Research workbench
Crystal structure of a putative dipeptidyl-peptidase VI (BACOVA_00612) from bacteroides ovatus at 1.72 a resolution
Analyse Crystal structure of a putative dipeptidyl-peptidase VI (BACOVA_00612) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NPF
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dipeptidyl-peptidase VI
- UniProt
- A7LS31
- Ligands
- CL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dipeptidyl-peptidase VI | protein | 305 | 17% helix, 40% strand | A7LS31 |
| B | Putative dipeptidyl-peptidase VI | protein | 297 | 18% helix, 41% strand | A7LS31 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.63 | 0.75 | 62 | GOL |
| 2 | 159 | 0.54 | 0.81 | 32 | GOL |
| 3 | 277 | 0.51 | 0.74 | 47 | GOL |
| 4 | 103 | 0.35 | 0.73 | 17 | empty |
| 5 | 96 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1471 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered, nonstandard).
Compared structures
- 3NPF · Crystal structure of a putative dipeptidyl-peptidase VI (BACOVA_00612) from Bacteroides… · the same entry in another collection · 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 A7LS31
- Elsewhere: RCSB PDB 3NPF · PDBe 3NPF · UniProt A7LS31
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