Research workbench
Cryo-EM of the S. islandicus filamentous virus, sifv
Analyse Cryo-EM of the S. islandicus filamentous virus, sifv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WQ2
- Type
- protein + DNA
- Length
- 6,500 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A-DNA; Structural protein MCP2; Structural protein MCP1
- UniProt
- Q914J5, Q914J4
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 4 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | A-DNA | dna | 225 | — | — |
| 2 | A-DNA | dna | 223 | — | — |
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, P, R, T | Structural protein MCP2 | protein | 154 | 71% helix, 6% strand | Q914J5 |
| a, b, c, d, e, f, g, h, i, j, k, l, m, n, p, r, t | Structural protein MCP1 | protein | 202 | 68% helix, 0% strand | Q914J4 |
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 | 925 | 0.91 | 0.94 | 93 | empty |
| 2 | 937 | 0.90 | 0.93 | 84 | empty |
| 3 | 896 | 0.90 | 0.94 | 87 | empty |
| 4 | 903 | 0.90 | 0.94 | 90 | empty |
| 5 | 747 | 0.90 | 0.94 | 84 | empty |
Interfaces
174 interfaces between chains.
- 1–2 · 10430 Ų buried · 910 hydrogen bonds · nucleic-nucleic
- 1–b · 1126 Ų buried · 16 hydrogen bonds · protein-nucleic
- 1–m · 1082 Ų buried · 18 hydrogen bonds · protein-nucleic
- 1–g · 1071 Ų buried · 23 hydrogen bonds · protein-nucleic
- 1–d · 1070 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 6WQ2 · Cryo-EM of the S. islandicus filamentous virus, SIFV · the same entry in another collection · chain 2 against 2, 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 Q914J5
- Every structure of UniProt Q914J4
- Elsewhere: RCSB PDB 6WQ2 · PDBe 6WQ2 · UniProt Q914J5 · UniProt Q914J4
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