Research workbench
Structural basis for the interaction of antibiotics with the peptidyl transferase center in eubacteria
Analyse Structural basis for the interaction of antibiotics with the peptidyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K01
- Type
- protein + RNA
- Length
- 3,159 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA; Ribosomal protein L4; Ribosomal protein L22; Ribosomal protein L32
- UniProt
- Q9RXK1, Q9RXJ7, P49228
- Ligands
- CLM, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA | rna | 2774 | — | — |
| K | Ribosomal protein L4 | protein | 197 | 0% helix, 0% strand | Q9RXK1 |
| L | Ribosomal protein L22 | protein | 130 | 0% helix, 0% strand | Q9RXJ7 |
| M | Ribosomal protein L32 | protein | 58 | 0% helix, 0% strand | P49228 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.86 | 0.89 | 87 | empty |
| 2 | 1030 | 0.85 | 0.87 | 76 | empty |
| 3 | 1027 | 0.84 | 0.86 | 92 | empty |
| 4 | 604 | 0.84 | 0.90 | 60 | empty |
| 5 | 623 | 0.82 | 0.88 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–K · 1720 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–L · 1119 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–M · 1000 Ų buried · 0 hydrogen bonds · protein-nucleic
- L–M · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1K01 · Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RXJ7 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (Q9RXJ7) · a predicted model of the same protein · chain L against A, TM-score 0.96
- Q9RXK1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (Q9RXK1) · a predicted model of the same protein · chain K against A, TM-score 0.90
- P49228 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L32 (P49228) · a predicted model of the same protein · chain M against A, TM-score 0.82
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9RXK1
- Every structure of UniProt Q9RXJ7
- Every structure of UniProt P49228
- Elsewhere: RCSB PDB 1K01 · PDBe 1K01 · UniProt Q9RXK1 · UniProt Q9RXJ7 · UniProt P49228
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