› 1kc8

X-ray diffraction
3.01Å resolution

Co-crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit

Released:
DOI: 10.2210/pdb1kc8/pdb
PDB 1kc8 coloured by chain and viewed from the front.
PDB 1kc8 coloured by chain and viewed from the side.
PDB 1kc8 coloured by chain and viewed from the top.
Source organism: Haloarcula marismortui
Primary publication:
Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit.
Hansen JL, Moore PB, Steitz TA
J Mol Biol 330 1061-75 (2003)
PMID: 12860128

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (30 distinct):
50S ribosomal protein L2 Chain: C
Molecule details ›
Chain: C
Length: 239 amino acids
Theoretical weight: 25.24 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20276 (Residues: 2-240; Coverage: 100%)
Gene names: rpl2, rrnAC1608
Structure domains:
50S ribosomal protein L3 Chain: D
Molecule details ›
Chain: D
Length: 337 amino acids
Theoretical weight: 37.27 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20279 (Residues: 2-338; Coverage: 100%)
Gene names: rpl3, rrnAC1611
Structure domains:
50S ribosomal protein L4 Chain: E
Molecule details ›
Chain: E
Length: 246 amino acids
Theoretical weight: 26.44 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12735 (Residues: 1-246; Coverage: 100%)
Gene names: rpl4, rrnAC1610
Structure domains: Ribosomal Protein L4; Chain: A;
50S ribosomal protein L5 Chain: F
Molecule details ›
Chain: F
Length: 176 amino acids
Theoretical weight: 19.42 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14124 (Residues: 2-177; Coverage: 99%)
Gene names: rpl5, rrnAC1598
Structure domains: 50s Ribosomal Protein L5; Chain: A,
50S ribosomal protein L6 Chain: G
Molecule details ›
Chain: G
Length: 177 amino acids
Theoretical weight: 19.83 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14135 (Residues: 2-178; Coverage: 99%)
Gene names: rpl6, rrnAC1596
Structure domains: Ribosomal protein L6, alpha-beta domain
50S ribosomal protein L7Ae Chain: H
Molecule details ›
Chain: H
Length: 119 amino acids
Theoretical weight: 12.6 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12743 (Residues: 2-120; Coverage: 99%)
Gene names: rpl7ae, rrnAC0103
Structure domains: 60s Ribosomal Protein L30; Chain: A;
50S ribosomal protein L10 Chain: I
Molecule details ›
Chain: I
Length: 348 amino acids
Theoretical weight: 37.21 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P15825 (Residues: 1-348; Coverage: 100%)
Gene names: rpl10, rpl10e, rplP0, rrnAC1417
50S ribosomal protein L10e Chain: J
Molecule details ›
Chain: J
Length: 167 amino acids
Theoretical weight: 18.02 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60617 (Residues: 4-166; Coverage: 90%)
Gene names: rpl10e, rrnAC2357
Structure domains: Ribosomal protein L10e/L16
50S ribosomal protein L13 Chain: K
Molecule details ›
Chain: K
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P29198 (Residues: 1-145; Coverage: 100%)
Gene names: rpl13, rrnAC0065
Structure domains: Ribosomal protein L13
50S ribosomal protein L14 Chain: L
Molecule details ›
Chain: L
Length: 132 amino acids
Theoretical weight: 14.22 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P22450 (Residues: 1-132; Coverage: 100%)
Gene names: rpl14, rrnAC1602
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
50S ribosomal protein L15 Chain: M
Molecule details ›
Chain: M
Length: 164 amino acids
Theoretical weight: 17.87 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12737 (Residues: 2-165; Coverage: 99%)
Gene names: rpl15, rrnAC1590
Structure domains:
50S ribosomal protein L15e Chain: N
Molecule details ›
Chain: N
Length: 194 amino acids
Theoretical weight: 22.86 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60618 (Residues: 2-194; Coverage: 99%)
Gene names: rpl15e, rrnAC2065
Structure domains: Ribosomal protein l15e
50S ribosomal protein L18 Chain: O
Molecule details ›
Chain: O
Length: 186 amino acids
Theoretical weight: 20.51 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14123 (Residues: 2-187; Coverage: 100%)
Gene names: rpl18, rrnAC1593
Structure domains: Nucleotidyltransferase; domain 5
50S ribosomal protein L18e Chain: P
Molecule details ›
Chain: P
Length: 115 amino acids
Theoretical weight: 12.31 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12733 (Residues: 2-116; Coverage: 99%)
Gene names: rpl18e, rrnAC0064
Structure domains: Ribosomal Protein L15; Chain: K; domain 2
50S ribosomal protein L19e Chain: Q
