3SI4 Hydrolase Hydrolase Inhibitor date Jun 17, 2011
title Human Thrombin In Complex With Ubthr104
authors A.Biela, A.Heine, G.Klebe
compound source
Molecule: Thrombin Light Chain
Chain: L
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Thrombin Heavy Chain
Chain: H
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hirudin Variant-2
Chain: I
Fragment: Residues In Unp 60-72
Engineered: Yes

Synthetic: Yes
Organism_scientific: Hirudo Medicinalis
Organism_common: Medicinal Leech
Organism_taxid: 6421
Other_details: Synthetic Fragment Of Hirudin From Hirudo Me
symmetry Space Group: C 1 2 1
R_factor 0.137 R_Free 0.159
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.350 71.230 72.590 90.00 100.36 90.00
method X-Ray Diffractionresolution 1.27 Å
ligand B04, GOL, NA, NAG, PO4, TYS enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
H


L


Primary referenceImpact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin., Biela A, Khayat M, Tan H, Kong J, Heine A, Hangauer D, Klebe G, J Mol Biol. 2012 May 18;418(5):350-66. Epub 2012 Feb 21. PMID:22366545
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk]
  • Biological Unit Coordinates (3si4.pdb1.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 3SI4
  • CSU: Contacts of Structural Units for 3SI4
  • Structure Factors (1135 Kb)
  • Retrieve 3SI4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SI4 from S2C, [Save to disk]
  • Re-refined 3si4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SI4 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 3SI4
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3SI4, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3si4_H] [3si4_L] [3si4_I] [3si4]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3SI4: [Tryp_SPc ] by SMART
  • Other resources with information on 3SI4
  • Community annotation for 3SI4 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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