Research workbench
Echovirus 18 open particle without three pentamers
Analyse Echovirus 18 open particle without three pentamers in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HBL
- Type
- protein
- Length
- 10,200 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Echovirus 18 capsid protein 1; Echovirus 18 capsid protein 2; Echovirus 18 capsid protein…
- UniProt
- Q8V635
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 6% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, q, n, k, h, e, b, Y, V, S, P, M, J, G, D | Echovirus 18 capsid protein 1 | protein | 224 | 6% helix, 30% strand | Q8V635 |
| r, o, l, i, f, c, Z, W, T, Q, N, K, H, E, B | Echovirus 18 capsid protein 2 | protein | 238 | 6% helix, 30% strand | Q8V635 |
| s, p, m, j, g, d, a, X, U, R, O, L, I, F, C | Echovirus 18 capsid protein 3 | protein | 218 | 6% helix, 35% strand | Q8V635 |
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 | 1102 | 0.83 | 0.84 | 118 | empty |
| 2 | 1147 | 0.82 | 0.83 | 117 | empty |
| 3 | 1120 | 0.81 | 0.82 | 104 | empty |
| 4 | 944 | 0.70 | 0.75 | 70 | empty |
| 5 | 898 | 0.70 | 0.75 | 72 | empty |
Interfaces
171 interfaces between chains.
- q–s · 3209 Ų buried · 37 hydrogen bonds · protein-protein
- Y–a · 3208 Ų buried · 37 hydrogen bonds · protein-protein
- n–p · 3208 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 3206 Ų buried · 37 hydrogen bonds · protein-protein
- S–U · 3206 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6HBL · Echovirus 18 Open particle without three pentamers · the same entry in another collection · chain q against q, 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 Q8V635
- Elsewhere: RCSB PDB 6HBL · PDBe 6HBL · UniProt Q8V635
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