MolNFT v1 · #11886 · protein + RNA
Structural basis for the interaction of antibiotics with the peptidyl transferase center in eubacteria
1K01 · 23S rRNA: “Structural basis for the interaction of antibiotics with the peptidyl transferase center in eubacteria”. X-ray diffraction, 2 ligands (CLM, MG), 20 pockets (best druggability 0.86). MolNFT v1 #11886 on GenesisL1: 3D…
- 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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