› 3pio

X-ray diffraction
3.25Å resolution

Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit

Released:
DOI: 10.2210/pdb3pio/pdb
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PDB entry 3pio coloured by chain, front view.
PDB entry 3pio coloured by chain, side view.
PDB entry 3pio coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
Belousoff MJ, Shapira T, Bashan A, Zimmerman E, Rozenberg H, Arakawa K, Kinashi H, Yonath A
Proc Natl Acad Sci U S A 108 2717-22 (2011)
PMID: 21282615

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-294208 (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (30 distinct):
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 29.98 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ9 (Residues: 2-275; Coverage: 100%)
Gene names: DR_0314, rplB
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 211 amino acids
Theoretical weight: 22.48 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK2 (Residues: 1-211; Coverage: 100%)
Gene names: DR_0311, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Large ribosomal subunit protein uL5 Chain: D
Large ribosomal subunit protein uL6 Chain: E
Large ribosomal subunit protein uL11 Chain: F
Large ribosomal subunit protein uL13 Chain: G
Large ribosomal subunit protein uL14 Chain: H
Large ribosomal subunit protein uL15 Chain: I
Large ribosomal subunit protein uL16 Chain: J
Large ribosomal subunit protein bL17 Chain: K
Large ribosomal subunit protein uL18 Chain: L
Large ribosomal subunit protein bL19 Chain: M
Large ribosomal subunit protein bL20 Chain: N
Large ribosomal subunit protein bL21 Chain: O
Large ribosomal subunit protein uL22 Chain: P
Large ribosomal subunit protein uL23 Chain: Q
Large ribosomal subunit protein uL24 Chain: R
Large ribosomal subunit protein bL25 Chain: S
Large ribosomal subunit protein bL27 Chain: T
Large ribosomal subunit protein bL28 Chain: U
Large ribosomal subunit protein uL29 Chain: V
Large ribosomal subunit protein uL30 Chain: W
Large ribosomal subunit protein bL32 Chain: Z
Large ribosomal subunit protein bL33 Chain: 1
Large ribosomal subunit protein bL34 Chain: 2
Large ribosomal subunit protein bL35 Chain: 3
Large ribosomal subunit protein bL36 Chain: 4
23S ribosomal RNA Chain: X
5S ribosomal RNA Chain: Y

Ligands and Environments

4 bound ligands:
Ligand LMA 1 x LMA
Ligand MG 154 x MG
Ligand NA 42 x NA
Ligand K 15 x K
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: I222
Unit cell:
a: 170.59Å b: 410.204Å c: 695.078Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.253 0.252 0.294

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Citations

11 review citations

Ribosome-targeting antibiotics and mechanisms of bacterial resistance.
Wilson DN. (2014)
10 more

3 mentions without citation

The future of the Protein Data Bank.
Berman et al. (2013)
2 more

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