3H32	Blood Clotting	date	Apr 15, 2009
title	Crystal Structure Of D-Dimer From Human Fibrin Complexed Wit Arg-Pro-Tyr-Amide
authors	R.F.Doolittle, L.Pandi
compound		source
Molecule: Fibrinogen Alpha Chain Chain: A, D Fragment: Unp Residues 20-216 Synonym: Fibrinopeptide A		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Plasma
Molecule: Fibrinogen Beta Chain Chain: B, E Fragment: Unp Residues 31-488 Synonym: Fibrinopeptide B		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Plasma
Molecule: Fibrinogen Gamma Chain, Isoform Gamma-A Chain: C, F Fragment: Unp Residues 27-437		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Plasma
Molecule: Fibrin B Knob Pentapeptide Chain: M, N Fragment: Unp Residues 22-26 Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide Based On The Bovine (Bos T Fibrinopeptide B, P02676, Fibb_bovin, Sequence Position 22-
symmetry	Space Group: C 1 2 1	R_factor 0.263 R_Free 0.320
crystal cell	length a length b length c angle alpha angle beta angle gamma 264.720 97.320 132.490 90.00 122.78 90.00
method	X-Ray Diffraction	resolution	3.60 Å
ligand	CA, GAL, MAN, NAG, SIA	enzyme
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	Two Families of Synthetic Peptides That Enhance Fibrin Turbidity and Delay Fibrinolysis by Different Mechanisms., Pandi L, Kollman JM, Lopez-Lira F, Burrows JM, Riley M, Doolittle RF, Biochemistry. 2009 Jul 9. PMID:19588915

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (239 Kb) [Save to disk] Biological Unit Coordinates (3h32.pdb1.gz) 228 Kb LPC: Ligand-Protein Contacts for 3H32 CSU: Contacts of Structural Units for 3H32 Likely Quarternary Molecular Structure file(s) for 3H32 Structure Factors (220 Kb) Retrieve 3H32 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3H32 from S2C, [Save to disk] Re-refined 3h32 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3H32 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 3H32

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 3H32, from MSDmotif at EBI Fold representative 3h32 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3h32_A] [3h32_B] [3h32_C] [3h32_D] [3h32_E] [3h32_F] [3h32_M] [3h32_N] SWISS-PROT database: [P02671] [P02676] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_BOVIN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 3H32: [FBG ] by SMART Alignments of the sequence of 3H32 with the sequences similar proteins can be viewed for 3H32's classification [FIBA_HUMAN] [FIBB_BOVIN] [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_BOVIN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3H32

Community annotation for 3H32 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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