Research workbench
Bacteriophage T4 isometric capsid
Analyse Bacteriophage T4 isometric capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VF3
- Type
- protein
- Length
- 6,796 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid vertex protein GP24; Major capsid protein; Small outer capsid protein; Highly…
- UniProt
- P19896, P04535, P03715, P18056
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Capsid vertex protein GP24 | protein | 415 | 22% helix, 21% strand | P19896 |
| A, B, C, D, E, F, G, H, I, J, K, L | Major capsid protein | protein | 456 | 22% helix, 23% strand | P04535 |
| O, P, Q, R, S, T, U, V, W, X, Y | Small outer capsid protein | protein | 79 | 22% helix, 30% strand | P03715 |
| Z | Highly immunogenic outer capsid protein | protein | 25 | 40% helix, 0% strand | P18056 |
| z | Highly immunogenic outer capsid protein | protein | 15 | 0% helix, 0% strand | — |
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 | 420 | 0.83 | 0.91 | 30 | empty |
| 2 | 438 | 0.82 | 0.90 | 30 | empty |
| 3 | 987 | 0.78 | 0.80 | 100 | empty |
| 4 | 926 | 0.78 | 0.80 | 87 | empty |
| 5 | 667 | 0.76 | 0.82 | 78 | empty |
Interfaces
91 interfaces between chains.
- K–L · 4251 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 4248 Ų buried · 55 hydrogen bonds · protein-protein
- H–I · 4247 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 4247 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 4211 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5VF3 · Bacteriophage T4 isometric capsid · 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 P19896
- Every structure of UniProt P04535
- Every structure of UniProt P03715
- Every structure of UniProt P18056
- Elsewhere: RCSB PDB 5VF3 · PDBe 5VF3 · UniProt P19896 · UniProt P04535 · UniProt P03715 · UniProt P18056
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