1YCP	Hydrolase Hydrolase Substrate	date	May 01, 1997
title	The Crystal Structure Of Fibrinogen-Aa Peptide 1-23 (F8y) Bo Bovine Thrombin Explains Why The Mutation Of Phe-8 To Tyros Strongly Inhibits Normal Cleavage At Arginine-16
authors	M.G.Malkowski, B.F.P.Edwards
compound		source
Molecule: Epsilon Thrombin Chain: L, J Ec: 3.4.21.5		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Tissue: Blood
Molecule: Alpha Thrombin Chain: H Ec: 3.4.21.5		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Tissue: Blood
Molecule: Fibrinopeptide A-Alpha Chain: F, N Fragment: Residues 1 - 23 Engineered: Yes Mutation: Yes
Molecule: Epsilon Thrombin Chain: K		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Tissue: Blood
Molecule: Epsilon Thrombin Chain: M		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Tissue: Blood
symmetry	Space Group: P 43 21 2	R_factor 0.183 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 88.270 88.270 195.530 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand		enzyme	Hydrolase E.C.3.4.21.5 BRENDA
related structures	by homologous chain: 1JWT, 1TMU
Primary reference	Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16., Malkowski MG, Martin PD, Lord ST, Edwards BF, Biochem J 1997 Sep 15;326 ( Pt 3):815-22. PMID:9307032

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk] Biological Unit Coordinates (1ycp.pdb1.gz) 52 Kb Biological Unit Coordinates (1ycp.pdb2.gz) 51 Kb CSU: Contacts of Structural Units for 1YCP Likely Quarternary Molecular Structure file(s) for 1YCP Retrieve 1YCP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YCP from S2C, [Save to disk]

View 1YCP 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 1YCP

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1YCP, from MSDmotif at EBI Genome occurence of 1YCP's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ycp.2, region J:,K:,M [Jmol] [rasmolscript] [script source]     - Domain d1ycp.1, region L:,H [Jmol] [rasmolscript] [script source] Fold representative 1ycp from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ycp_F] [1ycp_H] [1ycp_J] [1ycp_K] [1ycp_L] [1ycp_M] [1ycp_N] SWISS-PROT database: [P02671] [P00735] Domain organization of [FIBA_HUMAN] [THRB_BOVIN] by SWISSPFAM Domain found in 1YCP: [Tryp_SPc ] by SMART Alignments of the sequence of 1YCP with the sequences similar proteins can be viewed for 1YCP's classification [FIBA_HUMAN] [THRB_BOVIN] 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] [THRB_BOVIN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1YCP

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

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