Research workbench
Crystal structure of an empty vesicular stomatitis virus nucleocapsid protein complex
Analyse Crystal structure of an empty vesicular stomatitis virus nucleocapsid protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PTO
- Type
- protein
- Length
- 2,075 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- P03521
- Ligands
- IUM
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 416 | 42% helix, 5% strand | P03521 |
| B | Nucleoprotein | protein | 415 | 42% helix, 6% strand | P03521 |
| C | Nucleoprotein | protein | 413 | 42% helix, 6% strand | P03521 |
| D | Nucleoprotein | protein | 416 | 43% helix, 6% strand | P03521 |
| E | Nucleoprotein | protein | 415 | 42% helix, 5% strand | P03521 |
Ligands and binding sites
- IUM · Uranyl (VI) ion · metal · 15 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.72 | 0.82 | 46 | empty |
| 2 | 399 | 0.71 | 0.82 | 44 | empty |
| 3 | 1100 | 0.68 | 0.73 | 116 | empty |
| 4 | 201 | 0.67 | 0.86 | 21 | empty |
| 5 | 169 | 0.67 | 0.87 | 20 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2626 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 2609 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2565 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2548 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 350 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3PTO · Crystal Structure of an empty Vesicular Stomatitis Virus Nucleocapsid Protein 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 3PTO · PDBe 3PTO · UniProt P03521
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