Research workbench
Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from bacteroides thetaiotaomicron vpi-5482 at 1.75 a resolution
Analyse Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R0K
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl-peptidase VI
- UniProt
- Q8A860
- Ligands
- CL
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl-peptidase VI | protein | 303 | 19% helix, 40% strand | Q8A860 |
| B | Dipeptidyl-peptidase VI | protein | 304 | 19% helix, 40% strand | Q8A860 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.63 | 0.74 | 68 | EDO |
| 2 | 58 | 0.52 | 0.87 | 21 | empty |
| 3 | 229 | 0.48 | 0.74 | 36 | CL |
| 4 | 137 | 0.36 | 0.72 | 25 | empty |
| 5 | 81 | 0.35 | 0.75 | 16 | CL |
Interfaces
1 interface between chains.
- A–B · 1432 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered, nonstandard, oxidation).
Compared structures
- 4R0K · Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) 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 Q8A860
- Elsewhere: RCSB PDB 4R0K · PDBe 4R0K · UniProt Q8A860
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