6YPU Ribosome date Apr 16, 2020
title Acinetobacter Baumannii Ribosome-Amikacin Complex - 30s Subu
authors D.Nicholson, T.A.Edwards, A.J.O'Neill, N.A.Ranson
compound source
Molecule: 16s Ribosomal Rna
Chain: 2, 4
 Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S2
Chain: c
Other_details: Modelled Without Side Chains
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S4
Chain: e
Other_details: Residues 23-30 And 43-51 Modelled Without Si
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S5
Chain: f
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S6
Chain: g
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S8
Chain: I
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S11
Chain: l
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S12
Chain: m
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S15
Chain: p
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S16
Chain: q
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S17
Chain: r
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S18
Chain: s
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S20
Chain: u
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584

Molecule: 30s Ribosomal Protein S21
Chain: v
Other_details: Residues 2-36 Modelled Without Side Chains
Organism_scientific: Acinetobacter Baumannii (Strain Atcc 1 Dsm 30007 Cip 70.34 Jcm 6841 Nbrc 109757 Ncimb 1245 12156 81);
Organism_taxid: 575584
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 2.90 Å
ligand AKN, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
c


e


f


g


i


l


m


p


q


r


s


u


v


Primary referenceStructure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics., Nicholson D, Edwards TA, O'Neill AJ, Ranson NA, Structure. 2020 Aug 26. pii: S0969-2126(20)30286-0. doi:, 10.1016/j.str.2020.08.004. PMID:32857965
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (601 Kb) [Save to disk]
  • Biological Unit Coordinates (6ypu.pdb1.gz) 571 Kb
  • LPC: Ligand-Protein Contacts for 6YPU
  • CSU: Contacts of Structural Units for 6YPU
  • Retrieve 6YPU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YPU from S2C, [Save to disk]
    • View 6YPU in 3D
  • Proteopedia, because life has more than 2D.
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    • Visual 3D analysis of 6YPU
  • 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: [6ypu_e] [6ypu_g] [6ypu_v] [6ypu_2] [6ypu_r] [6ypu_p] [6ypu_l] [6ypu_u] [6ypu_i] [6ypu_c] [6ypu_4] [6ypu_f] [6ypu_s] [6ypu_m] [6ypu_q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6YPU
  • Community annotation for 6YPU at PDBWiki (http://pdbwiki.org)

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