2ZI2 Hydrolase Hydrolase Inhibitor date Feb 13, 2008
title Thrombin Inhibition
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: Unp 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
70.500 71.600 72.600 90.00 100.60 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand 24U, BEN, NA, TYS BindingDB enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
H


L


Primary referenceNon-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry., Baum B, Muley L, Smolinski M, Heine A, Hangauer D, Klebe G, J Mol Biol. 2010 Apr 9;397(4):1042-54. Epub 2010 Feb 12. PMID:20156458
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (2zi2.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 2ZI2
  • CSU: Contacts of Structural Units for 2ZI2
  • Likely Quarternary Molecular Structure file(s) for 2ZI2
  • Structure Factors (311 Kb)
  • Retrieve 2ZI2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZI2 from S2C, [Save to disk]
  • Re-refined 2zi2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZI2 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 2ZI2
  • 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
  • 3D motif for 2ZI2, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zi2_H] [2zi2] [2zi2_I] [2zi2_L]
  • SWISS-PROT database: [P01050] [P00734]
  • Domain organization of [HIRV1_HIRME] [THRB_HUMAN] by SWISSPFAM
  • Domain found in 2ZI2: [Tryp_SPc ] by SMART
  • Other resources with information on 2ZI2
  • Community annotation for 2ZI2 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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