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Crystal structure of yellow fever virus polymerase NS5A
Analyse Crystal structure of yellow fever virus polymerase NS5A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QSN
- Type
- protein
- Length
- 1,766 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- P03314
- Ligands
- SAH, ZN, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 882 | 44% helix, 13% strand | P03314 |
| B | Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 884 | 44% helix, 13% strand | P03314 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
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 | 992 | 0.83 | 0.84 | 103 | SO4 |
| 2 | 678 | 0.81 | 0.85 | 77 | empty |
| 3 | 874 | 0.81 | 0.83 | 95 | SO4 |
| 4 | 365 | 0.75 | 0.86 | 47 | empty |
| 5 | 516 | 0.68 | 0.78 | 48 | SAH |
Interfaces
1 interface between chains.
- A–B · 2287 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6QSN · Crystal structure of Yellow fever virus polymerase NS5A · 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 P03314
- Elsewhere: RCSB PDB 6QSN · PDBe 6QSN · UniProt P03314
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