3BF6	Hydrolase	date	Nov 20, 2007
title	Thrombin:Suramin Complex
authors	L.M.T.R.Lima, I.Polikarpov, R.Q.Monteiro
compound		source
Molecule: Thrombin, Light Chain Chain: L Fragment: Light Chain, Residues 328-363 Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Other_details: Human Plasma
Molecule: Thrombin, Heavy Chain Chain: H Fragment: Heavy Chain, Residues 364-622 Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Other_details: Human Plasma
Molecule: Phe-Pro-Arg Chain: I Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide
symmetry	Space Group: P 21 21 21	R_factor 0.228 R_Free 0.282
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.381 73.471 114.707 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	SVR	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
Gene Ontology	Chain Function Process Component H L
Primary reference	Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases., Lima LM, Becker CF, Giesel GM, Marques AF, Cargnelutti MT, de Oliveira Neto M, Monteiro RQ, Verli H, Polikarpov I, Biochim Biophys Acta. 2009 Jun;1794(6):873-81. Epub 2009 Mar 28. PMID:19332154

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk] Biological Unit Coordinates (3bf6.pdb1.gz) 54 Kb LPC: Ligand-Protein Contacts for 3BF6 CSU: Contacts of Structural Units for 3BF6 Likely Quarternary Molecular Structure file(s) for 3BF6 Structure Factors (211 Kb) Retrieve 3BF6 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3BF6 from S2C, [Save to disk] Re-refined 3bf6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BF6 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 3BF6

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 3BF6, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3bf6_H] [3bf6_I] [3bf6_L] [3bf6] SWISS-PROT database: [P00734] Domain organization of [THRB_HUMAN] by SWISSPFAM Domain found in 3BF6: [Tryp_SPc ] by SMART

Other resources with information on 3BF6

Community annotation for 3BF6 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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