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 Diffraction	resolution	2.43 Å
ligand	GDP, MG, MSE	enzyme	Transferase E.C.2.7.11.1 BRENDA
Primary reference	Structure 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3D6T

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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_B] SWISS-PROT database: [Q5S007] Domain organization of [LRRK2_HUMAN] by SWISSPFAM Domain found in 3D6T: [small_GTPase ] by SMART Alignments of the sequence of 3D6T with the sequences similar proteins can be viewed for 3D6T's classification [LRRK2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [LRRK2_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3D6T

Community annotation for 3D6T at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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