Research workbench
Crystal structure of adenovirus 8 protease with a nitrile inhibitor
Analyse Crystal structure of adenovirus 8 protease 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
- 4WX7
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease; Pvi
- UniProt
- B9A5C1, B9A5F5
- Ligands
- 3VJ
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protease | protein | 204 | 45% helix, 17% strand | B9A5C1 |
| B, D | Pvi | protein | 11 | 0% helix, 64% strand | B9A5F5 |
Ligands and binding sites
- 3VJ · 3-[2-(3,5-dichlorophenyl)-2-methylpropanoyl]-N-(2-{[(2Z)-2-iminoethyl]amino}-2-oxoethyl)-4-methoxybenzamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.70 | 0.77 | 76 | 3VJ |
| 2 | 140 | 0.45 | 0.77 | 29 | 3VJ |
| 3 | 96 | 0.36 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 885 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 855 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 4WX7 · Crystal structure of adenovirus 8 protease with a nitrile inhibitor · the same entry in another collection · chain B against B, 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
- Every structure of UniProt B9A5F5
- Elsewhere: RCSB PDB 4WX7 · PDBe 4WX7 · UniProt B9A5C1 · UniProt B9A5F5
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