MolNFT v1 · #115227 · protein
Crystal structure of israel acute paralysis virus
5CDC · VP1, structural polyprotein: “Crystal structure of israel acute paralysis virus”. X-ray diffraction, 8 pockets (best druggability 0.77). MolNFT v1 #115227 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CDC
- Type
- protein
- Length
- 791 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1, structural polyprotein; VP2, structural polyprotein; VP3, structural polyprotein; VP4
- UniProt
- D1FK67
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1, structural polyprotein | protein | 203 | 18% helix, 32% strand | D1FK67 |
| B | VP2, structural polyprotein | protein | 300 | 5% helix, 31% strand | D1FK67 |
| C | VP3, structural polyprotein | protein | 243 | 11% helix, 21% strand | D1FK67 |
| D | VP4 | protein | 45 | 0% helix, 0% strand | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.77 | 0.98 | 26 | empty |
| 2 | 673 | 0.66 | 0.76 | 74 | empty |
| 3 | 136 | 0.55 | 0.82 | 27 | empty |
| 4 | 259 | 0.53 | 0.76 | 36 | empty |
| 5 | 85 | 0.43 | 0.79 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4586 Ų buried · 64 hydrogen bonds · protein-protein
- B–C · 1586 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1094 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 563 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 83 Ų buried · 0 hydrogen bonds · protein-protein
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 D1FK67
- Elsewhere: RCSB PDB 5CDC · PDBe 5CDC · UniProt D1FK67
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