Research workbench
A virus that infects a hyperthermophile encapsidates a-form DNA
Analyse A virus that infects a hyperthermophile encapsidates a-form DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J9X
- Type
- protein + DNA
- Length
- 8,120 residues
- Chains
- 60
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein; DNA
- UniProt
- Q8V9P2
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, 1, 2, 3, 4, 5, 6 | Coat protein | protein | 128 | 80% helix, 0% strand | Q8V9P2 |
| 7, 8 | DNA | dna | 348 | — | — |
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 | 643 | 0.83 | 0.89 | 48 | empty |
| 2 | 630 | 0.83 | 0.89 | 47 | empty |
| 3 | 376 | 0.81 | 0.91 | 43 | empty |
| 4 | 508 | 0.80 | 0.87 | 80 | empty |
| 5 | 256 | 0.76 | 0.90 | 60 | empty |
Interfaces
329 interfaces between chains.
- 7–8 · 19040 Ų buried · 1,361 hydrogen bonds · nucleic-nucleic
- Q–R · 1547 Ų buried · 11 hydrogen bonds · protein-protein
- w–x · 1546 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1543 Ų buried · 11 hydrogen bonds · protein-protein
- 3–4 · 1543 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3J9X · A Virus that Infects a Hyperthermophile Encapsidates A-Form DNA · the same entry in another collection · chain C against C, 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 Q8V9P2
- Elsewhere: RCSB PDB 3J9X · PDBe 3J9X · UniProt Q8V9P2
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