MolNFT v1 · #75562 · protein + RNA
Crystal structure of a vesicular stomatitis virus nucleocapsid-polyu complex
3PU4 · Nucleoprotein: “Crystal structure of a vesicular stomatitis virus nucleocapsid-polyu complex”. X-ray diffraction, 1 ligand (IUM), 20 pockets (best druggability 0.85). MolNFT v1 #75562 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3PU4
- Type
- protein + RNA
- Length
- 2,131 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; RNA (45-mer)
- UniProt
- P03521
- Ligands
- IUM
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Nucleoprotein | protein | 421 | 42% helix, 4% strand | P03521 |
| B | Nucleoprotein | protein | 415 | 42% helix, 6% strand | P03521 |
| C | Nucleoprotein | protein | 413 | 44% helix, 6% strand | P03521 |
| D | Nucleoprotein | protein | 416 | 43% helix, 6% strand | P03521 |
| R | RNA (45-mer) | rna | 45 | — | — |
Ligands and binding sites
- IUM · Uranyl (VI) ion · metal · 20 copies · chains A, B, E, C, D, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1032 | 0.85 | 0.86 | 86 | IUM |
| 2 | 770 | 0.84 | 0.87 | 88 | IUM |
| 3 | 426 | 0.82 | 0.90 | 47 | IUM |
| 4 | 402 | 0.81 | 0.90 | 48 | IUM |
| 5 | 287 | 0.78 | 0.91 | 45 | IUM |
Interfaces
12 interfaces between chains.
- C–D · 2715 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 2701 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2677 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2641 Ų buried · 26 hydrogen bonds · protein-protein
- B–R · 1104 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 3PU4 · Crystal Structure of a vesicular stomatitis virus nucleocapsid-polyU complex · 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
- Elsewhere: RCSB PDB 3PU4 · PDBe 3PU4 · UniProt P03521
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