MolNFT v1 · #123855 · protein
Crystal structure of flavobacterium psychrophilum DPP11 in complex with dipeptide arg-asp
5JXF · ASP/GLU-specific dipeptidyl-peptidase: “Crystal structure of flavobacterium psychrophilum DPP11 in complex with dipeptide arg-asp”. X-ray diffraction, 2 ligands (NA, CL), 20 pockets (best druggability 0.84). MolNFT v1 #123855 on…
- PDB
- 5JXF
- Type
- protein
- Length
- 2,757 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASP/GLU-specific dipeptidyl-peptidase
- EC
- 3.4.14.-
- UniProt
- A6GWM2
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 696 | 48% helix, 15% strand | A6GWM2 |
| B | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 694 | 49% helix, 15% strand | A6GWM2 |
| C | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 682 | 45% helix, 15% strand | A6GWM2 |
| D | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 685 | 44% helix, 16% strand | A6GWM2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.84 | 0.85 | 94 | empty |
| 2 | 991 | 0.79 | 0.81 | 81 | CL |
| 3 | 156 | 0.73 | 0.91 | 24 | empty |
| 4 | 678 | 0.73 | 0.80 | 66 | CL |
| 5 | 749 | 0.72 | 0.78 | 67 | empty |
Interfaces
4 interfaces between chains.
- A–C · 557 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 417 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 206 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 192 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5JXF · Crystal structure of Flavobacterium psychrophilum DPP11 in complex with dipeptide Arg-Asp · the same entry in another collection · chain D against D, TM-score 1.00
- A6GWM2 · AlphaFold monomer V2.0 prediction for ASP/GLU-specific dipeptidyl- peptidase (A6GWM2) · a predicted model of the same protein · chain A 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 A6GWM2
- Elsewhere: RCSB PDB 5JXF · PDBe 5JXF · UniProt A6GWM2
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