Research workbench
Crystal structure of pbcv-1 VP54 fitted into a cryo-EM reconstruction of the virophage sputnik
Analyse Crystal structure of pbcv-1 VP54 fitted into a cryo-EM reconstruction of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KK5
- Type
- protein
- Length
- 5,369 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P30328
- Pockets
- 17 · best druggability 0.47
Structure
electron microscopy · 1 distinct chain · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M | Major capsid protein | protein | 413 | 0% helix, 0% strand | P30328 |
Pockets
17 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.47 | 0.73 | 45 | empty |
| 2 | 145 | 0.44 | 0.73 | 38 | empty |
| 3 | 153 | 0.43 | 0.72 | 38 | empty |
| 4 | 138 | 0.42 | 0.73 | 36 | empty |
| 5 | 128 | 0.42 | 0.73 | 32 | empty |
Interfaces
17 interfaces between chains.
- K–M · 259 Ų buried · 0 hydrogen bonds · protein-protein
- F–G · 257 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 256 Ų buried · 0 hydrogen bonds · protein-protein
- H–J · 256 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KK5 · Crystal structure of PBCV-1 VP54 fitted into a cryo-EM reconstruction of the virophage… · 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 P30328
- Elsewhere: RCSB PDB 3KK5 · PDBe 3KK5 · UniProt P30328
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