MolNFT v1 · #67930 · protein
Cryoem structure of cytoplasmic polyhedrosis virus
3IZ3 · Structural protein VP3: “Cryoem structure of cytoplasmic polyhedrosis virus”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #67930 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IZ3
- Type
- protein
- Length
- 4,053 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein VP3; Structural protein VP1; Viral structural protein 5
- UniProt
- Q914N6, D3JWE6, C6K2M8
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 25% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural protein VP3 | protein | 1047 | 29% helix, 14% strand | Q914N6 |
| B | Structural protein VP1 | protein | 1180 | 24% helix, 10% strand | D3JWE6 |
| C | Structural protein VP1 | protein | 1244 | 23% helix, 12% strand | D3JWE6 |
| D, E | Viral structural protein 5 | protein | 291 | 32% helix, 12% strand | C6K2M8 |
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 | 1096 | 0.86 | 0.87 | 146 | empty |
| 2 | 804 | 0.84 | 0.87 | 96 | empty |
| 3 | 659 | 0.82 | 0.87 | 65 | empty |
| 4 | 660 | 0.81 | 0.86 | 61 | empty |
| 5 | 467 | 0.81 | 0.88 | 50 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2451 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 2034 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 984 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 983 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 900 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3IZ3 · CryoEM structure of 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 D3JWE6
- Every structure of UniProt C6K2M8
- Elsewhere: RCSB PDB 3IZ3 · PDBe 3IZ3 · UniProt Q914N6 · UniProt D3JWE6 · UniProt C6K2M8
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