MolNFT v1 · #60142 · protein
Crystal structure of hepatitis C virus RNA-dependent RNA polymerase NS5B in complex with small molecule fragments
3CJ0 · RNA-directed RNA polymerase: “Crystal structure of hepatitis C virus RNA-dependent RNA polymerase NS5B in complex with small molecule…”. X-ray diffraction, 1 ligand (SX2), 14 pockets (best druggability 0.80). MolNFT v1 #60142 on…
- PDB
- 3CJ0
- Type
- protein
- Length
- 1,124 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P26663
- Ligands
- SX2
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 562 | 49% helix, 15% strand | P26663 |
Ligands and binding sites
- SX2 · 4-[(5-bromopyridin-2-yl)amino]-4-oxobutanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.80 | 0.81 | 83 | empty |
| 2 | 1085 | 0.80 | 0.81 | 79 | empty |
| 3 | 318 | 0.64 | 0.80 | 37 | empty |
| 4 | 362 | 0.64 | 0.79 | 38 | empty |
| 5 | 108 | 0.51 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 594 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3CJ0 · Crystal structure of hepatitis c virus rna-dependent rna polymerase ns5b in complex with… · 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 P26663
- Elsewhere: RCSB PDB 3CJ0 · PDBe 3CJ0 · UniProt P26663
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