1TA2 Hydrolase Hydrolase Inhibitor date May 19, 2004
title Crystal Structure Of Thrombin In Complex With Compound 1
authors T.J.Tucker, S.F.Brady, W.C.Lumma, S.D.Lewis, S.J.Gardel, A.M.Nayl Y.Yan, J.T.Sisko, K.J.Stauffer, B.Y.Lucas, J.J.Lynch, J.J.Cook, M.T.Stranieri, M.A.Holahan, E.A.Lyle, E.P.Baskin, I.W.Chen, K.B.Dancheck, J.A.Krueger, C.M.Cooper, J.P.Vacca
compound source
Molecule: Thrombin
Chain: A
Fragment: Alpha-Thrombin
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Pancreas

Molecule: Hirudin
Chain: B
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.150 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.810 72.360 72.960 90.00 100.90 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 176, TYS BindingDB enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1D9I, 1DIT
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDesign and synthesis of a series of potent and orally bioavailable noncovalent thrombin inhibitors that utilize nonbasic groups in the P1 position., Tucker TJ, Brady SF, Lumma WC, Lewis SD, Gardell SJ, Naylor-Olsen AM, Yan Y, Sisko JT, Stauffer KJ, Lucas BJ, Lynch JJ, Cook JJ, Stranieri MT, Holahan MA, Lyle EA, Baskin EP, Chen IW, Dancheck KB, Krueger JA, Cooper CM, Vacca JP, J Med Chem 1998 Aug 13;41(17):3210-9. PMID:9703466
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (1ta2.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 1TA2
  • CSU: Contacts of Structural Units for 1TA2
  • Likely Quarternary Molecular Structure file(s) for 1TA2
  • Retrieve 1TA2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TA2 from S2C, [Save to disk]
  • View 1TA2 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 1TA2
  • 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 1TA2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ta2a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1n1ta2, region A:1-406 [Jmol] [rasmolscript] [script source]
        - Domain d1g1ta2, region A:119-157 [Jmol] [rasmolscript] [script source]
        - Domain d1e1ta2, region A:161-502 [Jmol] [rasmolscript] [script source]
        - Domain d1d1ta2, region A:163-338 [Jmol] [rasmolscript] [script source]
        - Domain d1l1ta2, region A:2-134 [Jmol] [rasmolscript] [script source]
        - Domain d1m1ta2, region A:269-392 [Jmol] [rasmolscript] [script source]
        - Domain d1s1ta2, region A:3-429 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ta2 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: [1ta2] [1ta2_B] [1ta2_A]
  • SWISS-PROT database: [P00734]
  • Domain organization of [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1TA2: [Tryp_SPc ] by SMART
  • Other resources with information on 1TA2
  • Community annotation for 1TA2 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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