Research workbench
Crystal structure of the precursor (S250A mutant) of the N-terminal beta-aminopeptidase BapA
Analyse Crystal structure of the precursor (S250A mutant) of the N-terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N5I
- Type
- protein
- Length
- 1,453 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Sphingosinicella xenopeptidilytica
- Molecule
- Beta-peptidyl aminopeptidase
- UniProt
- Q52VH2
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.8 · 3 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-peptidyl aminopeptidase | protein | 360 | 29% helix, 30% strand | Q52VH2 |
| C | Beta-peptidyl aminopeptidase | protein | 362 | 28% helix, 31% strand | Q52VH2 |
| D | Beta-peptidyl aminopeptidase | protein | 371 | 28% helix, 30% strand | Q52VH2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains B, D
- GOL · Glycerol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.83 | 0.84 | 73 | empty |
| 2 | 240 | 0.71 | 0.86 | 43 | empty |
| 3 | 104 | 0.67 | 0.90 | 22 | empty |
| 4 | 110 | 0.67 | 0.90 | 22 | empty |
| 5 | 102 | 0.65 | 0.89 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1795 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1794 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1423 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1369 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 928 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3N5I · Crystal structure of the precursor (S250A mutant) of the N-terminal beta-aminopeptidase… · the same entry in another collection · chain D against D, TM-score 1.00
- Q52VH2 · AlphaFold monomer V2.0 prediction for beta-peptidyl aminopeptidase bapa (Q52VH2) · a predicted model of the same protein · chain D 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 Q52VH2
- Elsewhere: RCSB PDB 3N5I · PDBe 3N5I · UniProt Q52VH2
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