Research workbench
Crystal structure of porcine dipeptidyl peptidase IV (CD26) in complex with a low molecular weight inhibitor.
Analyse Crystal structure of porcine dipeptidyl peptidase IV (CD26) in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BUA
- Type
- protein
- Length
- 2,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV
- EC
- 3.4.14.5
- UniProt
- P22411
- Ligands
- 007, NAG, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 728 | 18% helix, 37% strand | P22411 |
Ligands and binding sites
- 007 · 1-methylamine-1-benzyl-cyclopentane · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.76 | 0.98 | 23 | empty |
| 2 | 79 | 0.75 | 0.97 | 22 | empty |
| 3 | 653 | 0.68 | 0.77 | 77 | 007, SO4 |
| 4 | 548 | 0.68 | 0.78 | 57 | 007, SO4 |
| 5 | 613 | 0.67 | 0.77 | 62 | 007, SO4 |
Interfaces
4 interfaces between chains.
- C–D · 2319 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2312 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 591 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 16 disulfide (N-glycosylation, disulfide).
Compared structures
- 2BUA · Crystal Structure Of Porcine Dipeptidyl Peptidase IV (Cd26) in Complex With a Low… · the same entry in another collection · chain D against D, TM-score 1.00
- P22411 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P22411) · a predicted model of the same protein · chain B 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 P22411
- Elsewhere: RCSB PDB 2BUA · PDBe 2BUA · UniProt P22411
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