Structure analysis

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with RB02

X-ray diffraction
3.442Å resolution
Assembly composition:
hetero 26-mer (preferred)
Entry contents: 24 distinct polypeptide molecules
2 distinct RNA molecules

Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 26-mer
Accessible surface area: 457385.67 Å2
Buried surface area: 158470.14 Å2
Dissociation area: 699.29 Å2
Dissociation energy (ΔGdiss): 4.49 kcal/mol
Dissociation entropy (TΔSdiss): 12.84 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-140920

Macromolecules

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Chain: C
Length: 207 amino acids
Theoretical weight: 22.5 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW07 (Residues: 1-207; Coverage: 100%)
Gene names: SAOUHSC_02511, rplD
Pfam: Ribosomal protein L4/L1 family
InterPro:

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Chain: K
Length: 122 amino acids
Theoretical weight: 13.77 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW33 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02484, rplQ
Pfam: Ribosomal protein L17
InterPro:
CATH: Ribosomal protein L17

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Chain: L
Length: 119 amino acids
Theoretical weight: 13.12 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW22 (Residues: 1-119; Coverage: 100%)
Gene names: SAOUHSC_02495, rplR
Pfam: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
InterPro:
CATH: Nucleotidyltransferase; domain 5

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Chain: N
Length: 118 amino acids
Theoretical weight: 13.72 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXQ1 (Residues: 1-118; Coverage: 100%)
Gene names: SAOUHSC_01784, rplT
Pfam: Ribosomal protein L20
InterPro:

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Chain: O
Length: 102 amino acids
Theoretical weight: 11.35 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXS8 (Residues: 1-102; Coverage: 100%)
Gene names: SAOUHSC_01757, rplU
Pfam: Ribosomal prokaryotic L21 protein
InterPro:

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Chain: T
Length: 94 amino acids
Theoretical weight: 10.33 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXT0 (Residues: 1-94; Coverage: 100%)
Gene names: SAOUHSC_01755, rpmA
Pfam: Ribosomal L27 protein
InterPro:

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Chain: V
Length: 69 amino acids
Theoretical weight: 8.11 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW14 (Residues: 1-69; Coverage: 100%)
Gene names: SAOUHSC_02504, rpmC
Pfam: Ribosomal L29 protein
InterPro:

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Chain: 2
Length: 45 amino acids
Theoretical weight: 5.45 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FUQ0 (Residues: 1-45; Coverage: 100%)
Gene names: SAOUHSC_03055, rpmH
Pfam: Ribosomal protein L34
InterPro:
CATH: Helix Hairpins

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Name: 23S ribosomal RNA
Representative chains: X
Length: 2923 nucleotides
Theoretical weight: 946.69 KDa
Rfam: Bacterial large subunit ribosomal RNA

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Name: 5S ribosomal RNA
Representative chains: Y
Length: 114 nucleotides
Theoretical weight: 36.69 KDa
Rfam: 5S ribosomal RNA

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