5HKV Ribosome date Jan 14, 2016
title The Crystal Structure Of The Large Ribosomal Subunit Of Stap Aureus In Complex With Lincomycin
authors A.Yonath, D.Matzov, Z.Eyal, R.Ben Hamou, E.Zimmerman, H.Rozenberg A.Bashan, M.Fridman
compound source
Molecule: 23s Ribosomal Rna
Chain: X
 Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 5s Ribosomal Rna
Chain: Y
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L2
Chain: A
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L3
Chain: B
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L4
Chain: C
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L5
Chain: D
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L6
Chain: E
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L13
Chain: G
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L14
Chain: H
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L15
Chain: I
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L16
Chain: J
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L17
Chain: K
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L18
Chain: L
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L19
Chain: M
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L20
Chain: N
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L21
Chain: O
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L22
Chain: P
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L23
Chain: Q
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L24
Chain: R
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L25
Chain: S
Synonym: General Stress Protein Ctc
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L27
Chain: T
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L28
Chain: U
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L29
Chain: V
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L30
Chain: W
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L32
Chain: Z
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L34
Chain: 2
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L35
Chain: 3
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061
symmetry Space Group: P 65 2 2
R_factor 0.187 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
280.885 280.885 873.522 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.66 Å
ligand 3QB, CA, EOH, MG, MN, MPD, SPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
2


3


A


B


C


D


E


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


Z


Primary referenceStructural insights of lincosamides targeting the ribosome of Staphylococcus aureus., Matzov D, Eyal Z, Benhamou RI, Shalev-Benami M, Halfon Y, Krupkin M, Zimmerman E, Rozenberg H, Bashan A, Fridman M, Yonath A, Nucleic Acids Res. 2017 Sep 29;45(17):10284-10292. doi: 10.1093/nar/gkx658. PMID:28973455
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3362 Kb) [Save to disk]
  • Biological Unit Coordinates (5hkv.pdb1.gz) 3329 Kb
  • LPC: Ligand-Protein Contacts for 5HKV
  • CSU: Contacts of Structural Units for 5HKV
  • Structure Factors (4072 Kb)
  • Retrieve 5HKV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HKV from S2C, [Save to disk]
  • Re-refined 5hkv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5HKV 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 5HKV
  • 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: [5hkv_Y] [5hkv_2] [5hkv_N] [5hkv_X] [5hkv_L] [5hkv_U] [5hkv_P] [5hkv_W] [5hkv_D] [5hkv_3] [5hkv_C] [5hkv_J] [5hkv_M] [5hkv_I] [5hkv_B] [5hkv_V] [5hkv_A] [5hkv_O] [5hkv_K] [5hkv_S] [5hkv_H] [5hkv_Z] [5hkv_T] [5hkv_E] [5hkv_G] [5hkv_R] [5hkv] [5hkv_Q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5HKV
  • Community annotation for 5HKV at PDBWiki (http://pdbwiki.org)

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