Research workbench
Crystal structure of adenovirus 8 protease in complex with a nitrile inhibitor
Analyse Crystal structure of adenovirus 8 protease in complex with a nitrile inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WX4
- Type
- protein
- Length
- 211 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease; Peptide
- UniProt
- B9A5C1
- Ligands
- 3VF, GLY
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease | protein | 201 | 44% helix, 17% strand | B9A5C1 |
| C | Peptide | protein | 10 | 0% helix, 70% strand | — |
Ligands and binding sites
- 3VF · N-[(2-cyanopyrimidin-4-yl)methyl]-3-[2-(3,5-dichlorophenyl)-2-methylpropanoyl]-4-methoxybenzamide · ligand · chains A
- GLY · Glycine · ligand · chains A, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.45 | 0.77 | 26 | 3VF |
Interfaces
1 interface between chains.
- A–C · 860 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 4WX4 · Crystal structure of adenovirus 8 protease in complex with a nitrile 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 B9A5C1
- Elsewhere: RCSB PDB 4WX4 · PDBe 4WX4 · UniProt B9A5C1
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