Research workbench
Crystal structure of KAPOSI'S sarcoma-associated herpesvirus (kshv) protease in complex with dimer disruptor
Analyse Crystal structure of KAPOSI'S sarcoma-associated herpesvirus (kshv) protease in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P3H
- Type
- protein
- Length
- 375 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kshv protease
- UniProt
- O36607
- Ligands
- 25G
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kshv protease | protein | 190 | 30% helix, 27% strand | O36607 |
| B | Kshv protease | protein | 185 | 31% helix, 28% strand | O36607 |
Ligands and binding sites
- 25G · N-[2-benzyl-4-(1H-tetrazol-5-yl)phenyl]-6-(cyclohexylmethyl)pyridine-2-carboxamide · ligand · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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 | 952 | 0.74 | 0.77 | 70 | DMS |
| 2 | 218 | 0.56 | 0.78 | 27 | 25G |
| 3 | 147 | 0.47 | 0.76 | 17 | 25G |
Interfaces
1 interface between chains.
- A–B · 851 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4P3H · Crystal structure of Kaposi's sarcoma-associated herpesvirus (KSHV) protease in complex… · 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 O36607
- Elsewhere: RCSB PDB 4P3H · PDBe 4P3H · UniProt O36607
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