MolNFT v1 · #128216 · protein
Flavivirus NS5 domain
5NJV: “Flavivirus NS5 domain”. X-ray diffraction, 2 ligands (SAM, CL), 7 pockets (best druggability 0.74). MolNFT v1 #128216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NJV
- Type
- protein
- Length
- 1,035 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5
- UniProt
- A0A146CJG7
- Ligands
- SAM, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS5 | protein | 261 | 38% helix, 15% strand | A0A146CJG7 |
| B | NS5 | protein | 262 | 37% helix, 15% strand | A0A146CJG7 |
| C | NS5 | protein | 256 | 35% helix, 17% strand | A0A146CJG7 |
| D | NS5 | protein | 256 | 37% helix, 18% strand | A0A146CJG7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.74 | 0.77 | 95 | empty |
| 2 | 1174 | 0.72 | 0.76 | 108 | SAM |
| 3 | 597 | 0.69 | 0.78 | 53 | SAM |
| 4 | 462 | 0.64 | 0.77 | 45 | SAM, CL |
| 5 | 519 | 0.64 | 0.76 | 52 | SAM, CL |
Interfaces
5 interfaces between chains.
- B–D · 602 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 485 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 275 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 222 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NJV · Flavivirus NS5 domain · 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 A0A146CJG7
- Elsewhere: RCSB PDB 5NJV · PDBe 5NJV · UniProt A0A146CJG7
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