Research workbench
Cryo-EM of the S. solfataricus rod-shaped virus, SSRV1
Analyse Cryo-EM of the S. solfataricus rod-shaped virus, SSRV1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WQ0
- Type
- protein + DNA
- Length
- 6,628 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (301-mer); Structural protein
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 7 | DNA (301-mer) | dna | 301 | — | — |
| 8 | DNA (301-mer) | dna | 301 | — | — |
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w | Structural protein | protein | 131 | 77% helix, 0% strand | — |
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 | 1054 | 0.91 | 0.94 | 103 | empty |
| 2 | 871 | 0.90 | 0.94 | 101 | empty |
| 3 | 1163 | 0.90 | 0.93 | 105 | empty |
| 4 | 859 | 0.90 | 0.94 | 90 | empty |
| 5 | 868 | 0.90 | 0.94 | 80 | empty |
Interfaces
257 interfaces between chains.
- 7–8 · 16558 Ų buried · 948 hydrogen bonds · nucleic-nucleic
- U–u · 1609 Ų buried · 10 hydrogen bonds · protein-protein
- W–w · 1601 Ų buried · 8 hydrogen bonds · protein-protein
- Q–q · 1601 Ų buried · 8 hydrogen bonds · protein-protein
- A–a · 1599 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6WQ0 · Cryo-EM of the S. solfataricus rod-shaped virus, SSRV1 · the same entry in another collection · chain 8 against 8, 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
- Elsewhere: RCSB PDB 6WQ0 · PDBe 6WQ0
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