5HL7 Ribosome date Jan 14, 2016
title The Crystal Structure Of The Large Ribosomal Subunit Of Stap Aureus In Complex With Lefamulin
authors Z.Eyal, D.Matzov, M.Krupkin, H.Rozenberg, E.Zimmerman, A.Bashan, A
compound source
Molecule: 50s Ribosomal Protein L2
Chain: A
 Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

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 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

Molecule: 50s Ribosomal Protein L36
Chain: 4
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061
symmetry Space Group: P 65 2 2
R_factor 0.187 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
282.112 282.112 875.343 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.55 Å
ligand 62B, EOH, EPE, MG, MN, MPD, SPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
2


3


4


A


B


C


D


E


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


Z


Primary referenceA novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism., Eyal Z, Matzov D, Krupkin M, Paukner S, Riedl R, Rozenberg H, Zimmerman E, Bashan A, Yonath A, Sci Rep. 2016 Dec 13;6:39004. doi: 10.1038/srep39004. PMID:27958389
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3373 Kb) [Save to disk]
  • Biological Unit Coordinates (5hl7.pdb1.gz) 3340 Kb
  • LPC: Ligand-Protein Contacts for 5HL7
  • CSU: Contacts of Structural Units for 5HL7
  • Structure Factors (3798 Kb)
  • Retrieve 5HL7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HL7 from S2C, [Save to disk]
  • Re-refined 5hl7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5HL7 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 5HL7
  • 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: [5hl7_X] [5hl7_3] [5hl7_T] [5hl7_U] [5hl7_K] [5hl7_D] [5hl7_G] [5hl7_A] [5hl7_M] [5hl7_N] [5hl7_W] [5hl7_B] [5hl7_V] [5hl7_S] [5hl7_R] [5hl7_L] [5hl7_Q] [5hl7] [5hl7_O] [5hl7_2] [5hl7_P] [5hl7_4] [5hl7_I] [5hl7_E] [5hl7_H] [5hl7_Y] [5hl7_C] [5hl7_Z] [5hl7_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5HL7
  • Community annotation for 5HL7 at PDBWiki (http://pdbwiki.org)

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