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
- 465 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kshv protease; Hexapeptide phosphonate inhibitor
- UniProt
- O36607
- Ligands
- ACE, GG7
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 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 | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, C, D
- GG7 · [(1R)-1-aminoethyl]phosphonic acid · ligand · 2 copies · chains B, C, A, D
- 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 | 146 | 0.45 | 0.76 | 18 | empty |
| 2 | 84 | 0.45 | 0.81 | 17 | empty |
| 3 | 153 | 0.42 | 0.74 | 19 | empty |
| 4 | 61 | 0.38 | 0.79 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1282 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 496 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 474 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 modified (covalent ligand, 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.