Research workbench
Crystal structure of dengue virus nonstructural protein NS5 (form 1)
Analyse Crystal structure of dengue virus nonstructural protein NS5 (form 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KR2
- Type
- protein
- Length
- 1,700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- Q91H74
- Ligands
- SAH, ZN
- Pockets
- 19 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 857 | 38% helix, 12% strand | Q91H74 |
| B | Genome polyprotein | protein | 843 | 43% helix, 12% strand | Q91H74 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.67 | 0.77 | 66 | empty |
| 2 | 621 | 0.66 | 0.76 | 61 | SAH |
| 3 | 549 | 0.65 | 0.76 | 65 | SAH |
| 4 | 315 | 0.58 | 0.76 | 43 | empty |
| 5 | 162 | 0.56 | 0.81 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 989 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6KR2 · Crystal structure of Dengue virus nonstructural protein NS5 (form 1) · 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 Q91H74
- Elsewhere: RCSB PDB 6KR2 · PDBe 6KR2 · UniProt Q91H74
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