5Y9F Viral Protein Immune System date Aug 24, 2017
title Crystal Structure Of Hpv59 Pentamer In Complex With The Fab Of Antibody 28f10
authors S.W.Li, Z.H.Li
compound source
Molecule: Major Capsid Protein L1
Chain: A, B, C, D, E, F, G, H, I, J
Fragment: Unp Residues 10-508
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Papillomavirus Type 59
Organism_taxid: 37115
Gene: Orf Putative L1, L1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Light Chains Of Fab Fragment Of Antibody 28f10
Chain: K, O, Q, S, M, c, W, Y, a, U

Organism_scientific: Mus Musculus
Organism_taxid: 10090

Molecule: Heavy Chain Of Fab Fragment Of Antibody 28f10
Chain: L, P, R, T, N, d, V, X, Z, b

Organism_scientific: Mus Musculus
Organism_taxid: 10090
symmetry Space Group: P 1 21 1
R_factor 0.230 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
116.265 417.233 134.942 90.00 111.02 90.00
method X-Ray Diffractionresolution 3.35 Å
F, A, J, E, B, H, C, D, I, G

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] (2881 Kb) [Save to disk]
  • Biological Unit Coordinates (5y9f.pdb1.gz) 1431 Kb
  • Biological Unit Coordinates (5y9f.pdb2.gz) 1439 Kb
  • CSU: Contacts of Structural Units for 5Y9F
  • Structure Factors (3917 Kb)
  • Retrieve 5Y9F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y9F from S2C, [Save to disk]
  • View 5Y9F 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 5Y9F
  • Cartoon representation from PDB Cartoon
  • 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
  • Fold representative 5y9f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5y9f_N] [5y9f_J] [5y9f_Y] [5y9f_Z] [5y9f_O] [5y9f_F] [5y9f_L] [5y9f_T] [5y9f_W] [5y9f_K] [5y9f_c] [5y9f_C] [5y9f_D] [5y9f_U] [5y9f_P] [5y9f_S] [5y9f_G] [5y9f_a] [5y9f_I] [5y9f_Q] [5y9f_H] [5y9f_E] [5y9f_M] [5y9f_B] [5y9f_b] [5y9f_R] [5y9f_A] [5y9f_X] [5y9f_V] [5y9f_d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Y9F
  • Community annotation for 5Y9F at PDBWiki (http://pdbwiki.org)

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