Research workbench
Pz peptidase a with inhibitor 2
Analyse Pz peptidase a with inhibitor 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AHO
- Type
- protein
- Length
- 1,126 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptidase
- UniProt
- Q4W803
- Ligands
- 3A2, ZN
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligopeptidase | protein | 564 | 70% helix, 4% strand | Q4W803 |
| B | Oligopeptidase | protein | 562 | 70% helix, 4% strand | Q4W803 |
Ligands and binding sites
- 3A2 · 1-{3-[(R)-{(1R)-1-[(glycyl-L-prolyl)amino]-2-phenylethyl}(hydroxy)phosphoryl]propanoyl}-L-prolyl-D-norleucine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.84 | 0.85 | 74 | 3A2, ACT |
| 2 | 550 | 0.84 | 0.89 | 62 | empty |
| 3 | 1119 | 0.83 | 0.84 | 70 | 3A2, ACT |
| 4 | 893 | 0.76 | 0.79 | 73 | empty |
| 5 | 243 | 0.74 | 0.88 | 34 | ACT |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3AHO · PZ PEPTIDASE A with inhibitor 2 · 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 Q4W803
- Elsewhere: RCSB PDB 3AHO · PDBe 3AHO · UniProt Q4W803
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