Research workbench
Crystal structure of KSHV protease in complex with hexapeptide phosphonate inhibitor
Analyse Crystal structure of KSHV protease in complex with hexapeptide phosphonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PBK
- Type
- protein
- Length
- 467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.73
- Source
- Human herpesvirus; SYNTHETIC CONSTRUCT
- Molecule
- KSHV protease; hexapeptide phosphonate inhibitor
- UniProt
- O36607
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · resolution 1.73 · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KSHV protease | protein | 228 | 35% helix, 24% strand | O36607 |
| B | KSHV protease | protein | 227 | 37% helix, 24% strand | O36607 |
| C, D | hexapeptide phosphonate inhibitor | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.45 | 0.81 | 17 | empty |
| 2 | 139 | 0.44 | 0.76 | 19 | empty |
| 3 | 144 | 0.41 | 0.74 | 19 | empty |
| 4 | 61 | 0.39 | 0.79 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1282 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 586 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 568 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2PBK · Crystal structure of kshv protease in complex with hexapeptide phosphonate inhibitor · 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 2PBK · PDBe 2PBK · UniProt O36607
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