MolNFT v1 · #67903 · protein
Leishmania tarentolae mitonchondrial ribosome small subunit
3IY8 · 30S ribosomal protein S5: “Leishmania tarentolae mitonchondrial ribosome small subunit”. Electron microscopy, 3 pockets (best druggability 0.49). MolNFT v1 #67903 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IY8
- Type
- protein
- Length
- 1,051 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 30S ribosomal protein S5; 30S ribosomal protein S6; 30S ribosomal protein S8; 30S…
- UniProt
- P0A7W1, P02358, P0A7W7, P0A7X3, P0A7R9, P0A7S3, Q8X9M2, P0A7T3, P0AG63, Q1R358
- Pockets
- 3 · best druggability 0.49
Structure
electron microscopy · 10 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 30S ribosomal protein S5 | protein | 150 | 0% helix, 0% strand | P0A7W1 |
| F | 30S ribosomal protein S6 | protein | 100 | 0% helix, 0% strand | P02358 |
| H | 30S ribosomal protein S8 | protein | 129 | 0% helix, 0% strand | P0A7W7 |
| I | 30S ribosomal protein S9 | protein | 127 | 0% helix, 0% strand | P0A7X3 |
| K | 30S ribosomal protein S11 | protein | 117 | 0% helix, 0% strand | P0A7R9 |
| L | 30S ribosomal protein S12 | protein | 123 | 0% helix, 0% strand | P0A7S3 |
| O | 30S ribosomal protein S15 | protein | 88 | 0% helix, 0% strand | Q8X9M2 |
| P | 30S ribosomal protein S16 | protein | 82 | 0% helix, 0% strand | P0A7T3 |
| Q | 30S ribosomal protein S17 | protein | 80 | 0% helix, 0% strand | P0AG63 |
| R | 30S ribosomal protein S18 | protein | 55 | 0% helix, 0% strand | Q1R358 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.49 | 0.73 | 44 | empty |
| 2 | 82 | 0.36 | 0.74 | 25 | empty |
| 3 | 79 | 0.34 | 0.73 | 29 | empty |
Interfaces
4 interfaces between chains.
- H–Q · 312 Ų buried · 0 hydrogen bonds · protein-protein
- K–R · 65 Ų buried · 0 hydrogen bonds · protein-protein
- E–H · 19 Ų buried · 0 hydrogen bonds · protein-protein
- H–O · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IY8 · Leishmania tarentolae Mitonchondrial Ribosome small subunit · the same entry in another collection · chain R against R, TM-score 1.00
- Q8X9M2 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S15 (Q8X9M2) · a predicted model of the same protein · chain O against A, TM-score 0.94
- Q1R358 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S18 (Q1R358) · a predicted model of the same protein · chain R against A, TM-score 0.86
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 P0A7W1
- Every structure of UniProt P02358
- Every structure of UniProt P0A7W7
- Every structure of UniProt P0A7X3
- Every structure of UniProt P0A7R9
- Every structure of UniProt P0A7S3
- Every structure of UniProt Q8X9M2
- Every structure of UniProt P0A7T3
- Every structure of UniProt P0AG63
- Every structure of UniProt Q1R358
- Elsewhere: RCSB PDB 3IY8 · PDBe 3IY8 · UniProt P0A7W1 · UniProt P02358 · UniProt P0A7W7 · UniProt P0A7X3 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt Q8X9M2 · UniProt P0A7T3 · UniProt P0AG63 · UniProt Q1R358
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