Research workbench
Hepatitis C virus polymerase NS5B genotype 1B (bk) in complex with inhibitor 2 (3-(3-tert-butyl-4-METHOXYPHENYL)PYRIDIN-2(1H)-one)
Analyse Hepatitis C virus polymerase NS5B genotype 1B (bk) in complex with inhibitor 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MK7
- Type
- protein
- Length
- 1,116 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
- 28O, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 557 | 48% helix, 15% strand | P26663 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 559 | 48% helix, 15% strand | P26663 |
Ligands and binding sites
- 28O · 3-(3-tert-butyl-4-methoxyphenyl)pyridin-2(1H)-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.81 | 0.82 | 90 | DMS, 28O |
| 2 | 575 | 0.79 | 0.85 | 64 | DMS, 28O |
| 3 | 322 | 0.61 | 0.79 | 38 | empty |
| 4 | 202 | 0.61 | 0.82 | 28 | empty |
| 5 | 114 | 0.51 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 361 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4MK7 · Hepatitis C Virus polymerase NS5B genotype 1b (BK) in complex with inhibitor 2… · 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 4MK7 · PDBe 4MK7 · UniProt P26663
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