Research workbench
Structure of ipnv subviral particle
Analyse Structure of ipnv subviral particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IDE
- Type
- protein
- Length
- 2,077 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP2
- UniProt
- Q703G9
- Ligands
- CO, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Capsid protein VP2 | protein | 415 | 13% helix, 41% strand | Q703G9 |
| B, D | Capsid protein VP2 | protein | 416 | 13% helix, 41% strand | Q703G9 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 3 copies · chains A, C, E
- CL · Chloride ion · ion · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.74 | 0.90 | 25 | empty |
| 2 | 187 | 0.74 | 0.90 | 26 | empty |
| 3 | 234 | 0.74 | 0.88 | 34 | empty |
| 4 | 237 | 0.73 | 0.88 | 33 | empty |
| 5 | 249 | 0.72 | 0.87 | 36 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1000 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 980 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 908 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 903 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 836 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3IDE · Structure of IPNV subviral particle · 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 Q703G9
- Elsewhere: RCSB PDB 3IDE · PDBe 3IDE · UniProt Q703G9
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