2ZO3 Hydrolase Hydrolase Inhibitor date May 05, 2008
title Bisphenylic Thrombin Inhibitors
authors B.Baum, A.Heine, G.Klebe
compound source
Molecule: Thrombin Light Chain
Chain: L
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood Plasma

Molecule: Thrombin Heavy Chain
Chain: H
Synonym: Coagulation Factor II
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood Plasma

Molecule: Hirudin Variant-1
Chain: I
Fragment: Residues 54-64
Synonym: Lepirudin
Engineered: Yes

Synthetic: Yes
Organism_scientific: Hirudo Medicinalis
Organism_taxid: 6421
Other_details: Synthetic Fragment Of Hirudin From Hirudo Me
symmetry Space Group: C 1 2 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.950 71.640 71.910 90.00 100.10 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand 33U, NA, TYS BindingDB enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
H


L


Primary referenceThink twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin., Baum B, Muley L, Heine A, Smolinski M, Hangauer D, Klebe G, J Mol Biol. 2009 Aug 21;391(3):552-64. Epub 2009 Jun 9. PMID:19520086
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (2zo3.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 2ZO3
  • CSU: Contacts of Structural Units for 2ZO3
  • Likely Quarternary Molecular Structure file(s) for 2ZO3
  • Structure Factors (273 Kb)
  • Retrieve 2ZO3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZO3 from S2C, [Save to disk]
  • Re-refined 2zo3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZO3 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 2ZO3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2ZO3, from MSDmotif at EBI
  • Fold representative 2zo3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zo3_I] [2zo3_L] [2zo3] [2zo3_H]
  • SWISS-PROT database: [P01050] [P00734]
  • Domain organization of [HIRV1_HIRME] [THRB_HUMAN] by SWISSPFAM
  • Domain found in 2ZO3: [Tryp_SPc ] by SMART
  • Other resources with information on 2ZO3
  • Community annotation for 2ZO3 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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