MolNFT v1 · #138463 · protein
Structure of the major capsid protein and the capsid stabilizing protein of the marine siphovirus TW1
5WK1: “Structure of the major capsid protein and the capsid stabilizing protein of the marine siphovirus TW1”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #138463 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WK1
- Type
- protein
- Length
- 3,094 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid stabilizing protein; Major capsid protein
- UniProt
- S5MS27, S5M825
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 12% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, L, Y, M, S, Z, K | Capsid stabilizing protein | protein | 148 | 2% helix, 30% strand | S5MS27 |
| A, B, C, D, E, F, G | Major capsid protein | protein | 294 | 16% helix, 22% strand | S5M825 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.84 | 0.85 | 55 | empty |
| 2 | 937 | 0.83 | 0.84 | 56 | empty |
| 3 | 811 | 0.74 | 0.78 | 71 | empty |
| 4 | 638 | 0.73 | 0.80 | 69 | empty |
| 5 | 821 | 0.72 | 0.77 | 79 | empty |
Interfaces
29 interfaces between chains.
- B–C · 2666 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2614 Ų buried · 31 hydrogen bonds · protein-protein
- F–G · 2576 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2576 Ų buried · 31 hydrogen bonds · protein-protein
- B–G · 2533 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5WK1 · Structure of the major capsid protein and the capsid stabilizing protein of the marine… · the same entry in another collection · chain X against X, 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 S5MS27
- Every structure of UniProt S5M825
- Elsewhere: RCSB PDB 5WK1 · PDBe 5WK1 · UniProt S5MS27 · UniProt S5M825
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