› 1n8r

X-ray diffraction
3Å resolution

Structure of large ribosomal subunit in complex with virginiamycin M

Released:
DOI: 10.2210/pdb1n8r/pdb
Model geometry
Fit model/data
Data not deposited
PDB entry 1n8r coloured by chain, front view.
PDB entry 1n8r coloured by chain, side view.
PDB entry 1n8r coloured by chain, top view.
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)
Assembly name:
PDBe Complex ID:
PDB-CPX-289888 (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (30 distinct):
Large ribosomal subunit protein uL2 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
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL3 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
Sequence domains: Ribosomal protein L3
Structure domains:
Large ribosomal subunit protein uL4 Chain: E
Large ribosomal subunit protein uL5 Chain: F
Large ribosomal subunit protein uL6 Chain: G
Large ribosomal subunit protein eL8 Chain: H
Large ribosomal subunit protein uL10 Chain: I
Large ribosomal subunit protein uL16 Chain: J
Large ribosomal subunit protein uL13 Chain: K
Large ribosomal subunit protein uL14 Chain: L
Large ribosomal subunit protein uL15 Chain: M
Large ribosomal subunit protein eL15 Chain: N
Large ribosomal subunit protein uL18 Chain: O
Large ribosomal subunit protein eL18 Chain: P
Large ribosomal subunit protein eL19 Chain: Q
Large ribosomal subunit protein eL21 Chain: R
Large ribosomal subunit protein uL22 Chain: S
Large ribosomal subunit protein uL23 Chain: T
Large ribosomal subunit protein uL24 Chain: U
Large ribosomal subunit protein eL24 Chain: V
Large ribosomal subunit protein uL29 Chain: W
Large ribosomal subunit protein uL30 Chain: X
Large ribosomal subunit protein eL31 Chain: Y
Large ribosomal subunit protein eL32 Chain: Z
Large ribosomal subunit protein eL43 Chain: 1
Large ribosomal subunit protein eL37 Chain: 2
Large ribosomal subunit protein eL39 Chain: 3
Large ribosomal subunit protein eL42 Chain: 4
23S ribosomal RNA Chain: A
5S ribosomal RNA Chain: B

Ligands and Environments

6 bound ligands:
Ligand VIR 1 x VIR
Ligand MG 117 x MG
Ligand K 1 x K
Ligand NA 86 x NA
Ligand CL 22 x CL
Ligand CD 5 x CD
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS BEAMLINE X25
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
0.201 0.201 0.242

Quick links

Citations

60 review citations

Antibiotics and bacterial resistance in the 21st century.
Fair et al. (2014)
59 more

2 mentions without citation

POPSCOMP: an automated interaction analysis of biomolecular complexes.
Kleinjung et al. (2005)
1 more