Molecule details ›
Chain: Q
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14119 (Residues: 2-149; Coverage: 99%)
Gene names: rpl19e, rrnAC1594
Structure domains:
50S ribosomal protein L21e Chain: R
Molecule details ›
Chain: R
Length: 95 amino acids
Theoretical weight: 10.44 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12734 (Residues: 2-96; Coverage: 99%)
Gene names: rpl21e, rrnAC0260
Structure domains: Ribosomal protein L21
50S ribosomal protein L22 Chain: S
Molecule details ›
Chain: S
Length: 154 amino acids
Theoretical weight: 16.84 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10970 (Residues: 2-155; Coverage: 99%)
Gene names: rpl22, rrnAC1606
Structure domains: Ribosomal protein L22/L17
50S ribosomal protein L23 Chain: T
Molecule details ›
Chain: T
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12732 (Residues: 2-85; Coverage: 99%)
Gene names: rpl23, rrnAC1609
Structure domains: Alpha-Beta Plaits
50S ribosomal protein L24 Chain: U
Molecule details ›
Chain: U
Length: 119 amino acids
Theoretical weight: 13.54 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10972 (Residues: 2-120; Coverage: 99%)
Gene names: rpl24, rrnAC1601
Structure domains: SH3 type barrels.
50S ribosomal protein L24e Chain: V
Molecule details ›
Chain: V
Length: 66 amino acids
Theoretical weight: 7.23 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14116 (Residues: 2-67; Coverage: 99%)
Gene names: rpl24e, rrnAC0104
Structure domains: Ribosomal protein L24e
50S ribosomal protein L29 Chain: W
Molecule details ›
Chain: W
Length: 70 amino acids
Theoretical weight: 7.76 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10971 (Residues: 2-71; Coverage: 99%)
Gene names: rpl29, rrnAC1604
Structure domains: Helix Hairpins
50S ribosomal protein L30 Chain: X
Molecule details ›
Chain: X
Length: 154 amino acids
Theoretical weight: 17.06 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14121 (Residues: 1-154; Coverage: 100%)
Gene names: rpl30, rrnAC1591
Structure domains:
50S ribosomal protein L31e Chain: Y
Molecule details ›
Chain: Y
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P18138 (Residues: 2-92; Coverage: 99%)
Gene names: rpl31e, rrnAC3113
Structure domains: Ribosomal Protein L31e; Chain: W;
50S ribosomal protein L32e Chain: Z
Molecule details ›
Chain: Z
Length: 240 amino acids
Theoretical weight: 26.32 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12736 (Residues: 2-241; Coverage: 100%)
Gene names: rpl32e, rrnAC1595
50S ribosomal protein L37Ae Chain: 1
Molecule details ›
Chain: 1
Length: 73 amino acids
Theoretical weight: 8.1 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60619 (Residues: 11-82; Coverage: 78%)
Gene names: rpl37ae, rrnAC1669
Structure domains: N-terminal domain of TfIIb
50S ribosomal protein L37e Chain: 2
Molecule details ›
Chain: 2
Length: 56 amino acids
Theoretical weight: 6.2 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P32410 (Residues: 2-57; Coverage: 98%)
Gene names: rpl37e, rrnAC0797.1
Structure domains: N-terminal domain of TfIIb
50S ribosomal protein L39e Chain: 3
Molecule details ›
Chain: 3
Length: 48 amino acids
Theoretical weight: 5.84 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P22452 (Residues: 2-50; Coverage: 96%)
Gene names: rpl39e, rrnAC3112
Structure domains: Ribosomal protein L39e
50S ribosomal protein L44e Chain: 4
Molecule details ›
Chain: 4
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P32411 (Residues: 1-92; Coverage: 100%)
Gene names: rpl44e, rrnAC3514
Structure domains: Nuclear Transport Factor 2; Chain: A,
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2922 nucleotides
Theoretical weight: 946.03 KDa
Sequence domains: Archaeal large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 122 nucleotides
Theoretical weight: 39.32 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

6 bound ligands:
Ligand BLS 2 x BLS
Ligand MG 117 x MG
Ligand K 3 x K
Ligand NA 86 x NA
Ligand CL 22 x CL
Ligand CD 5 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 212.902Å b: 300.474Å c: 575.176Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.195 0.235

Quick links

Citations

54 review citations

Pulling the Brakes on Fast and Furious Multiple Drug-Resistant (MDR) Bacteria.
Khan et al. (2021)
53 more

2 mentions without citation

A structural model for the large subunit of the mammalian mitochondrial ribosome.
Mears et al. (2006)
1 more