2H43	Blood Clotting	date	May 23, 2006
title	Crystal Structure Of Human Fragment D Complexed With Ala-His Amide
authors	R.F.Doolittle, L.Pandi
compound		source
Molecule: Fibrinogen Alpha Chain Chain: A, D		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Fibrinogen Beta Chain Chain: B, E		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Fibrinogen Gamma Chain Chain: C, F		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Gly-His-Arg-Pro-Amide Peptide Ligand Chain: I, J Engineered: Yes		Synthetic: Yes Other_details: The Peptide Was Chemically Synthesized.
symmetry	Space Group: P 1 21 1	R_factor 0.251 R_Free 0.307
crystal cell	length a length b length c angle alpha angle beta angle gamma 105.000 47.900 171.400 90.00 105.41 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	CA, NAG, NDG, NH2	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	Differences in Binding Specificity for the Homologous gamma- and beta-Chain "Holes" on Fibrinogen: Exclusive Binding of Ala-His-Arg-Pro-amide by the beta-Chain Hole(,)., Doolittle RF, Chen A, Pandi L, Biochemistry. 2006 Nov 28;45(47):13962-13969. PMID:17115691

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (228 Kb) [Save to disk] Biological Unit Coordinates (2h43.pdb1.gz) 113 Kb Biological Unit Coordinates (2h43.pdb2.gz) 113 Kb LPC: Ligand-Protein Contacts for 2H43 CSU: Contacts of Structural Units for 2H43 Likely Quarternary Molecular Structure file(s) for 2H43 Structure Factors (477 Kb) Retrieve 2H43 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2H43 from S2C, [Save to disk] Re-refined 2h43 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2H43 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 2H43

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 2H43, from MSDmotif at EBI Fold representative 2h43 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2h43_A] [2h43_B] [2h43_C] [2h43_D] [2h43_E] [2h43_F] [2h43_I] [2h43_J] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 2H43: [FBG ] by SMART Alignments of the sequence of 2H43 with the sequences similar proteins can be viewed for 2H43'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 2H43

Community annotation for 2H43 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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