1YPL	Blood Clotting Hydrolase Inhibitor	date	Jan 31, 2005
title	X-Ray Crystal Structure Of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008
authors	J.Fokkens, G.Radau
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
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
Molecule: Hirudin Chain: I Fragment: Residues 1-10 Engineered: Yes		Synthetic: Yes Organism_scientific: Hirudo Medicinalis Organism_taxid: 6421 Other_details: Chemically Synthesized
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 70.131 71.630 72.198 90.00 100.45 90.00
method	X-Ray Diffraction	resolution	1.85 Å
ligand	GOL, NA, RA8, TYS	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
Gene Ontology	Chain Function Process Component H L
Primary reference	Design and X-ray crystal structures of human thrombin with synthetic cyanopeptide-analogues., Radau G, Fokkens J, Pharmazie. 2007 Feb;62(2):83-8. PMID:17341023

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk] Biological Unit Coordinates (1ypl.pdb1.gz) 53 Kb LPC: Ligand-Protein Contacts for 1YPL CSU: Contacts of Structural Units for 1YPL Likely Quarternary Molecular Structure file(s) for 1YPL Structure Factors (246 Kb) Retrieve 1YPL in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YPL from S2C, [Save to disk] Re-refined 1ypl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YPL 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 1YPL

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 1YPL, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ypl_L] [1ypl] [1ypl_H] [1ypl_I] SWISS-PROT database: [P00734] Domain organization of [THRB_HUMAN] by SWISSPFAM Domain found in 1YPL: [Tryp_SPc ] by SMART

Other resources with information on 1YPL

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

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---