1FIB	Blood Coagulation Factor	date	Apr 02, 1996
title	Recombinant Human Gamma-Fibrinogen Carboxyl Terminal Fragment (Residues 143-411) Bound To Calcium At Ph 6.0
authors	V.C.Yee, D.C.Teller
compound		source
Molecule: Gamma-Fibrinogen Carboxyl Terminal Fragment Chain: A Fragment: Carboxyl Terminus, Residues 143 - 411 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Gene: Human Fibrinogen Gamma Chain C Expression_system: Pichia Pastoris Expression_system_taxid: 4922 Expression_system_plasmid: Ppic9k Expression_system_gene: Human Fibrinogen Gamma Chain Cdna Encoding Val 143 - Val 411
symmetry	Space Group: P 1 21 1	R_factor 0.159 R_Free 0.227
crystal cell	length a length b length c angle alpha angle beta angle gamma 37.530 68.420 47.670 90.00 105.36 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	CA	enzyme
related structures	by homologous chain: 1FID, 3FIB
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	Crystal structure of a 30 kDa C-terminal fragment from the gamma chain of human fibrinogen., Yee VC, Pratt KP, Cote HC, Trong IL, Chung DW, Davie EW, Stenkamp RE, Teller DC, Structure 1997 Jan 15;5(1):125-38. PMID:9016719

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk] Biological Unit Coordinates (1fib.pdb1.gz) 44 Kb LPC: Ligand-Protein Contacts for 1FIB CSU: Contacts of Structural Units for 1FIB Likely Quarternary Molecular Structure file(s) for 1FIB Structure Factors (104 Kb) Retrieve 1FIB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1FIB from S2C, [Save to disk] Re-refined 1fib structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1FIB 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 1FIB

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 1FIB, from MSDmotif at EBI Genome occurence of 1FIB's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1fib__, region [Jmol] [rasmolscript] [script source] Fold representative 1fib 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: [1fib_A] SWISS-PROT database: [P02679] Domain organization of [FIBG_HUMAN] by SWISSPFAM Domain found in 1FIB: [FBG ] by SMART Alignments of the sequence of 1FIB with the sequences similar proteins can be viewed for 1FIB'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 1FIB

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

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