Research workbench
Satellite phage P4 procapsid including size determination (sid) protein
Analyse Satellite phage P4 procapsid including size determination (sid) protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JW1
- Type
- protein
- Length
- 2,858 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein gpn; Size determination protein sid
- UniProt
- P25477, P05461
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 5 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Major capsid protein gpn | protein | 279 | 27% helix, 25% strand | P25477 |
| B, b | Major capsid protein gpn | protein | 327 | 28% helix, 24% strand | P25477 |
| C, c | Major capsid protein gpn | protein | 281 | 23% helix, 27% strand | P25477 |
| D, d | Major capsid protein gpn | protein | 307 | 25% helix, 24% strand | P25477 |
| E, e | Size determination protein sid | protein | 235 | 74% helix, 0% strand | P05461 |
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 | 1028 | 0.77 | 0.79 | 103 | empty |
| 2 | 978 | 0.76 | 0.78 | 100 | empty |
| 3 | 101 | 0.72 | 0.94 | 24 | empty |
| 4 | 970 | 0.72 | 0.76 | 85 | empty |
| 5 | 524 | 0.72 | 0.81 | 59 | empty |
Interfaces
22 interfaces between chains.
- c–d · 2934 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2880 Ų buried · 33 hydrogen bonds · protein-protein
- D–b · 2777 Ų buried · 32 hydrogen bonds · protein-protein
- B–d · 2727 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2254 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7JW1 · Satellite phage P4 procapsid including size determination (Sid) protein · 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 P25477
- Every structure of UniProt P05461
- Elsewhere: RCSB PDB 7JW1 · PDBe 7JW1 · UniProt P25477 · UniProt P05461
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