Research workbench
Crystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile inhibitor
Analyse Crystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PID
- Type
- protein
- Length
- 215 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease; Pre-protein VI
- EC
- 3.4.22.39
- UniProt
- P03252, P03274
- Ligands
- 2UQ
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease (EC 3.4.22.39) | protein | 204 | 42% helix, 16% strand | P03252 |
| B | Pre-protein VI | protein | 11 | 0% helix, 64% strand | P03274 |
Ligands and binding sites
- 2UQ · N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide · ligand · chains A
- ACT · Acetate ion · 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 | 62 | 0.31 | 0.75 | 21 | 2UQ |
Interfaces
1 interface between chains.
- A–B · 888 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 4PID · Crystal structure of human adenovirus 2 protease with a weak pyrimidine 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 P03252
- Every structure of UniProt P03274
- Elsewhere: RCSB PDB 4PID · PDBe 4PID · UniProt P03252 · UniProt P03274
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