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Crystal structure of human dipeptidyl peptidase IV at 2.1 ang. resolution.
Analyse Crystal structure of human dipeptidyl peptidase IV at 2.1 ang. resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R9M
- Type
- protein
- Length
- 2,914 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
- P27487
- Ligands
- NAG, MAN, FUC
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 727 | 18% helix, 37% strand | P27487 |
| B | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 733 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 37 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.65 | 0.76 | 64 | empty |
| 2 | 514 | 0.65 | 0.77 | 71 | empty |
| 3 | 470 | 0.64 | 0.77 | 64 | empty |
| 4 | 295 | 0.60 | 0.78 | 41 | empty |
| 5 | 384 | 0.56 | 0.74 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2325 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2318 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 212 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 glycan, 20 disulfide (N-glycosylation, disulfide).
Compared structures
- 1R9M · Crystal Structure of Human Dipeptidyl Peptidase IV at 2.1 Ang. Resolution. · the same entry in another collection · chain D against D, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · 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 P27487
- Elsewhere: RCSB PDB 1R9M · PDBe 1R9M · UniProt P27487
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