1K21 Hydrolase Hydrolase Inhibitor date Sep 26, 2001
title Human Thrombin-Inhibitor Complex
authors M.T.Stubbs, D.Musil
compound source
Molecule: Prothrombin
Chain: L
Fragment: Thrombin Light Chain, Residues 323-363
Synonym: Alpha-Thrombin, Coagulation Factor II
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Prothrombin
Chain: H
Fragment: Thrombin Heavy Chain, Residues 364-622
Synonym: Alpha-Thrombin, Coagulation Factor II
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hirudin Variant-2
Chain: I
Fragment: Residues 60-71

Organism_scientific: Hirudo Medicinalis
Organism_common: Medicinal Leech
Organism_taxid: 6421
symmetry Space Group: C 1 2 1
R_factor 0.216 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.619 71.546 71.821 90.00 100.12 90.00
method X-Ray Diffractionresolution 1.86 Å
ligand IGN, NA, NAG, TYS BindingDB enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1NO9, 1XMN
Gene
Ontology
ChainFunctionProcessComponent
H


L


Primary referenceFactorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition., Dullweber F, Stubbs MT, Musil D, Sturzebecher J, Klebe G, J Mol Biol 2001 Oct 26;313(3):593-614. PMID:11676542
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (1k21.pdb1.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 1K21
  • CSU: Contacts of Structural Units for 1K21
  • Likely Quarternary Molecular Structure file(s) for 1K21
  • Structure Factors (85 Kb)
  • Retrieve 1K21 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K21 from S2C, [Save to disk]
  • View 1K21 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 1K21
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1K21, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k21.1, region L:,H [Jmol] [rasmolscript] [script source]
  • 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: [1k21] [1k21_H] [1k21_I] [1k21_L]
  • SWISS-PROT database: [P09945] [P00734]
  • Domain organization of [HIRV2_HIRME] [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1K21: [Tryp_SPc ] by SMART
  • Other resources with information on 1K21
  • Community annotation for 1K21 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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