1FZE	Blood Coagulation	date	Dec 23, 1998
title	Crystal Structure Of Fragment Double-D From Human Fibrin
authors	S.J.Everse, G.Spraggon, L.Veerapandian, R.F.Doolittle
compound		source
Molecule: Fibrinogen Chain: A, D Fragment: Fragment D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
Molecule: Fibrinogen Chain: B, E Fragment: Fragment D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
Molecule: Fibrinogen Chain: C, F Fragment: Fragment D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Blood
symmetry	Space Group: P 1 21 1	R_factor 0.251 R_Free 0.318
crystal cell	length a length b length c angle alpha angle beta angle gamma 108.000 48.600 166.400 90.00 104.40 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	CA, NAG	enzyme
related structures	by homologous chain: 1FZA
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	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] (236 Kb) [Save to disk] Biological Unit Coordinates (1fze.pdb1.gz) 229 Kb Biological Unit Coordinates (1fze.pdb2.gz) 117 Kb Biological Unit Coordinates (1fze.pdb3.gz) 117 Kb LPC: Ligand-Protein Contacts for 1FZE CSU: Contacts of Structural Units for 1FZE Likely Quarternary Molecular Structure file(s) for 1FZE Retrieve 1FZE in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1FZE from S2C, [Save to disk]

View 1FZE 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 1FZE

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 1FZE, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1fzea_, region A [Jmol] [rasmolscript] [script source]     - Domain d1fzeb2, region B:151-199 [Jmol] [rasmolscript] [script source]     - Domain d1fzeb1, region B:200-459 [Jmol] [rasmolscript] [script source]     - Domain d1fzec1, region C:142-394 [Jmol] [rasmolscript] [script source]     - Domain d1fzec2, region C:92-141 [Jmol] [rasmolscript] [script source]     - Domain d1fzed_, region D [Jmol] [rasmolscript] [script source]     - Domain d1fzee2, region E:151-199 [Jmol] [rasmolscript] [script source]     - Domain d1fzee1, region E:200-458 [Jmol] [rasmolscript] [script source]     - Domain d1fzef1, region F:142-393 [Jmol] [rasmolscript] [script source]     - Domain d1fzef2, region F:92-141 [Jmol] [rasmolscript] [script source] Fold representative 1fze 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: [1fze_A] [1fze_B] [1fze_C] [1fze_D] [1fze_E] [1fze_F] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 1FZE: [FBG ] by SMART Alignments of the sequence of 1FZE with the sequences similar proteins can be viewed for 1FZE'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 1FZE

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

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