5VYP Antimicrobial Protein date May 25, 2017
title Crystal Structure Of The Plant Defensin Nsd7 Bound To Pip2
authors M.Jarva, F.T.Lay, M.Hulett, M.Kvansakul
compound source
Molecule: Defensin Nsd7
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R V, W, X;
Engineered: Yes
 Organism_scientific: Nicotiana Suaveolens
Organism_common: Australian Tobacco
Organism_taxid: 200320
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_plasmid: Ppic9
symmetry Space Group: P 1 21 1
R_factor 0.215 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.605 83.489 105.194 90.00 93.99 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand GOL, PIO, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
S, F, T, N, K, E, V, Q, M, C, L, A, J, O, W, X, P, B, H, D, R, I, G, U


Primary referenceStructure of the defensin NsD7 in complex with PIP2 reveals that defensin:lipid oligomer topologies are dependent on lipid type., Jarva M, Lay FT, Hulett MD, Kvansakul M, FEBS Lett. 2017 Jul 25. doi: 10.1002/1873-3468.12761. PMID:28741756
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (220 Kb) [Save to disk]
  • Biological Unit Coordinates (5vyp.pdb1.gz) 206 Kb
  • LPC: Ligand-Protein Contacts for 5VYP
  • CSU: Contacts of Structural Units for 5VYP
  • Structure Factors (1614 Kb)
  • Retrieve 5VYP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VYP from S2C, [Save to disk]
  • Re-refined 5vyp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VYP 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 5VYP
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vyp_P] [5vyp_F] [5vyp_K] [5vyp_L] [5vyp_D] [5vyp_Q] [5vyp_O] [5vyp_B] [5vyp_M] [5vyp_I] [5vyp_V] [5vyp_W] [5vyp_R] [5vyp_C] [5vyp_E] [5vyp_H] [5vyp_X] [5vyp_G] [5vyp_A] [5vyp_U] [5vyp_J] [5vyp_S] [5vyp_T] [5vyp_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VYP
  • Community annotation for 5VYP at PDBWiki (http://pdbwiki.org)

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