1FZF	Blood Coagulation	date	Dec 28, 1998
title	Crystal Structure Of Fragment Double-D From Human Fibrin Wit Peptide Ligand Gly-His-Arg-Pro-Amide
authors	S.J.Everse, G.Spraggon, L.Veerapandian, R.F.Doolittle
compound		source
Molecule: Fibrinogen Chain: A, D Fragment: Fragment Double-D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
Molecule: Fibrinogen Chain: B, E Fragment: Fragment Double-D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
Molecule: Fibrinogen Chain: C, F Fragment: Fragment Double-D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
Molecule: Fibrinogen Chain: S, T, M, N Fragment: Fragment Double-D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood
symmetry	Space Group: P 21 21 21	R_factor 0.233 R_Free 0.302
crystal cell	length a length b length c angle alpha angle beta angle gamma 54.800 149.400 234.700 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	CA, NAG	enzyme
related structures	by homologous chain: 1LTJ, 1M1J, 1RE4
Gene Ontology	Chain Function Process Component 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 S, T, N, E, B, M 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
Primary reference	Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide., Everse SJ, Spraggon G, Veerapandian L, Doolittle RF, Biochemistry 1999 Mar 9;38(10):2941-6. PMID:10074346

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (224 Kb) [Save to disk] Biological Unit Coordinates (1fzf.pdb1.gz) 216 Kb LPC: Ligand-Protein Contacts for 1FZF CSU: Contacts of Structural Units for 1FZF Likely Quarternary Molecular Structure file(s) for 1FZF Retrieve 1FZF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1FZF from S2C, [Save to disk]

View 1FZF 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 1FZF

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 1FZF, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1fzfa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1fzfb2, region B:157-199 [Jmol] [rasmolscript] [script source]     - Domain d1fzfb1, region B:200-459 [Jmol] [rasmolscript] [script source]     - Domain d1fzfc2, region C:102-141 [Jmol] [rasmolscript] [script source]     - Domain d1fzfc1, region C:142-393 [Jmol] [rasmolscript] [script source]     - Domain d1fzfd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1fzfe2, region E:164-199 [Jmol] [rasmolscript] [script source]     - Domain d1fzfe1, region E:200-459 [Jmol] [rasmolscript] [script source]     - Domain d1fzff2, region F:109-141 [Jmol] [rasmolscript] [script source]     - Domain d1fzff1, region F:142-393 [Jmol] [rasmolscript] [script source] Fold representative 1fzf 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: [1fzf_A] [1fzf_B] [1fzf_C] [1fzf_D] [1fzf_E] [1fzf_F] [1fzf_M] [1fzf_N] [1fzf_S] [1fzf_T] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 1FZF: [FBG ] by SMART Alignments of the sequence of 1FZF with the sequences similar proteins can be viewed for 1FZF'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 1FZF

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

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