4V24 Transferase date Oct 05, 2014
title Sphingosine Kinase 1 In Complex With Pf-543
authors J.M.Elkins, J.Wang, F.Sorrell, C.Tallant, D.Wang, L.Shrestha, C.Bo F.Von Delft, S.Knapp, A.Edwards
compound source
Molecule: Sphingosine Kinase 1
Chain: A, B
Fragment: Kinase Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1 21 1
R_factor 0.182 R_Free 0.210
length a length b length c angle alpha angle beta angle gamma
86.570 60.549 89.592 90.00 107.17 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand ACT, GYR enzyme Transferase E.C. BRENDA
A, B
  • lipid kinase activity
  • sphinganine kinase activity
  • sphingosine-1-phosphate rece...

  • Primary referenceCrystal Structure of Sphingosine Kinase 1 with PF-543., Wang J, Knapp S, Pyne NJ, Pyne S, Elkins JM, ACS Med Chem Lett. 2014 Oct 27;5(12):1329-33. doi: 10.1021/ml5004074. eCollection, 2014 Dec 11. PMID:25516793
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (4v24.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (4v24.pdb2.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 4V24
  • CSU: Contacts of Structural Units for 4V24
  • Structure Factors (4535 Kb)
  • Retrieve 4V24 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V24 from S2C, [Save to disk]
  • Re-refined 4v24 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • Visual 3D analysis of 4V24
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  • 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 4V24, from MSDmotif at EBI
  • Fold representative 4v24 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4v24_A] [4v24] [4v24_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4V24: [DAGKc ] by SMART
  • Other resources with information on 4V24
  • Community annotation for 4V24 at PDBWiki (http://pdbwiki.org)

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