MolNFT v1 · #129220 · protein + RNA
Structure of watermelon mosaic virus potyvirus.
5ODV · Coat protein: “Structure of watermelon mosaic virus potyvirus.”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #129220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ODV
- Type
- protein + RNA
- Length
- 5,088 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein; RNA (5'-R(P*UP*UP*UP*UP*U)-3')
- UniProt
- Q70J31
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 38% helix, 3% 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 | Coat protein | protein | 207 | 38% helix, 3% strand | Q70J31 |
| a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x | RNA (5'-R(P*UP*UP*UP*UP*U)-3') | rna | 5 | — | — |
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 | 737 | 0.89 | 0.93 | 121 | empty |
| 2 | 583 | 0.88 | 0.93 | 113 | empty |
| 3 | 664 | 0.87 | 0.91 | 88 | empty |
| 4 | 507 | 0.86 | 0.93 | 87 | empty |
| 5 | 594 | 0.86 | 0.91 | 82 | empty |
Interfaces
214 interfaces between chains.
- O–P · 1890 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1890 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1889 Ų buried · 18 hydrogen bonds · protein-protein
- J–K · 1889 Ų buried · 18 hydrogen bonds · protein-protein
- N–O · 1889 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5ODV · Structure of Watermelon mosaic virus potyvirus. · 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 Q70J31
- Elsewhere: RCSB PDB 5ODV · PDBe 5ODV · UniProt Q70J31
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