5EBB Hydrolase date Oct 19, 2015
title Structure Of Human Sphingomyelinase Phosphodiesterase Like 3 (Smpdl3a) With Zn2+
authors S.M.Lim, K.Yeung, L.Tresaugues, H.L.Teo, P.Nordlund
compound source
Molecule: Acid Sphingomyelinase-Like Phosphodiesterase 3a
Chain: A, B, C
Fragment: Unp Residues 34-433
Synonym: Asm-Like Phosphodiesterase 3a
Ec: 3.1.4.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Smpdl3a, Asml3a
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_plasmid: Pfb-Sec-Nh
symmetry Space Group: P 32 2 1
R_factor 0.237 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
147.790 147.790 139.900 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand GOL, MLI, NAG, ZN enzyme Hydrolase E.C.3.1.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceThe structure and catalytic mechanism of Human Sphingomyelin Phosphodiesterase like 3a - an acid sphingomyelinase homolog with a novel nucleotide hydrolase activity., Lim SM, Yeung K, Tresaugues L, Ling TH, Nordlund P, FEBS J. 2016 Jan 18. doi: 10.1111/febs.13655. PMID:26783088
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (212 Kb) [Save to disk]
  • Biological Unit Coordinates (5ebb.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (5ebb.pdb2.gz) 71 Kb
  • Biological Unit Coordinates (5ebb.pdb3.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 5EBB
  • CSU: Contacts of Structural Units for 5EBB
  • Structure Factors (3643 Kb)
  • Retrieve 5EBB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EBB from S2C, [Save to disk]
  • Re-refined 5ebb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EBB 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 5EBB
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ebb] [5ebb_B] [5ebb_C] [5ebb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EBB
  • Community annotation for 5EBB at PDBWiki (http://pdbwiki.org)

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