MolNFT v1 · #146030 · protein + DNA
Cryo-EM reconstruction of membrane-enveloped filamentous virus SFV1 (sulfolobus filamentous virus 1)
6D5F · Fimbrial protein: “Cryo-EM reconstruction of membrane-enveloped filamentous virus SFV1 (sulfolobus filamentous virus 1)”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #146030 on GenesisL1: 3D structure…
- PDB
- 6D5F
- Type
- protein + DNA
- Length
- 9,122 residues
- Chains
- 54
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fimbrial protein; DNA (336-mer)
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 64% helix, 2% 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 | Fimbrial protein | protein | 194 | 60% helix, 4% strand | — |
| 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 | Fimbrial protein | protein | 131 | 69% helix, 0% strand | — |
| 1, 2 | DNA (336-mer) | dna | 336 | — | — |
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 | 900 | 0.88 | 0.91 | 70 | empty |
| 2 | 782 | 0.88 | 0.92 | 70 | empty |
| 3 | 815 | 0.88 | 0.92 | 71 | empty |
| 4 | 880 | 0.88 | 0.91 | 74 | empty |
| 5 | 768 | 0.88 | 0.92 | 70 | empty |
Interfaces
292 interfaces between chains.
- 1–2 · 15998 Ų buried · 706 hydrogen bonds · nucleic-nucleic
- Z–z · 1742 Ų buried · 10 hydrogen bonds · protein-protein
- G–g · 1742 Ų buried · 9 hydrogen bonds · protein-protein
- H–h · 1737 Ų buried · 10 hydrogen bonds · protein-protein
- N–n · 1736 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide (disulfide).
Compared structures
- 6D5F · Cryo-EM reconstruction of membrane-enveloped filamentous virus SFV1 (Sulfolobus… · the same entry in another collection · chain A against A, 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 6D5F · PDBe 6D5F
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