Research workbench
Crystal structure of the S228A mutant of the aminopeptidase from vibrio proteolyticus in complex with leucine phosphonic acid
Analyse Crystal structure of the S228A mutant of the aminopeptidase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B7I
- Type
- protein
- Length
- 291 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial leucyl aminopeptidase
- EC
- 3.4.11.10
- UniProt
- Q01693
- Ligands
- PLU, LEU, ZN, NA, K, SCN
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacterial leucyl aminopeptidase (EC 3.4.11.10) | protein | 291 | 42% helix, 19% strand | Q01693 |
Ligands and binding sites
- PLU · Leucine phosphonic acid · ligand · chains A
- LEU · Leucine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- SCN · Thiocyanate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.50 | 0.83 | 20 | K, PLU, LEU |
| 2 | 55 | 0.30 | 0.76 | 12 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3B7I · Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01693 · AlphaFold monomer V2.0 prediction for bacterial leucyl aminopeptidase (Q01693) · 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 Q01693
- Elsewhere: RCSB PDB 3B7I · PDBe 3B7I · UniProt Q01693
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