MolNFT v1 · #142893 · protein
The structure of enterovirus D68 procapsid
6AJ3 · Capsid protein VP1: “The structure of enterovirus D68 procapsid”. Electron microscopy, 6 pockets (best druggability 0.76). MolNFT v1 #142893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AJ3
- Type
- protein
- Length
- 573 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- A0A097F8Q2, A0A0A7X639
- Pockets
- 6 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 7% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 187 | 6% helix, 37% strand | A0A097F8Q2 |
| B | Capsid protein VP2 | protein | 166 | 8% helix, 27% strand | A0A0A7X639 |
| C | Capsid protein VP3 | protein | 220 | 6% helix, 29% strand | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.76 | 0.91 | 34 | empty |
| 2 | 136 | 0.61 | 0.85 | 19 | empty |
| 3 | 93 | 0.48 | 0.81 | 22 | empty |
| 4 | 105 | 0.42 | 0.77 | 20 | empty |
| 5 | 100 | 0.40 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2004 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1540 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1530 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6AJ3 · The structure of Enterovirus D68 procapsid · 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 A0A097F8Q2
- Every structure of UniProt A0A0A7X639
- Elsewhere: RCSB PDB 6AJ3 · PDBe 6AJ3 · UniProt A0A097F8Q2 · UniProt A0A0A7X639
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