Research workbench
Satellite tobacco mosaic virus refined to 1.4 a resolution using non- crystallographic symmetry restraints
Analyse Satellite tobacco mosaic virus refined to 1.4 a resolution using non… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OQ9
- Type
- protein + RNA
- Length
- 2,475 residues
- Chains
- 60
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein; RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'); RNA…
- UniProt
- P17574
- Ligands
- NA, MG, SO4, PO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O | Coat protein | protein | 144 | 7% helix, 46% strand | P17574 |
| P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | rna | 10 | — | — |
| e, f, g, h, i, j, k, l, m, n, o, p, q, r, s | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 10 | — | — |
| t, u, v, w, x, y, z, 1, 2, 3, 4, 5, 6, 7, 8 | RNA (5'-R(P*UP*U)-3') | rna | 1 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 17 copies · chains A, O, B, C, D, E, F, G, H, I, J, K, L, M, N
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 260 | 0.77 | 0.90 | 53 | empty |
| 2 | 509 | 0.73 | 0.82 | 53 | empty |
| 3 | 557 | 0.73 | 0.82 | 52 | empty |
| 4 | 549 | 0.73 | 0.82 | 53 | empty |
| 5 | 483 | 0.73 | 0.83 | 75 | empty |
Interfaces
189 interfaces between chains.
- A–O · 2139 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2127 Ų buried · 36 hydrogen bonds · protein-protein
- J–K · 2123 Ų buried · 31 hydrogen bonds · protein-protein
- d–e · 1131 Ų buried · 403 hydrogen bonds · nucleic-nucleic
- U–i · 1126 Ų buried · 409 hydrogen bonds · nucleic-nucleic
Compared structures
- 4OQ9 · Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic… · the same entry in another collection · chain K against K, 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 P17574
- Elsewhere: RCSB PDB 4OQ9 · PDBe 4OQ9 · UniProt P17574
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