Research workbench
Structure of the major capsid protein and the capsid stabilizing protein of the marine siphovirus TW1
Analyse Structure of the major capsid protein and the capsid stabilizing protein of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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