MolNFT v1 · #68170 · protein
Atomic model of transcribing cytoplasmic polyhedrosis virus
3JAY · Structural protein VP3: “Atomic model of transcribing cytoplasmic polyhedrosis virus”. Electron microscopy, 4 ligands (SAM, ATP, GTP), 20 pockets (best druggability 0.85). MolNFT v1 #68170 on GenesisL1: 3D structure, binding sites…
- PDB
- 3JAY
- 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, ATP, GTP, MG
- 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 | 36% helix, 17% strand | Q914N6 |
| B | Capsid protein VP1 | protein | 1191 | 36% helix, 17% strand | Q6TS43 |
| C | Capsid protein VP1 | protein | 1251 | 33% helix, 18% strand | Q6TS43 |
| D, E | Viral structural protein 5 | protein | 292 | 44% helix, 18% strand | C6K2M8 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- GTP · Guanosine-5'-triphosphate · ligand · 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 | 553 | 0.85 | 0.91 | 50 | empty |
| 2 | 1101 | 0.84 | 0.85 | 107 | empty |
| 3 | 607 | 0.82 | 0.87 | 53 | empty |
| 4 | 888 | 0.80 | 0.82 | 85 | empty |
| 5 | 802 | 0.80 | 0.83 | 81 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3301 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 2298 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2020 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 994 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 812 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3JAY · Atomic model of transcribing cytoplasmic polyhedrosis virus · 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 Q914N6
- Every structure of UniProt Q6TS43
- Every structure of UniProt C6K2M8
- Elsewhere: RCSB PDB 3JAY · PDBe 3JAY · UniProt Q914N6 · UniProt Q6TS43 · UniProt C6K2M8
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