Research workbench
Echovirus 18 open particle without one pentamer
Analyse Echovirus 18 open particle without one pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HBK
- Type
- protein
- Length
- 7,480 residues
- Chains
- 33
- 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 0.80
Structure
electron microscopy · 3 distinct chains · 6% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, e, b, Y, V, S, P, M, J, G, D | Echovirus 18 capsid protein 1 | protein | 224 | 7% helix, 30% strand | Q8V635 |
| g, d, a, X, U, R, O, L, I, F, C | Echovirus 18 capsid protein 2 | protein | 218 | 6% helix, 35% strand | Q8V635 |
| f, c, Z, W, T, Q, N, K, H, E, B | Echovirus 18 capsid protein 3 | protein | 238 | 6% helix, 31% strand | Q8V635 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.80 | 0.82 | 107 | empty |
| 2 | 1159 | 0.80 | 0.82 | 100 | empty |
| 3 | 926 | 0.71 | 0.76 | 73 | empty |
| 4 | 228 | 0.60 | 0.80 | 49 | empty |
| 5 | 177 | 0.57 | 0.81 | 36 | empty |
Interfaces
113 interfaces between chains.
- J–L · 3232 Ų buried · 43 hydrogen bonds · protein-protein
- Y–a · 3231 Ų buried · 40 hydrogen bonds · protein-protein
- g–e · 3224 Ų buried · 38 hydrogen bonds · protein-protein
- V–X · 3214 Ų buried · 42 hydrogen bonds · protein-protein
- D–F · 3214 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 6HBK · Echovirus 18 Open particle without one pentamer · the same entry in another collection · chain g against g, 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 6HBK · PDBe 6HBK · UniProt Q8V635
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