3QDZ Hydrolase Hydrolase Receptor date Jan 19, 2011
title Crystal Structure Of The Human Thrombin Mutant D102n In Comp The Extracellular Fragment Of Human Par4.
authors P.Gandhi, Z.Chen, E.Appelbaum, F.Zapata, E.Di Cera
compound source
Molecule: Thrombin Light Chain
Chain: A, C
Synonym: Coagulation Factor II, Activation Peptide Fragment Activation Peptide Fragment 2, Thrombin Light Chain, Thromb Chain;
Ec: 3.4.21.5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F2
Expression_system: Mesocricetus Auratus
Expression_system_taxid: 10036
Expression_system_cell_line: Bhk

Molecule: Thrombin Heavy Chain
Chain: B, D
Synonym: Coagulation Factor II, Activation Peptide Fragment Activation Peptide Fragment 2, Thrombin Light Chain, Thromb Chain;
Ec: 3.4.21.5
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F2
Expression_system: Mesocricetus Auratus
Expression_system_taxid: 10036
Expression_system_cell_line: Bhk

Molecule: Proteinase-Activated Receptor 4
Chain: E, F
Synonym: Par-4, Coagulation Factor II Receptor-Like 3, Thro Receptor-Like 3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F2rl3, Par4
Expression_system: Mesocricetus Auratus
Expression_system_taxid: 10036
Expression_system_cell_line: Bhk
symmetry Space Group: C 2 2 21
R_factor 0.304 R_Free 0.364
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.414 102.876 146.390 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand
enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (101 Kb) [Save to disk]
  • Biological Unit Coordinates (3qdz.pdb1.gz) 49 Kb
  • Biological Unit Coordinates (3qdz.pdb2.gz) 49 Kb
  • CSU: Contacts of Structural Units for 3QDZ
  • Structure Factors (207 Kb)
  • Retrieve 3QDZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QDZ from S2C, [Save to disk]
  • Re-refined 3qdz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QDZ 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 3QDZ
  • 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 3QDZ, from MSDmotif at EBI
  • Fold representative 3qdz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qdz_E] [3qdz] [3qdz_A] [3qdz_B] [3qdz_F] [3qdz_C] [3qdz_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3QDZ: [Tryp_SPc ] by SMART
  • Other resources with information on 3QDZ
  • Community annotation for 3QDZ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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