› 5hl7

X-ray diffraction
3.55Å resolution

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

Released:
DOI: 10.2210/pdb5hl7/pdb
PDB entry 5hl7 coloured by chain, front view.
PDB entry 5hl7 coloured by chain, side view.
PDB entry 5hl7 coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Primary publication:
A 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 6 39004 (2016)
PMID: 27958389

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140918 (preferred)
Entry contents:
26 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (28 distinct):
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 277 amino acids
Theoretical weight: 30.22 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P60430 (Residues: 1-277; Coverage: 100%)
Gene names: SAOUHSC_02509, rplB
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 220 amino acids
Theoretical weight: 23.76 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW06 (Residues: 1-220; Coverage: 100%)
Gene names: SAOUHSC_02512, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
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
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: D
Molecule details ›
Chain: D
Length: 179 amino acids
Theoretical weight: 20.3 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW18 (Residues: 1-179; Coverage: 100%)
Gene names: SAOUHSC_02500, rplE
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
Large ribosomal subunit protein uL6 Chain: E
Molecule details ›
Chain: E
Length: 178 amino acids
Theoretical weight: 19.89 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW21 (Residues: 1-178; Coverage: 100%)
Gene names: SAOUHSC_02496, rplF
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
Large ribosomal subunit protein uL13 Chain: G
Molecule details ›
Chain: G
Length: 145 amino acids
Theoretical weight: 16.36 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW38 (Residues: 1-145; Coverage: 100%)
Gene names: SAOUHSC_02478, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: H
Molecule details ›
Chain: H
Length: 122 amino acids
Theoretical weight: 13.16 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW16 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02502, rplN
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
Large ribosomal subunit protein uL15 Chain: I
Molecule details ›
Chain: I
Length: 140 amino acids
Theoretical weight: 15.02 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0F8 (Residues: 1-140; Coverage: 96%)
Gene names: SAOUHSC_02492, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: J
Molecule details ›
Chain: J
Length: 144 amino acids
Theoretical weight: 16.27 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW13 (Residues: 1-144; Coverage: 100%)
Gene names: SAOUHSC_02505, rplP
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein bL17 Chain: K
Molecule details ›
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
Sequence domains: Ribosomal protein L17
Structure domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: L
Molecule details ›
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
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Structure domains: Nucleotidyltransferase; domain 5
Large ribosomal subunit protein bL19 Chain: M
Molecule details ›
Chain: M
Length: 116 amino acids
Theoretical weight: 13.39 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ42 (Residues: 1-116; Coverage: 100%)
Gene names: SAOUHSC_01211, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: N
Molecule details ›
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
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: O
Molecule details ›
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
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: P
Molecule details ›
Chain: P
Length: 117 amino acids
Theoretical weight: 12.86 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW11 (Residues: 1-117; Coverage: 100%)
Gene names: SAOUHSC_02507, rplV
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
Large ribosomal subunit protein uL23 Chain: Q
Molecule details ›
Chain: Q
Length: 91 amino acids
Theoretical weight: 10.63 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW08 (Residues: 1-91; Coverage: 100%)
Gene names: SAOUHSC_02510, rplW
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24 Chain: R
Molecule details ›
Chain: R
Length: 105 amino acids
Theoretical weight: 11.56 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW17 (Residues: 1-105; Coverage: 100%)
Gene names: SAOUHSC_02501, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: S
Molecule details ›
Chain: S
Length: 217 amino acids
Theoretical weight: 23.81 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G0S0 (Residues: 1-217; Coverage: 100%)
Gene names: SAOUHSC_00474, ctc, rplY
Sequence domains:
Structure domains:
Large ribosomal subunit protein bL27 Chain: T
Molecule details ›
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
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: U
Molecule details ›
Chain: U
Length: 62 amino acids
Theoretical weight: 7 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ60 (Residues: 1-62; Coverage: 100%)
Gene names: SAOUHSC_01191, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: V
Molecule details ›
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
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: W
Molecule details ›
Chain: W
Length: 59 amino acids
Theoretical weight: 6.57 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0G2 (Residues: 1-59; Coverage: 100%)
Gene names: SAOUHSC_02493, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Structure domains: Ribosomal protein L30, ferredoxin-like fold domain
Large ribosomal subunit protein bL32 Chain: Z
Molecule details ›
Chain: Z
Length: 58 amino acids
Theoretical weight: 6.66 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZF1 (Residues: 1-58; Coverage: 100%)
Gene names: SAOUHSC_01078, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL34 Chain: 2
Molecule details ›
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
Sequence domains: Ribosomal protein L34
Structure domains: Helix Hairpins
Large ribosomal subunit protein bL35 Chain: 3
Molecule details ›
Chain: 3
Length: 66 amino acids
Theoretical weight: 7.72 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXQ0 (Residues: 1-66; Coverage: 100%)
Gene names: SAOUHSC_01785, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: 4
Molecule details ›
Chain: 4
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW29 (Residues: 1-37; Coverage: 100%)
Gene names: SAOUHSC_02488, rpmJ
Sequence domains: Ribosomal protein L36
23S ribosomal RNA Chain: X
Molecule details ›
Chain: X
Length: 2923 nucleotides
Theoretical weight: 946.69 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: Y
Molecule details ›
Chain: Y
Length: 114 nucleotides
Theoretical weight: 36.69 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

7 bound ligands:
Ligand MN 274 x MN
Ligand MG 240 x MG
Ligand 62B 1 x 62B
Ligand MPD 11 x MPD
Ligand SPD 8 x SPD
Ligand EOH 3 x EOH
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P6522
Unit cell:
a: 282.112Å b: 282.112Å c: 875.343Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.189 0.187 0.227

Quick links

Citations

12 review citations

Developing New Antimicrobial Therapies: Are Synergistic Combinations of Plant Extracts/Compounds with Conventional Antibiotics the Solution?
Cheesman et al. (2017)
11 more

6 mentions without citation

Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design.
Lin et al. (2018)
5 more