MolNFT v1 · #168890 · protein + RNA
30S subunit (head) of 70S ribosome enterococcus faecalis multibody refinement
6WUB · 16S rRNA: “30S subunit (head) of 70S ribosome enterococcus faecalis multibody refinement”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #168890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WUB
- Type
- protein + RNA
- Length
- 2,374 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 30S ribosomal protein S4; 30S ribosomal protein S5; 30S ribosomal protein S6…
- UniProt
- A0A1B4XRV7, A0A1B4XKW0, A0A1B4XKB6, A0A1B4XKS6, A0A1B4XKV1, A0A1B4XKQ7, A0A1B4XRW3, A0A1B4XP69, A0A1B4XKS3, A0A1B4XKB3, A0A1B4XQJ7
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 12 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | 16S rRNA | rna | 1121 | — | — |
| d | 30S ribosomal protein S4 | protein | 201 | 37% helix, 8% strand | A0A1B4XRV7 |
| e | 30S ribosomal protein S5 | protein | 163 | 25% helix, 30% strand | A0A1B4XKW0 |
| f | 30S ribosomal protein S6 | protein | 97 | 23% helix, 40% strand | A0A1B4XKB6 |
| h | 30S ribosomal protein S8 | protein | 131 | 26% helix, 27% strand | A0A1B4XKS6 |
| k | 30S ribosomal protein S11 | protein | 117 | 28% helix, 26% strand | A0A1B4XKV1 |
| l | 30S ribosomal protein S12 | protein | 136 | 7% helix, 26% strand | A0A1B4XKQ7 |
| o | 30S ribosomal protein S15 | protein | 88 | 73% helix, 0% strand | A0A1B4XRW3 |
| p | 30S ribosomal protein S16 | protein | 89 | 25% helix, 29% strand | A0A1B4XP69 |
| q | 30S ribosomal protein S17 | protein | 83 | 0% helix, 53% strand | A0A1B4XKS3 |
| r | 30S ribosomal protein S18 | protein | 66 | 42% helix, 3% strand | A0A1B4XKB3 |
| t | 30S ribosomal protein S20 | protein | 82 | 76% helix, 0% strand | A0A1B4XQJ7 |
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 | 1024 | 0.85 | 0.87 | 81 | empty |
| 2 | 643 | 0.83 | 0.89 | 63 | empty |
| 3 | 779 | 0.83 | 0.87 | 63 | empty |
| 4 | 576 | 0.80 | 0.86 | 55 | empty |
| 5 | 491 | 0.79 | 0.87 | 51 | empty |
Interfaces
18 interfaces between chains.
- a–l · 3127 Ų buried · 53 hydrogen bonds · protein-nucleic
- a–d · 2766 Ų buried · 48 hydrogen bonds · protein-nucleic
- a–p · 2333 Ų buried · 38 hydrogen bonds · protein-nucleic
- a–t · 2056 Ų buried · 34 hydrogen bonds · protein-nucleic
- a–q · 1930 Ų buried · 32 hydrogen bonds · protein-nucleic
Compared structures
- 6WUB · 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement · the same entry in another collection · chain a against a, TM-score 1.00
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 A0A1B4XRV7
- Every structure of UniProt A0A1B4XKW0
- Every structure of UniProt A0A1B4XKB6
- Every structure of UniProt A0A1B4XKS6
- Every structure of UniProt A0A1B4XKV1
- Every structure of UniProt A0A1B4XKQ7
- Every structure of UniProt A0A1B4XRW3
- Every structure of UniProt A0A1B4XP69
- Every structure of UniProt A0A1B4XKS3
- Every structure of UniProt A0A1B4XKB3
- Every structure of UniProt A0A1B4XQJ7
- Elsewhere: RCSB PDB 6WUB · PDBe 6WUB · UniProt A0A1B4XRV7 · UniProt A0A1B4XKW0 · UniProt A0A1B4XKB6 · UniProt A0A1B4XKS6 · UniProt A0A1B4XKV1 · UniProt A0A1B4XKQ7 · UniProt A0A1B4XRW3 · UniProt A0A1B4XP69 · UniProt A0A1B4XKS3 · UniProt A0A1B4XKB3 · UniProt A0A1B4XQJ7
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