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 Diffraction	resolution	2.81 Å
ligand	CA, NAG	enzyme
related structures	by homologous chain: 1FZB, 1LT9
Gene Ontology	Chain Function Process Component A, D E, B F, C
Primary reference	Calcium-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] (221 Kb) [Save to disk] Biological Unit Coordinates (1rf0.pdb1.gz) 109 Kb Biological Unit Coordinates (1rf0.pdb2.gz) 109 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

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 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] 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

Other resources with information on 1RF0

Community annotation for 1RF0 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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