1RF0 Blood Clotting date Nov 07, 2003
title Crystal Structure Of Fragment D Of Gammae132a Fibrinogen
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
symmetry Space Group: P 21 21 21
R_factor 0.233 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.408 94.948 227.614 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand CA, NAG enzyme
related structures by homologous chain: 1FZB, 1LT9
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


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] (225 Kb) [Save to disk]
  • Biological Unit Coordinates (1rf0.pdb1.gz) 112 Kb
  • Biological Unit Coordinates (1rf0.pdb2.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 1RF0
  • CSU: Contacts of Structural Units for 1RF0
  • Likely Quarternary Molecular Structure file(s) for 1RF0
  • Structure Factors (525 Kb)
  • Retrieve 1RF0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RF0 from S2C, [Save to disk]
  • Re-refined 1rf0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RF0 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 1RF0
  • 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 1RF0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rf0a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rf0b2, region B:154-199 [Jmol] [rasmolscript] [script source]
        - Domain d1rf0b1, region B:200-459 [Jmol] [rasmolscript] [script source]
        - Domain d1rf0c1, region C:142-393 [Jmol] [rasmolscript] [script source]
        - Domain d1rf0c2, region C:96-141 [Jmol] [rasmolscript] [script source]
        - Domain d1rf0d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1rf0e2, region E:160-199 [Jmol] [rasmolscript] [script source]
        - Domain d1rf0e1, region E:200-459 [Jmol] [rasmolscript] [script source]
        - Domain d1rf0f1, region F:142-394 [Jmol] [rasmolscript] [script source]
        - Domain d1rf0f2, region F:96-141 [Jmol] [rasmolscript] [script source]
  • Fold representative 1rf0 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: [1rf0_B] [1rf0] [1rf0_F] [1rf0_D] [1rf0_C] [1rf0_E] [1rf0_A]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 1RF0: [FBG ] by SMART
  • Alignments of the sequence of 1RF0 with the sequences similar proteins can be viewed for 1RF0's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1RF0
  • Community annotation for 1RF0 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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