1YPK	Hydrolase Hydrolase Inhibitor	date	Jan 31, 2005
title	Thrombin Inhibitor Complex
authors	P.Czodrowski, C.Sotriffer, J.Fokkens, A.Heine, G.Klebe
compound		source
Molecule: Prothrombin Light Chain Chain: L Synonym: Thrombin Light Chain Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood
Molecule: Prothrombin Heavy Chain Chain: H Synonym: Thrombin Heavy Chain Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood
Molecule: 10-Mer Peptide From Acety-Hirudin(54-65) Sulfated Chain: I Engineered: Yes		Synthetic: Yes Organism_scientific: Hirudo Medicinalis Organism_taxid: 6421 Other_details: This Sequence Occurs Naturally
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 70.885 71.744 72.274 90.00 100.93 90.00
method	X-Ray Diffraction	resolution	1.78 Å
ligand	CCR, TYS	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
Gene Ontology	Chain Function Process Component H L
Primary reference	A Simple Protocol To Estimate Differences in Protein Binding Affinity for Enantiomers without Prior Resolution of Racemates., Fokkens J, Klebe G, Angew Chem Int Ed Engl. 2005 Dec 22;. PMID:16374786

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk] Biological Unit Coordinates (1ypk.pdb1.gz) 54 Kb LPC: Ligand-Protein Contacts for 1YPK CSU: Contacts of Structural Units for 1YPK Likely Quarternary Molecular Structure file(s) for 1YPK Structure Factors (276 Kb) Retrieve 1YPK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YPK from S2C, [Save to disk] Re-refined 1ypk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YPK 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 1YPK

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 1YPK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ypk] [1ypk_H] [1ypk_L] [1ypk_I] SWISS-PROT database: [P00734] Domain organization of [THRB_HUMAN] by SWISSPFAM Domain found in 1YPK: [Tryp_SPc ] by SMART

Other resources with information on 1YPK

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

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