1FZB	Blood Coagulation	date	Aug 05, 1997
title	Crystal Structure Of Crosslinked Fragment D
authors	G.Spraggon, S.J.Everse, R.F.Doolittle
compound		source
Molecule: Fibrinogen Chain: A, D Fragment: Double Fragment D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
Molecule: Fibrinogen Chain: B, E Fragment: Double Fragment D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
Molecule: Fibrinogen Chain: C, F Fragment: Double Fragment D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
Molecule: Peptide Ligand Gprg Chain: G, H Engineered: Yes Other_details: Bound Peptide Causes The Fibrin Clot Conform
symmetry	Space Group: P 1 21 1	R_factor 0.241 R_Free 0.318
crystal cell	length a length b length c angle alpha angle beta angle gamma 93.820 95.500 113.760 90.00 96.08 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	CA, NAG	enzyme
related structures	by homologous chain: 1FZA, 1RF0
Gene Ontology	Chain Function Process Component E, B eukaryotic cell surface bind... chaperone 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 F, C 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 structures of fragment D from human fibrinogen and its crosslinked counterpart from fibrin., Spraggon G, Everse SJ, Doolittle RF, Nature 1997 Oct 2;389(6650):455-62. PMID:9333233

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (239 Kb) [Save to disk] Biological Unit Coordinates (1fzb.pdb1.gz) 234 Kb LPC: Ligand-Protein Contacts for 1FZB CSU: Contacts of Structural Units for 1FZB Likely Quarternary Molecular Structure file(s) for 1FZB Retrieve 1FZB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1FZB from S2C, [Save to disk]

View 1FZB 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 1FZB

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1FZB, from MSDmotif at EBI Genome occurence of 1FZB's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1fzba_, region A [Jmol] [rasmolscript] [script source]     - Domain d1fzbb2, region B:148-199 [Jmol] [rasmolscript] [script source]     - Domain d1fzbb1, region B:200-459 [Jmol] [rasmolscript] [script source]     - Domain d1fzbc1, region C:142-396 [Jmol] [rasmolscript] [script source]     - Domain d1fzbc2, region C:88-141 [Jmol] [rasmolscript] [script source]     - Domain d1fzbd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1fzbe2, region E:148-199 [Jmol] [rasmolscript] [script source]     - Domain d1fzbe1, region E:200-459 [Jmol] [rasmolscript] [script source]     - Domain d1fzbf1, region F:142-398 [Jmol] [rasmolscript] [script source]     - Domain d1fzbf2, region F:88-141 [Jmol] [rasmolscript] [script source] Fold representative 1fzb 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: [1fzb_A] [1fzb_B] [1fzb_C] [1fzb_D] [1fzb_E] [1fzb_F] [1fzb_G] [1fzb_H] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 1FZB: [FBG ] by SMART Alignments of the sequence of 1FZB with the sequences similar proteins can be viewed for 1FZB'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 1FZB

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

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