MolNFT v1 · #158886 · protein + RNA
30S initiation complex
6O7K · Translation initiation factor if-1: “30S initiation complex”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #158886 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O7K
- Type
- protein + RNA
- Length
- 4,556 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor if-1; Translation initiation factor if-2; 16S ribosomal…
- UniProt
- A0A069XYI1, A0A080IK26, D7X302, P0A7R9, V6FZ95, A0A1X3KX08, A0A090BZT4, D7XN21, B7MIU7, L3BXG0, F4SQ43, U9ZNW8, T6N332, A0A0K5Z365, A0A376HTV6, L3PZ69, B6I217, S1CG62, S1D5F0, D8A1L7, T9TH92
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 25 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 5 | Translation initiation factor if-1 | protein | 71 | 7% helix, 46% strand | — |
| f | Translation initiation factor if-2 | protein | 509 | 26% helix, 34% strand | A0A069XYI1 |
| g | 16S ribosomal RNA | rna | 1539 | — | — |
| P | 30S ribosomal protein S17 | protein | 80 | 0% helix, 51% strand | A0A080IK26 |
| r | 30S ribosomal protein S10 | protein | 98 | 26% helix, 33% strand | D7X302 |
| q | 30S ribosomal protein S11 | protein | 117 | 27% helix, 29% strand | P0A7R9 |
| t | 30S ribosomal protein S12 | protein | 123 | 5% helix, 21% strand | V6FZ95 |
| s | 30S ribosomal protein S13 | protein | 114 | 52% helix, 2% strand | A0A1X3KX08 |
| w | 30S ribosomal protein S14 | protein | 96 | 39% helix, 7% strand | A0A090BZT4 |
| u | 30S ribosomal protein S15 | protein | 88 | 75% helix, 0% strand | D7XN21 |
| y | 30S ribosomal protein S16 | protein | 82 | 23% helix, 29% strand | B7MIU7 |
| 1 | 30S ribosomal protein S18 | protein | 55 | 49% helix, 4% strand | L3BXG0 |
| z | 30S ribosomal protein S19 | protein | 79 | 30% helix, 19% strand | F4SQ43 |
| j | 30S ribosomal protein S2 | protein | 218 | 50% helix, 10% strand | U9ZNW8 |
| 3 | 30S ribosomal protein S20 | protein | 85 | 81% helix, 0% strand | T6N332 |
| 2 | 30S ribosomal protein S21 | protein | 51 | 53% helix, 2% strand | A0A0K5Z365 |
| h | 30S ribosomal protein S3 | protein | 206 | 37% helix, 25% strand | A0A376HTV6 |
| l | 30S ribosomal protein S4 | protein | 205 | 43% helix, 9% strand | L3PZ69 |
| k | 30S ribosomal protein S5 | protein | 150 | 27% helix, 37% strand | B6I217 |
| n | 30S ribosomal protein S6 | protein | 100 | 33% helix, 34% strand | S1CG62 |
| m | 30S ribosomal protein S7 | protein | 151 | 56% helix, 7% strand | S1D5F0 |
| p | 30S ribosomal protein S8 | protein | 129 | 27% helix, 32% strand | D8A1L7 |
| o | 30S ribosomal protein S9 | protein | 127 | 29% helix, 20% strand | T9TH92 |
| v | TRNA | rna | 77 | — | — |
| N | MRNA | rna | 6 | — | — |
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 | 826 | 0.85 | 0.88 | 81 | empty |
| 2 | 784 | 0.84 | 0.88 | 68 | empty |
| 3 | 1123 | 0.84 | 0.86 | 77 | empty |
| 4 | 1169 | 0.84 | 0.86 | 99 | empty |
| 5 | 564 | 0.84 | 0.90 | 60 | empty |
Interfaces
53 interfaces between chains.
- g–l · 3281 Ų buried · 103 hydrogen bonds · protein-nucleic
- g–o · 3083 Ų buried · 89 hydrogen bonds · protein-nucleic
- g–t · 3059 Ų buried · 94 hydrogen bonds · protein-nucleic
- g–3 · 2412 Ų buried · 68 hydrogen bonds · protein-nucleic
- g–w · 2308 Ų buried · 73 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 isopeptide, 1 disulfide (isopeptide, disulfide).
Compared structures
- 6O7K · 30S initiation complex · the same entry in another collection · chain h against h, 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 A0A069XYI1
- Every structure of UniProt A0A080IK26
- Every structure of UniProt D7X302
- Every structure of UniProt P0A7R9
- Every structure of UniProt V6FZ95
- Every structure of UniProt A0A1X3KX08
- Every structure of UniProt A0A090BZT4
- Every structure of UniProt D7XN21
- Every structure of UniProt B7MIU7
- Every structure of UniProt L3BXG0
- Every structure of UniProt F4SQ43
- Every structure of UniProt U9ZNW8
- Every structure of UniProt T6N332
- Every structure of UniProt A0A0K5Z365
- Every structure of UniProt A0A376HTV6
- Every structure of UniProt L3PZ69
- Every structure of UniProt B6I217
- Every structure of UniProt S1CG62
- Every structure of UniProt S1D5F0
- Every structure of UniProt D8A1L7
- Every structure of UniProt T9TH92
- Elsewhere: RCSB PDB 6O7K · PDBe 6O7K · UniProt A0A069XYI1 · UniProt A0A080IK26 · UniProt D7X302 · UniProt P0A7R9 · UniProt V6FZ95 · UniProt A0A1X3KX08 · UniProt A0A090BZT4 · UniProt D7XN21 · UniProt B7MIU7 · UniProt L3BXG0 · UniProt F4SQ43 · UniProt U9ZNW8 · UniProt T6N332 · UniProt A0A0K5Z365 · UniProt A0A376HTV6 · UniProt L3PZ69 · UniProt B6I217 · UniProt S1CG62 · UniProt S1D5F0 · UniProt D8A1L7 · UniProt T9TH92
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