2FIB	Complex (Blood Coagulation Peptide)	date	Jun 03, 1997
title	Recombinant Human Gamma-Fibrinogen Carboxyl Terminal Fragment (Residues 143-411) Complexed To The Peptide Gly- Pro-Arg-Pro At Ph 6.0
authors	K.P.Pratt, H.C.F.Cote, D.W.Chung, R.E.Stenkamp, E.W.Davie
compound		source
Molecule: Fibrinogen Chain: A Fragment: Gamma Chain, Carboxyl Terminal Fragment Residues 143 - 411; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood Plasma Gene: Human Fibrinogen Gamma Chain Cdna Encoding Val 143 - Val 411; Expression_system: Pichia Pastoris Expression_system_taxid: 4922 Expression_system_plasmid: Ppic9k
Molecule: Gly-Pro-Arg-Pro Chain: B Engineered: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.186 R_Free 0.282
crystal cell	length a length b length c angle alpha angle beta angle gamma 37.330 68.200 47.600 90.00 105.02 90.00
method	X-Ray Diffraction	resolution	2.01 Å
ligand	CA	enzyme
related structures	by homologous chain: 1FID, 1FZC
Gene Ontology	Chain Function Process Component A eukaryotic cell surface bind... metal ion binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle
Primary reference	The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro., Pratt KP, Cote HC, Chung DW, Stenkamp RE, Davie EW, Proc Natl Acad Sci U S A 1997 Jul 8;94(14):7176-81. PMID:9207064

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk] Biological Unit Coordinates (2fib.pdb1.gz) 44 Kb LPC: Ligand-Protein Contacts for 2FIB CSU: Contacts of Structural Units for 2FIB Likely Quarternary Molecular Structure file(s) for 2FIB Structure Factors (118 Kb) Retrieve 2FIB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2FIB from S2C, [Save to disk] Re-refined 2fib structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2FIB 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2FIB

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 2FIB, from MSDmotif at EBI Genome occurence of 2FIB's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d2fiba_, region A [Jmol] [rasmolscript] [script source] Fold representative 2fib 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: [2fib_A] [2fib_B] SWISS-PROT database: [P02679] Domain organization of [FIBG_HUMAN] by SWISSPFAM Domain found in 2FIB: [FBG ] by SMART Alignments of the sequence of 2FIB with the sequences similar proteins can be viewed for 2FIB's classification [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 [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2FIB

Community annotation for 2FIB at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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