Research workbench
Structure of vesicular stomatitis virus (local reconstruction, 3.5 a resolution)
Analyse Structure of vesicular stomatitis virus (local reconstruction, 3.5 a resolution) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UML
- Type
- protein + RNA
- Length
- 825 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; Matrix protein; RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
- UniProt
- P03521, P03519
- Pockets
- 10 · best druggability 0.75
Structure
electron microscopy · 7 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 379 | 45% helix, 4% strand | P03521 |
| B | Matrix protein | protein | 171 | 20% helix, 36% strand | P03519 |
| C | Matrix protein | protein | 172 | 24% helix, 30% strand | P03519 |
| D | Nucleoprotein | protein | 34 | 21% helix, 15% strand | P03521 |
| E | Nucleoprotein | protein | 39 | 0% helix, 8% strand | P03521 |
| F | Matrix protein | protein | 17 | 0% helix, 0% strand | P03519 |
| R | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 13 | — | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.75 | 0.79 | 77 | empty |
| 2 | 223 | 0.65 | 0.83 | 40 | empty |
| 3 | 245 | 0.57 | 0.78 | 29 | empty |
| 4 | 296 | 0.55 | 0.76 | 43 | empty |
| 5 | 177 | 0.47 | 0.76 | 29 | empty |
Interfaces
9 interfaces between chains.
- A–R · 1105 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 915 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 887 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 719 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 432 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7UML · Structure of vesicular stomatitis virus (local reconstruction, 3.5 A resolution) · 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 P03521
- Every structure of UniProt P03519
- Elsewhere: RCSB PDB 7UML · PDBe 7UML · UniProt P03521 · UniProt P03519
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