Research workbench
Crystal structure of porcine dipeptidyl peptidase IV (CD26) in complex with a peptidomimetic 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
- 1ORW
- Type
- protein
- Length
- 2,920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV
- EC
- 3.4.14.5
- Ligands
- NAG, BMA, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 730 | 17% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 4 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.74 | 0.98 | 23 | empty |
| 2 | 887 | 0.71 | 0.76 | 101 | SO4 |
| 3 | 898 | 0.71 | 0.75 | 104 | SO4 |
| 4 | 489 | 0.64 | 0.76 | 61 | empty |
| 5 | 442 | 0.62 | 0.76 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2280 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2270 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 590 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 16 disulfide, 8 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 1ORW · Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with a… · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 1ORW · PDBe 1ORW
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