1A3B Hydrolase Hydrolase Inhibitor date Jan 20, 1998
title Complex Of Human Alpha-Thrombin With The Bifunctional Borona Inhibitor Borolog1
authors E.Skordalakes, S.Elgendy, G.Dodson, C.A.Goodwin, D.Green, M.F.Scu J.H.Freyssinet, V.V.Kakkar, J.Deadman
compound source
Molecule: Alpha-Thrombin (Small Subunit)
Chain: L
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Alpha-Thrombin (Large Subunit)
Chain: H

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hirudin
Chain: I

Organism_scientific: Hirudo Medicinalis
Organism_common: Medicinal Leech
Organism_taxid: 6421
symmetry Space Group: C 1 2 1
R_factor 0.170 R_Free 0.230
length a length b length c angle alpha angle beta angle gamma
70.150 71.340 71.650 90.00 100.23 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand T29 enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1AY6, 1TOM


Primary referenceBifunctional peptide boronate inhibitors of thrombin: crystallographic analysis of inhibition enhanced by linkage to an exosite 1 binding peptide., Skordalakes E, Elgendy S, Goodwin CA, Green D, Scully MF, Kakkar VV, Freyssinet JM, Dodson G, Deadman JJ, Biochemistry. 1998 Oct 13;37(41):14420-7. PMID:9772168
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (1a3b.pdb1.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 1A3B
  • CSU: Contacts of Structural Units for 1A3B
  • Likely Quarternary Molecular Structure file(s) for 1A3B
  • Retrieve 1A3B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1A3B from S2C, [Save to disk]
  • View 1A3B 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 1A3B
  • 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 1A3B, from MSDmotif at EBI
  • Genome occurence of 1A3B's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1a3b.1, region L:,H [Jmol] [rasmolscript] [script source]
  • Fold representative 1a3b 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: [1a3b] [1a3b_L] [1a3b_H] [1a3b_I]
  • SWISS-PROT database: [P28504] [P00734]
  • Domain organization of [HIR2_HIRME] [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1A3B: [Tryp_SPc ] by SMART
  • Other resources with information on 1A3B
  • Community annotation for 1A3B 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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