MolNFT v1 · #91526 · protein
Crystal structure of dipeptidyl peptidase IV (DPP4, dpp-IV, CD26) in complex with Fab + sitagliptin
4FFW · Dipeptidyl peptidase 4: “Crystal structure of dipeptidyl peptidase IV (DPP4, dpp-IV, CD26) in complex with Fab + sitagliptin”. X-ray diffraction, 1 ligand (715), 20 pockets (best druggability 0.72). MolNFT v1 #91526 on GenesisL1: 3D…
- PDB
- 4FFW
- Type
- protein
- Length
- 2,282 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4; Fab light chain; Fab heavy chain
- EC
- 3.4.14.5
- UniProt
- P14740
- Ligands
- 715
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 18% helix, 36% strand | P14740 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 729 | 18% helix, 37% strand | P14740 |
| C | Fab light chain | protein | 207 | 3% helix, 45% strand | — |
| D | Fab heavy chain | protein | 209 | 5% helix, 48% strand | — |
| H | Fab heavy chain | protein | 208 | 3% helix, 46% strand | — |
| L | Fab light chain | protein | 202 | 5% helix, 46% strand | — |
Ligands and binding sites
- 715 · (2R)-4-oxo-4-[3-(trifluoromethyl)-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]-1-(2,4,5-trifluorophenyl)butan-2-A mine · ligand · 2 copies · chains A, B
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 | 1105 | 0.72 | 0.76 | 122 | 715 |
| 2 | 57 | 0.72 | 0.98 | 16 | empty |
| 3 | 917 | 0.71 | 0.76 | 84 | empty |
| 4 | 897 | 0.70 | 0.75 | 91 | empty |
| 5 | 725 | 0.69 | 0.77 | 84 | 715 |
Interfaces
9 interfaces between chains.
- A–B · 2294 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1827 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1782 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 691 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 684 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4FFW · Crystal Structure of Dipeptidyl Peptidase IV (DPP4, DPP-IV, CD26) in Complex with Fab +… · the same entry in another collection · chain L against L, TM-score 1.00
- P14740 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P14740) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P14740
- Elsewhere: RCSB PDB 4FFW · PDBe 4FFW · UniProt P14740
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