Research workbench
Structure of an N-terminal domain of a reptarenavirus L protein
Analyse Structure of an N-terminal domain of a reptarenavirus L protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MV0
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L protein
- UniProt
- J7HBG8
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L protein | protein | 200 | 56% helix, 13% strand | J7HBG8 |
| B | L protein | protein | 206 | 54% helix, 12% strand | J7HBG8 |
| C | L protein | protein | 193 | 55% helix, 13% strand | J7HBG8 |
| D | L protein | protein | 197 | 55% helix, 13% strand | J7HBG8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.85 | 0.86 | 109 | PO4 |
| 2 | 938 | 0.85 | 0.86 | 94 | PO4 |
| 3 | 587 | 0.74 | 0.82 | 62 | empty |
| 4 | 85 | 0.59 | 0.88 | 16 | PO4 |
| 5 | 87 | 0.48 | 0.83 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1419 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1363 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 326 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 318 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MV0 · Structure of an N-terminal domain of a reptarenavirus L protein · 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 J7HBG8
- Elsewhere: RCSB PDB 5MV0 · PDBe 5MV0 · UniProt J7HBG8
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