Research workbench
Crystal structure of the full-length japanese encephalitis virus NS5
Analyse Crystal structure of the full-length japanese encephalitis virus NS5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K6M
- Type
- protein
- Length
- 1,776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein
- UniProt
- Q5NT71
- Ligands
- SAH, ZN, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polyprotein | protein | 888 | 43% helix, 13% strand | Q5NT71 |
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 · 18 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.79 | 0.82 | 83 | SAH, SO4 |
| 2 | 1041 | 0.78 | 0.80 | 94 | SAH, SO4 |
| 3 | 1163 | 0.78 | 0.80 | 106 | SO4 |
| 4 | 1198 | 0.78 | 0.79 | 97 | SO4 |
| 5 | 387 | 0.69 | 0.81 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1689 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4K6M · Crystal Structure of the full-length Japanese encephalitis virus NS5 · the same entry in another collection · chain B against B, 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 Q5NT71
- Elsewhere: RCSB PDB 4K6M · PDBe 4K6M · UniProt Q5NT71
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