Research workbench
Crystal structure of KAPOSI'S sarcoma-associated herpesvirus protease in complex with dimer disruptor
Analyse Crystal structure of KAPOSI'S sarcoma-associated herpesvirus protease in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NJQ
- Type
- protein
- Length
- 379 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orf 17
- UniProt
- P88911
- Ligands
- NJQ, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orf 17 | protein | 190 | 27% helix, 27% strand | P88911 |
| B | Orf 17 | protein | 189 | 30% helix, 29% strand | P88911 |
Ligands and binding sites
- NJQ · 3-benzyl-4-({[6-(cyclohexylmethyl)pyridin-2-yl]carbonyl}amino)benzoic acid · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains B
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.73 | 0.78 | 81 | GOL |
| 2 | 178 | 0.55 | 0.79 | 20 | NJQ |
| 3 | 135 | 0.45 | 0.76 | 17 | NJQ |
Interfaces
1 interface between chains.
- A–B · 849 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 3NJQ · Crystal structure of Kaposi's sarcoma-associated herpesvirus protease 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 P88911
- Elsewhere: RCSB PDB 3NJQ · PDBe 3NJQ · UniProt P88911
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