Research workbench
Vsv N protein in complex with inhibitory nanobody 1004
Analyse Vsv N protein in complex with inhibitory nanobody 1004 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UKB
- Type
- protein + RNA
- Length
- 2,750 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-vesicular stomatitis virus N vhh; Nucleocapsid; RNA (45-mer)
- UniProt
- A0A192B6J5, A6H4P1
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| d, c, b, a, e | Anti-vesicular stomatitis virus N vhh | protein | 122 | 5% helix, 44% strand | A0A192B6J5 |
| D, C, B, A, E | Nucleocapsid | protein | 419 | 42% helix, 6% strand | A6H4P1 |
| R | RNA (45-mer) | rna | 45 | — | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.83 | 0.84 | 99 | empty |
| 2 | 841 | 0.82 | 0.85 | 65 | empty |
| 3 | 705 | 0.82 | 0.86 | 63 | empty |
| 4 | 758 | 0.78 | 0.82 | 67 | empty |
| 5 | 698 | 0.76 | 0.82 | 71 | empty |
Interfaces
17 interfaces between chains.
- B–A · 2605 Ų buried · 13 hydrogen bonds · protein-protein
- C–B · 2580 Ų buried · 17 hydrogen bonds · protein-protein
- D–C · 2578 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 2572 Ų buried · 12 hydrogen bonds · protein-protein
- A–R · 1114 Ų buried · 27 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5UKB · Vsv N protein in complex with inhibitory nanobody 1004 · the same entry in another collection · chain d against d, 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 A0A192B6J5
- Every structure of UniProt A6H4P1
- Elsewhere: RCSB PDB 5UKB · PDBe 5UKB · UniProt A0A192B6J5 · UniProt A6H4P1
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