MolNFT v1 · #148304 · protein + DNA
Cryoem structure of ageratum yellow vein virus (ayvv)
6F2S · Capsid protein: “Cryoem structure of ageratum yellow vein virus (ayvv)”. Electron microscopy, 20 pockets (best druggability 0.67). MolNFT v1 #148304 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F2S
- Type
- protein + DNA
- Length
- 2,252 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Ssdna loop; Coat protein subunit I; Coat protein subunit H; Ssdna loop…
- UniProt
- W5RUR4
- Pockets
- 20 · best druggability 0.67
Structure
electron microscopy · 5 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, E, D, C, K, J, G | Capsid protein | protein | 195 | 7% helix, 52% strand | W5RUR4 |
| L, M, Q, P, O, N, V, U, T, R | Ssdna loop | dna | 7 | — | — |
| I | Coat protein subunit I | protein | 203 | 5% helix, 50% strand | W5RUR4 |
| H | Coat protein subunit H | protein | 218 | 11% helix, 48% strand | W5RUR4 |
| S | Ssdna loop associated with subunit H | dna | 6 | — | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.67 | 0.77 | 52 | empty |
| 2 | 519 | 0.66 | 0.77 | 48 | empty |
| 3 | 221 | 0.63 | 0.82 | 36 | empty |
| 4 | 214 | 0.63 | 0.82 | 33 | empty |
| 5 | 229 | 0.60 | 0.81 | 39 | empty |
Interfaces
39 interfaces between chains.
- I–H · 1046 Ų buried · 14 hydrogen bonds · protein-protein
- K–J · 1019 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1010 Ų buried · 15 hydrogen bonds · protein-protein
- F–E · 1000 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 999 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6F2S · CryoEM structure of Ageratum Yellow Vein virus (AYVV) · 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
- Every structure of UniProt W5RUR4
- Elsewhere: RCSB PDB 6F2S · PDBe 6F2S · UniProt W5RUR4
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