Research workbench
Crystal structure of tetrahedral aminopeptidase from P. horikoshii in complex with amastatin
Analyse Crystal structure of tetrahedral aminopeptidase from P. horikoshii in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y0Y
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Frv operon protein frvx; Amastatin
- UniProt
- O59196
- Ligands
- L2O, ZN
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Frv operon protein frvx | protein | 335 | 30% helix, 31% strand | O59196 |
| B | Amastatin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- L2O · (2S,3R)-3-amino-2-hydroxy-5-methylhexanoic acid · ligand · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.52 | 0.88 | 23 | L2O |
Interfaces
1 interface between chains.
- A–B · 250 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1Y0Y · Crystal structure of tetrahedral aminopeptidase from P. horikoshii in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O59196 · AlphaFold monomer V2.0 prediction for tetrahedral aminopeptidase (O59196) · a predicted model of the same protein · 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 O59196
- Elsewhere: RCSB PDB 1Y0Y · PDBe 1Y0Y · UniProt O59196
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