MolNFT v1 · #23702 · protein
Human dipeptidyl peptidase IV/CD26 mutant Y547F
1U8E: “Human dipeptidyl peptidase IV/CD26 mutant Y547F”. X-ray diffraction, 5 ligands (NAG, FUC, NDG), 13 pockets (best druggability 0.75). MolNFT v1 #23702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1U8E
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- NAG, FUC, NDG, BMA, MAN
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 726 | 17% helix, 37% strand | P27487 |
| B | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 728 | 19% helix, 38% strand | P27487 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.75 | 0.99 | 23 | empty |
| 2 | 1151 | 0.71 | 0.75 | 133 | empty |
| 3 | 531 | 0.65 | 0.76 | 57 | empty |
| 4 | 306 | 0.56 | 0.76 | 35 | empty |
| 5 | 416 | 0.55 | 0.73 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 2285 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
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 P27487
- Elsewhere: RCSB PDB 1U8E · PDBe 1U8E · UniProt P27487
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