Research workbench
Crystal structure of DPP8 in complex with the eil peptide (slrflfegqriadnh)
Analyse Crystal structure of DPP8 in complex with the eil peptide (slrflfegqriadnh) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TRW
- Type
- protein
- Length
- 2,541 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 8; Ser-leu-arg-phe-leu-phe-glu-gly-gln-arg
- EC
- 3.4.14.5
- UniProt
- Q6V1X1
- Ligands
- NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 839 | 19% helix, 34% strand | Q6V1X1 |
| B | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 834 | 18% helix, 35% strand | Q6V1X1 |
| C | Dipeptidyl peptidase 8 (EC 3.4.14.5) | protein | 838 | 19% helix, 34% strand | Q6V1X1 |
| D, E, F | Ser-leu-arg-phe-leu-phe-glu-gly-gln-arg | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.85 | 0.87 | 96 | empty |
| 2 | 977 | 0.85 | 0.86 | 105 | NA |
| 3 | 1047 | 0.83 | 0.84 | 103 | NA |
| 4 | 512 | 0.81 | 0.88 | 50 | empty |
| 5 | 686 | 0.81 | 0.85 | 67 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2406 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1008 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 967 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 955 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 478 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6TRW · Crystal structure of DPP8 in complex with the EIL peptide (SLRFLFEGQRIADNH) · the same entry in another collection · chain F against F, TM-score 1.00
- Q6V1X1 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 8 (Q6V1X1) · 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 Q6V1X1
- Elsewhere: RCSB PDB 6TRW · PDBe 6TRW · UniProt Q6V1X1
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