MolNFT v1 · #166983 · protein + DNA
Cryo-EM reconstruction of pyrobaculum filamentous virus 2 (PFV2)
6V7B · A-DNA: “Cryo-EM reconstruction of pyrobaculum filamentous virus 2 (PFV2)”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #166983 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V7B
- Type
- protein + DNA
- Length
- 6,281 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A-DNA; Structural protein VP1; Structural protein VP2
- UniProt
- A0A140F3K6, A0A140F3K7
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | A-DNA | dna | 323 | — | — |
| 2 | A-DNA | dna | 323 | — | — |
| 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 VP1 | protein | 119 | 76% helix, 0% strand | A0A140F3K6 |
| 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 VP2 | protein | 126 | 69% helix, 0% strand | A0A140F3K7 |
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 | 1173 | 0.84 | 0.86 | 100 | empty |
| 2 | 612 | 0.80 | 0.86 | 62 | empty |
| 3 | 581 | 0.80 | 0.86 | 51 | empty |
| 4 | 535 | 0.79 | 0.86 | 51 | empty |
| 5 | 541 | 0.79 | 0.86 | 45 | empty |
Interfaces
213 interfaces between chains.
- 1–2 · 16142 Ų buried · 1,120 hydrogen bonds · nucleic-nucleic
- R–r · 1498 Ų buried · 15 hydrogen bonds · protein-protein
- W–w · 1495 Ų buried · 12 hydrogen bonds · protein-protein
- G–g · 1487 Ų buried · 13 hydrogen bonds · protein-protein
- S–s · 1487 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide (disulfide).
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 A0A140F3K6
- Every structure of UniProt A0A140F3K7
- Elsewhere: RCSB PDB 6V7B · PDBe 6V7B · UniProt A0A140F3K6 · UniProt A0A140F3K7
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