5Y9E Structural Protein date Aug 24, 2017
title Crystal Structure Of Hpv58 Pentamer
authors S.W.Li, Z.H.Li
compound source
Molecule: Major Capsid Protein L1
Chain: A, B, C, D, E
Fragment: Unp Residues 36-524
Engineered: Yes
Mutation: Yes
 Organism_scientific: Human Papillomavirus Type 58
Organism_taxid: 10598
Gene: L1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.168 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
187.213 101.804 136.195 90.00 95.68 90.00
method X-Ray Diffractionresolution 2.04 Å
ligand GOL, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, E, B


Primary referenceCrystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus., Li Z, Wang D, Gu Y, Song S, He M, Shi J, Liu X, Wei S, Li J, Yu H, Zheng Q, Yan X, Baker TS, Zhang J, McLellan JS, Li S, Xia N, MBio. 2017 Sep 26;8(5). pii: e00787-17. doi: 10.1128/mBio.00787-17. PMID:28951471
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (715 Kb) [Save to disk]
  • Biological Unit Coordinates (5y9e.pdb1.gz) 700 Kb
  • LPC: Ligand-Protein Contacts for 5Y9E
  • CSU: Contacts of Structural Units for 5Y9E
  • Structure Factors (4433 Kb)
  • Retrieve 5Y9E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y9E from S2C, [Save to disk]
    • View 5Y9E 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 5Y9E
  • 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: [5y9e_B] [5y9e_A] [5y9e_E] [5y9e_C] [5y9e_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5Y9E
  • Community annotation for 5Y9E at PDBWiki (http://pdbwiki.org)

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