Research workbench
Crystal structure of the base of the ribosomal P stalk from methanococcus jannaschii with antibiotic thiostrepton
Analyse Crystal structure of the base of the ribosomal P stalk from methanococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D8H
- Type
- protein + RNA
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 50S ribosomal protein L10; 50S ribosomal protein L11; Thiostrepton
- UniProt
- P54049, P54030
- Ligands
- QUA, MG, NA, NH2
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S ribosomal RNA | rna | 74 | — | — |
| B | 50S ribosomal protein L10 | protein | 207 | 37% helix, 22% strand | P54049 |
| C | 50S ribosomal protein L11 | protein | 158 | 39% helix, 18% strand | P54030 |
| D | Thiostrepton | protein | 17 | 0% helix, 0% strand | — |
Ligands and binding sites
- QUA · 8-hydroxy-4-(1-hydroxyethyl)quinoline-2-carboxylic acid · ligand · chains A, D
- MG · Magnesium ion · metal · 11 copies · chains A, C
- NA · Sodium ion · metal · 4 copies · chains A, B
- NH2 · Amino group · ion · chains D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B
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 | 690 | 0.73 | 0.80 | 42 | MG, TRS |
| 2 | 502 | 0.69 | 0.80 | 48 | MG |
| 3 | 169 | 0.45 | 0.75 | 23 | NA |
| 4 | 87 | 0.35 | 0.76 | 12 | empty |
| 5 | 68 | 0.34 | 0.77 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1157 Ų buried · 42 hydrogen bonds · protein-nucleic
- A–B · 1131 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–D · 263 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–D · 152 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified, 2 covalent, 1 d-amino (engineered, nonstandard, covalent ligand, D-amino acid).
Compared structures
- P54049 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L10 (P54049) · a predicted model of the same protein · chain B against A, TM-score 0.90
- P54030 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L11 (P54030) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 P54049
- Every structure of UniProt P54030
- Elsewhere: RCSB PDB 5D8H · PDBe 5D8H · UniProt P54049 · UniProt P54030
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