Research workbench
Atomic model of cytoplasmic polyhedrosis virus with SAM
Analyse Atomic model of cytoplasmic polyhedrosis virus with SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JB1
- Type
- protein
- Length
- 4,082 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein VP3; Capsid protein VP1; Viral structural protein 5
- UniProt
- Q914N6, Q6TS43, C6K2M8
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural protein VP3 | protein | 1057 | 37% helix, 17% strand | Q914N6 |
| B | Capsid protein VP1 | protein | 1191 | 36% helix, 17% strand | Q6TS43 |
| C | Capsid protein VP1 | protein | 1250 | 33% helix, 17% strand | Q6TS43 |
| D, E | Viral structural protein 5 | protein | 292 | 43% helix, 15% strand | C6K2M8 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 702 | 0.85 | 0.89 | 99 | empty |
| 2 | 1006 | 0.81 | 0.83 | 102 | empty |
| 3 | 897 | 0.81 | 0.83 | 83 | empty |
| 4 | 731 | 0.80 | 0.84 | 62 | empty |
| 5 | 1144 | 0.79 | 0.81 | 102 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3483 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 2301 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1319 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1005 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 828 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3JB1 · Atomic model of cytoplasmic polyhedrosis virus with SAM · the same entry in another collection · chain B against B, 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 Q914N6
- Every structure of UniProt Q6TS43
- Every structure of UniProt C6K2M8
- Elsewhere: RCSB PDB 3JB1 · PDBe 3JB1 · UniProt Q914N6 · UniProt Q6TS43 · UniProt C6K2M8
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