Research workbench
Atomic model of cytoplasmic polyhedrosis virus with SAM and GTP
Analyse Atomic model of cytoplasmic polyhedrosis virus with SAM and GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JB2
- Type
- protein
- Length
- 4,083 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, GTP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 35% 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 | 35% helix, 17% strand | Q6TS43 |
| C | Capsid protein VP1 | protein | 1251 | 33% helix, 18% strand | Q6TS43 |
| D, E | Viral structural protein 5 | protein | 292 | 43% helix, 18% strand | C6K2M8 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 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 | 518 | 0.85 | 0.91 | 46 | empty |
| 2 | 1059 | 0.84 | 0.85 | 104 | empty |
| 3 | 725 | 0.84 | 0.87 | 60 | empty |
| 4 | 926 | 0.82 | 0.84 | 101 | empty |
| 5 | 854 | 0.80 | 0.83 | 82 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3431 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 2323 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2023 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1048 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 832 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3JB2 · Atomic model of cytoplasmic polyhedrosis virus with SAM and GTP · 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 3JB2 · PDBe 3JB2 · UniProt Q914N6 · UniProt Q6TS43 · UniProt C6K2M8
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