3VZC	Transferase Inhibitor	date	Oct 11, 2012
title	Crystal Structure Of Sphingosine Kinase 1 With Inhibitor
authors	X.Min, N.P.Walker, Z.Wang
compound		source
Molecule: Sphingosine Kinase 1 Chain: A, B, C, D, E, F Fragment: Unp Residues 9-364 Synonym: Sk 1, Spk 1 Ec: 2.7.1.91 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Cell_line: Sf9 Gene: Sphk1, Sphk, Spk Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pfastbac Htb
symmetry	Space Group: P 21 21 21	R_factor 0.229 R_Free 0.285
crystal cell	length a length b length c angle alpha angle beta angle gamma 102.220 106.610 226.180 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	EDO, UUL	enzyme	Transferase E.C.2.7.1.91 BRENDA
Gene Ontology	Chain Function Process Component F, A, D, C, E, B lipid kinase activity sphinganine kinase activity sphingosine-1-phosphate rece...
Primary reference	Molecular Basis of Sphingosine Kinase 1 Substrate Recognition and Catalysis., Wang Z, Min X, Xiao SH, Johnstone S, Romanow W, Meininger D, Xu H, Liu J, Dai J, An S, Thibault S, Walker N, Structure. 2013 Apr 16. pii: S0969-2126(13)00086-5. doi:, 10.1016/j.str.2013.02.025. PMID:23602659

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (333 Kb) [Save to disk] Biological Unit Coordinates (3vzc.pdb1.gz) 59 Kb Biological Unit Coordinates (3vzc.pdb2.gz) 59 Kb Biological Unit Coordinates (3vzc.pdb3.gz) 59 Kb Biological Unit Coordinates (3vzc.pdb4.gz) 59 Kb Biological Unit Coordinates (3vzc.pdb5.gz) 59 Kb Biological Unit Coordinates (3vzc.pdb6.gz) 59 Kb LPC: Ligand-Protein Contacts for 3VZC CSU: Contacts of Structural Units for 3VZC Structure Factors (1638 Kb) Retrieve 3VZC in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3VZC from S2C, [Save to disk] Re-refined 3vzc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3VZC 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 3VZC

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 3VZC, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3vzc] [3vzc_C] [3vzc_B] [3vzc_F] [3vzc_A] [3vzc_D] [3vzc_E] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3VZC: [DAGKc ] by SMART

Other resources with information on 3VZC

Community annotation for 3VZC at PDBWiki (http://pdbwiki.org)

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