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 Diffractionresolution 2.50 Å
ligand
enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1JWT, 1TMU
Gene
Ontology
ChainFunctionProcessComponent
H, K


J, L


M


Primary referenceCrystal 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.
  • 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_N] [1ycp_L] [1ycp_J] [1ycp_H] [1ycp] [1ycp_K] [1ycp_M]
  • SWISS-PROT database: [P02671] [P00735]
  • Domain organization of [FIBA_HUMAN] [THRB_BOVIN] by SWISSPFAM
  • Domain found in 1YCP: [Tryp_SPc ] by SMART
  • Other resources with information on 1YCP
  • Community annotation for 1YCP at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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