3DHK	Blood Clotting Hydrolase Inhibitor	date	Jun 18, 2008
title	Bisphenylic Thrombin Inhibitors
authors	B.Baum, A.Heine, G.Klebe
compound		source
Molecule: Thrombin Light Chain Chain: L Synonym: Coagulation Factor II Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Plasma
Molecule: Thrombin Heavy Chain Chain: H Synonym: Coagulation Factor II Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Plasma
Molecule: Hirudin Variant-1 Chain: I Fragment: Residues 54-64 Synonym: Lepirudin Engineered: Yes		Synthetic: Yes Other_details: Synthetic Fragment Of Hirudin From Hirudo Me
symmetry	Space Group: C 1 2 1	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 69.950 71.340 72.440 90.00 100.32 90.00
method	X-Ray Diffraction	resolution	1.73 Å
ligand	23U, NA, TYS BindingDB	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
Gene Ontology	Chain Function Process Component H L
Primary reference	Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin., Baum B, Muley L, Heine A, Smolinski M, Hangauer D, Klebe G, J Mol Biol. 2009 Aug 21;391(3):552-64. Epub 2009 Jun 9. PMID:19520086

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk] Biological Unit Coordinates (3dhk.pdb1.gz) 50 Kb LPC: Ligand-Protein Contacts for 3DHK CSU: Contacts of Structural Units for 3DHK Likely Quarternary Molecular Structure file(s) for 3DHK Structure Factors (229 Kb) Retrieve 3DHK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DHK from S2C, [Save to disk] Re-refined 3dhk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DHK 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.

Visual 3D analysis of 3DHK

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 3D motif for 3DHK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dhk_I] [3dhk_H] [3dhk] [3dhk_L] SWISS-PROT database: [P00734] Domain organization of [THRB_HUMAN] by SWISSPFAM Domain found in 3DHK: [Tryp_SPc ] by SMART

Other resources with information on 3DHK

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

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Images from IMB Jena Image Library of Biological Macromolecules.

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