MolNFT v1 · #154928 · protein
Crystal structure of dengue virus nonstructural protein NS5 (form 2)
6KR3 · Genome polyprotein: “Crystal structure of dengue virus nonstructural protein NS5 (form 2)”. X-ray diffraction, 3 ligands (SAH, ZN, IOD), 20 pockets (best druggability 0.81). MolNFT v1 #154928 on GenesisL1: 3D structure, binding…
- PDB
- 6KR3
- Type
- protein
- Length
- 1,678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- Q91H74
- Ligands
- SAH, ZN, IOD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 842 | 45% helix, 12% strand | Q91H74 |
| B | Genome polyprotein | protein | 836 | 44% helix, 13% strand | Q91H74 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- IOD · Iodide ion · ion · 15 copies · chains A, B
- GOL · Glycerol · additive · 5 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.81 | 0.86 | 84 | empty |
| 2 | 979 | 0.81 | 0.82 | 120 | empty |
| 3 | 343 | 0.75 | 0.86 | 51 | IOD, GOL |
| 4 | 90 | 0.74 | 0.96 | 30 | IOD |
| 5 | 426 | 0.61 | 0.76 | 41 | IOD, SAH |
Interfaces
1 interface between chains.
- A–B · 1597 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6KR3 · Crystal structure of Dengue virus nonstructural protein NS5 (form 2) · 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 6KR3 · PDBe 6KR3 · UniProt Q91H74
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