Research workbench
Crystal structure of the N-terminal beta-aminopeptidase bapa from sphingosinicella xenopeptidilytica
Analyse Crystal structure of the N-terminal beta-aminopeptidase bapa from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N2W
- Type
- protein
- Length
- 1,460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-peptidyl aminopeptidase
- UniProt
- Q52VH2
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-peptidyl aminopeptidase | protein | 367 | 28% helix, 29% strand | Q52VH2 |
| B | Beta-peptidyl aminopeptidase | protein | 365 | 30% helix, 28% strand | Q52VH2 |
| D | Beta-peptidyl aminopeptidase | protein | 361 | 29% helix, 30% strand | Q52VH2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B, D
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.84 | 0.85 | 87 | empty |
| 2 | 665 | 0.72 | 0.79 | 71 | GOL, SO4 |
| 3 | 480 | 0.71 | 0.81 | 59 | GOL, SO4 |
| 4 | 557 | 0.70 | 0.79 | 62 | SO4 |
| 5 | 442 | 0.68 | 0.80 | 49 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 1709 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1697 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1471 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1465 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 921 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3N2W · Crystal structure of the N-terminal beta-aminopeptidase BapA from Sphingosinicella… · 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 3N2W · PDBe 3N2W · UniProt Q52VH2
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