Research workbench
Crystal structure of dipeptidyl peptidase IV (dppiv or CD26) in complex with adenosine deaminase
Analyse Crystal structure of dipeptidyl peptidase IV (dppiv or CD26) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W1I
- Type
- protein
- Length
- 4,320 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV; Adenosine deaminase
- EC
- 3.4.14.5, 3.5.4.4
- UniProt
- P27487, P56658
- Ligands
- NAG, FUC, BMA, MAN, ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% 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 | P27487 |
| E, F, G, H | Adenosine deaminase (EC 3.5.4.4) | protein | 352 | 51% helix, 14% strand | P56658 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains A, F, B, E, C, G, D, H
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains F, E, G, H
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains F, E, G, H
- ZN · Zinc ion · metal · 4 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.76 | 0.99 | 22 | empty |
| 2 | 79 | 0.76 | 0.98 | 24 | empty |
| 3 | 104 | 0.73 | 0.94 | 24 | empty |
| 4 | 181 | 0.68 | 0.87 | 33 | empty |
| 5 | 184 | 0.66 | 0.86 | 34 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2301 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2284 Ų buried · 39 hydrogen bonds · protein-protein
- C–G · 908 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 889 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 873 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 glycan, 20 disulfide (N-glycosylation, disulfide).
Compared structures
- 1W1I · Crystal structure of dipeptidyl peptidase IV (DPPIV or CD26) in complex with adenosine… · the same entry in another collection · chain H against H, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · 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 P27487
- Every structure of UniProt P56658
- Elsewhere: RCSB PDB 1W1I · PDBe 1W1I · UniProt P27487 · UniProt P56658
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