Research workbench
High pH native structure of leucine aminopeptidase from pseudomonas putida
Analyse High pH native structure of leucine aminopeptidase from pseudomonas putida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H8F
- Type
- protein
- Length
- 2,982 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosol aminopeptidase
- EC
- 3.4.11.1
- UniProt
- O86436
- Ligands
- BCT, ZN, MN, K
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Cytosol aminopeptidase (EC 3.4.11.1) | protein | 497 | 38% helix, 21% strand | O86436 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.73 | 0.76 | 100 | BCT |
| 2 | 921 | 0.72 | 0.77 | 78 | empty |
| 3 | 957 | 0.72 | 0.76 | 85 | BCT |
| 4 | 588 | 0.68 | 0.78 | 45 | empty |
| 5 | 594 | 0.67 | 0.77 | 46 | empty |
Interfaces
12 interfaces between chains.
- B–F · 1251 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1244 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1178 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1019 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 993 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3H8F · High pH native structure of leucine aminopeptidase from Pseudomonas putida · the same entry in another collection · chain F against F, TM-score 1.00
- O86436 · AlphaFold monomer V2.0 prediction for cytosol aminopeptidase (O86436) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O86436
- Elsewhere: RCSB PDB 3H8F · PDBe 3H8F · UniProt O86436
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