Research workbench
Crystal structure of human depiptidyl peptidase IV (dpp-4) in complex with mp-513
Analyse Crystal structure of human depiptidyl peptidase IV (dpp-4) 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
- 3VJK
- Type
- protein
- Length
- 1,458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- M51, NAG
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 729 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- M51 · {(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-yl}(1,3-thiazolidin-3-yl)methanone · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.73 | 0.97 | 22 | empty |
| 2 | 734 | 0.70 | 0.77 | 88 | M51 |
| 3 | 718 | 0.68 | 0.76 | 86 | M51 |
| 4 | 221 | 0.52 | 0.77 | 31 | empty |
| 5 | 339 | 0.51 | 0.73 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 2334 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 3VJK · Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with MP-513 · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 3VJK · PDBe 3VJK · UniProt P27487
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