3LCD	Transferase	date	Jan 10, 2010
title	Inhibitor Bound To A Dfg-In Structure Of The Kinase Domain O
authors	S.Kamtekar, J.E.Day, B.A.Reitz, K.J.Mathis, M.J.Meyers
compound		source
Molecule: Macrophage Colony-Stimulating Factor 1 Receptor Chain: A Fragment: Kinase Domain Synonym: Csf-1-R, Fms Proto-Oncogene, C-Fms Ec: 2.7.10.1 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Csf-1r, Csf1r, Fms Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108 Expression_system_vector_type: Baculovirus
symmetry	Space Group: P 21 21 21	R_factor 0.216 R_Free 0.265
crystal cell	length a length b length c angle alpha angle beta angle gamma 57.649 74.125 91.024 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	BDY, SO4	enzyme	Transferase E.C.2.7.10.1 BRENDA
Primary reference	Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode., Meyers MJ, Pelc M, Kamtekar S, Day J, Poda GI, Hall MK, Michener ML, Reitz BA, Mathis KJ, Pierce BS, Parikh MD, Mischke DA, Long SA, Parlow JJ, Anderson DR, Thorarensen A, Bioorg Med Chem Lett. 2010 Mar 1;20(5):1543-1547. Epub 2010 Jan 21. PMID:20137931

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk] Biological Unit Coordinates (3lcd.pdb1.gz) 48 Kb LPC: Ligand-Protein Contacts for 3LCD CSU: Contacts of Structural Units for 3LCD Structure Factors (206 Kb) Retrieve 3LCD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3LCD from S2C, [Save to disk] Re-refined 3lcd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3LCD 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 3LCD

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 3LCD, from MSDmotif at EBI Fold representative 3lcd from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3lcd_A] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3LCD with the sequences similar proteins can be viewed for 3LCD's classification 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 at ProtoMap. Click on the Cluster number.

Other resources with information on 3LCD

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

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