Research workbench
Pz peptidase a with inhibitor 1
Analyse Pz peptidase a with inhibitor 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AHN
- Type
- protein
- Length
- 1,127 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptidase
- UniProt
- Q4W803
- Ligands
- 3A1, ZN
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligopeptidase | protein | 564 | 69% helix, 4% strand | Q4W803 |
| B | Oligopeptidase | protein | 563 | 70% helix, 4% strand | Q4W803 |
Ligands and binding sites
- 3A1 · N~2~-{(2S)-3-[(R)-hydroxy{(1R)-2-phenyl-1-[(phenylacetyl)amino]ethyl}phosphoryl]-2-methylpropanoyl}-L-lysyl-D-serine · 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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.85 | 0.87 | 74 | 3A1 |
| 2 | 630 | 0.85 | 0.89 | 72 | 3A1 |
| 3 | 696 | 0.82 | 0.86 | 70 | 3A1, ACT |
| 4 | 374 | 0.79 | 0.89 | 57 | ACT |
| 5 | 740 | 0.77 | 0.81 | 62 | empty |
Interfaces
1 interface between chains.
- A–B · 683 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3AHN · PZ PEPTIDASE A with Inhibitor 1 · 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 3AHN · PDBe 3AHN · UniProt Q4W803
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.