MolNFT v1 · #14857 · protein + RNA
Crystal structure of the ribosomal protein L11-RNA complex
1MMS · 23S ribosomal RNA: “Crystal structure of the ribosomal protein L11-RNA complex”. X-ray diffraction, 3 ligands (MG, CD, MMC), 5 pockets (best druggability 0.76). MolNFT v1 #14857 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1MMS
- Type
- protein + RNA
- Length
- 319 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; Protein (ribosomal protein L11)
- UniProt
- P29395
- Ligands
- MG, CD, MMC
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 23S ribosomal RNA | rna | 58 | — | — |
| A | Protein (ribosomal protein L11) | protein | 133 | 38% helix, 19% strand | P29395 |
| B | Protein (ribosomal protein L11) | protein | 70 | 51% helix, 9% strand | P29395 |
Ligands and binding sites
- MG · Magnesium ion · metal · 19 copies · chains C, D, A
- CD · Cadmium ion · metal · 8 copies · chains C, D, A
- MMC · Methyl mercury ion · metal · 8 copies · chains C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.76 | 0.79 | 70 | CD, MMC |
| 2 | 289 | 0.61 | 0.81 | 21 | CD, MG |
| 3 | 106 | 0.37 | 0.76 | 15 | empty |
| 4 | 87 | 0.34 | 0.76 | 15 | MG |
| 5 | 56 | 0.27 | 0.75 | 12 | empty |
Interfaces
4 interfaces between chains.
- C–A · 1274 Ų buried · 41 hydrogen bonds · protein-nucleic
- D–B · 1044 Ų buried · 40 hydrogen bonds · protein-nucleic
- C–D · 212 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- D–A · 43 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 1MMS · Crystal structure of the ribosomal PROTEIN L11-RNA complex · the same entry in another collection · chain C against C, TM-score 1.00
- 1OLN · Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA · a predicted model of the same protein · chain A against A, TM-score 1.00
- 1OLN · Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA · a predicted model of the same protein · chain A against A, TM-score 1.00
- P29395 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L11 (P29395) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P29395
- Elsewhere: RCSB PDB 1MMS · PDBe 1MMS · UniProt P29395
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