Research workbench
Vsv nucleocapsid with polyamide bound
Analyse Vsv nucleocapsid with polyamide bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BJY
- Type
- protein + RNA
- Length
- 2,131 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (45-mer); Nucleoprotein
- UniProt
- P03521
- Ligands
- DV4, IUM
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA (45-mer) | rna | 45 | — | — |
| A, E | Nucleoprotein | protein | 421 | 43% helix, 5% strand | P03521 |
| B | Nucleoprotein | protein | 415 | 44% helix, 6% strand | P03521 |
| C | Nucleoprotein | protein | 413 | 43% helix, 5% strand | P03521 |
| D | Nucleoprotein | protein | 416 | 43% helix, 5% strand | P03521 |
Ligands and binding sites
- DV4 · 4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide · ligand · chains R, A, B
- IUM · Uranyl (VI) ion · metal · 15 copies · chains A, B, E, C, D
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 | 806 | 0.84 | 0.87 | 97 | empty |
| 2 | 695 | 0.83 | 0.87 | 84 | empty |
| 3 | 643 | 0.82 | 0.87 | 76 | empty |
| 4 | 854 | 0.81 | 0.84 | 73 | empty |
| 5 | 256 | 0.72 | 0.87 | 44 | empty |
Interfaces
12 interfaces between chains.
- A–E · 2820 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2791 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2702 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2625 Ų buried · 22 hydrogen bonds · protein-protein
- R–D · 1150 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 6BJY · VSV Nucleocapsid with Polyamide Bound · the same entry in another collection · chain R against R, 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
- Elsewhere: RCSB PDB 6BJY · PDBe 6BJY · UniProt P03521
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