MolNFT v1 · #67944 · protein
3.1 ångström cryoem structure of cytoplasmic polyhedrosis virus
3IZX · Structural protein VP3: “3.1 ångström cryoem structure of cytoplasmic polyhedrosis virus”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #67944 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IZX
- Type
- protein
- Length
- 4,077 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
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 31% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural protein VP3 | protein | 1057 | 33% helix, 13% strand | Q914N6 |
| B | Capsid protein VP1 | protein | 1191 | 31% helix, 11% strand | Q6TS43 |
| C | Capsid protein VP1 | protein | 1249 | 29% helix, 11% strand | Q6TS43 |
| D, E | Viral structural protein 5 | protein | 290 | 38% helix, 7% 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 | 843 | 0.86 | 0.89 | 102 | empty |
| 2 | 1200 | 0.86 | 0.87 | 130 | empty |
| 3 | 821 | 0.82 | 0.85 | 73 | empty |
| 4 | 609 | 0.80 | 0.85 | 59 | empty |
| 5 | 1047 | 0.80 | 0.81 | 95 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3215 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 2375 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1181 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 902 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 788 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3IZX · 3.1 Angstrom 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 Q6TS43
- Every structure of UniProt C6K2M8
- Elsewhere: RCSB PDB 3IZX · PDBe 3IZX · UniProt Q914N6 · UniProt Q6TS43 · UniProt C6K2M8
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