3D6T Transferase date May 20, 2008
title Structure Of The Roc Domain From The Parkinson'S Disease-Ass Leucine-Rich Repeat Kinase 2 Reveals A Dimeric Gtpase
authors J.Deng
compound source
Molecule: Leucine-Rich Repeat Serinethreonine-Protein Kina
Chain: B
Fragment: Miro Domain
Synonym: Dardarin
Ec: 2.7.11.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Strain: Bl21goldde3
Gene: Lrrk2, Park8
Expression_system: Escherichia Coli
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pskb3
symmetry Space Group: C 1 2 1
R_factor 0.211 R_Free 0.307
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.919 53.167 42.736 90.00 112.76 90.00
method X-Ray Diffractionresolution 2.43 Å
ligand GDP, MG, MSE enzyme Transferase E.C.2.7.11.1 BRENDA
Primary referenceStructure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase., Deng J, Lewis PA, Greggio E, Sluch E, Beilina A, Cookson MR, Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1499-504. Epub 2008 Jan 29. PMID:18230735
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (3d6t.pdb1.gz) 22 Kb
  • Biological Unit Coordinates (3d6t.pdb2.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 3D6T
  • CSU: Contacts of Structural Units for 3D6T
  • Likely Quarternary Molecular Structure file(s) for 3D6T
  • Structure Factors (84 Kb)
  • Retrieve 3D6T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D6T from S2C, [Save to disk]
  • Re-refined 3d6t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D6T 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 3D6T
  • 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 3D6T, from MSDmotif at EBI
  • Fold representative 3d6t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d6t] [3d6t_B]
  • SWISS-PROT database: [Q5S007]
  • Domain organization of [LRRK2_HUMAN] by SWISSPFAM
  • Other resources with information on 3D6T
  • Community annotation for 3D6T 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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