [Jmol] [rasmolscript] [script source]
        - Domain d1rf1d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1rf1e2, region E:165-199 [Jmol] [rasmolscript] [script source]
        - Domain d1rf1e1, region E:200-459 [Jmol] [rasmolscript] [script source]
        - Domain d1rf1f2, region F:103-141 [Jmol] [rasmolscript] [script source]
        - Domain d1rf1f1, region F:142-393 [Jmol] [rasmolscript] [script source]
        - Domain d1e1rf1, region F:358-474 [Jmol] [rasmolscript] [script source]
  • Fold representative 1rf1 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: [1rf1_A] [1rf1_J] [1rf1_I] [1rf1_H] [1rf1_G] [1rf1] [1rf1_E] [1rf1_B] [1rf1_F] [1rf1_D] [1rf1_C]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 1RF1: [FBG ] by SMART
  • Other resources with information on 1RF1
  • Community annotation for 1RF1 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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