Research workbench
Structure of P. gingivalis DPP11 in complex with the dipeptide arg-asp
Analyse Structure of P. gingivalis DPP11 in complex with the dipeptide arg-asp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R51
- Type
- protein
- Length
- 1,397 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASP/GLU-specific dipeptidyl-peptidase; Arg-asp
- EC
- 3.4.14.-
- UniProt
- B2RID1
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 695 | 49% helix, 16% strand | B2RID1 |
| B | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 698 | 49% helix, 16% strand | B2RID1 |
| C, D | Arg-asp | protein | 2 | 0% helix, 0% strand | — |
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.73 | 0.76 | 103 | empty |
| 2 | 869 | 0.72 | 0.77 | 73 | empty |
| 3 | 256 | 0.67 | 0.83 | 26 | empty |
| 4 | 182 | 0.66 | 0.85 | 27 | empty |
| 5 | 176 | 0.48 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 644 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 367 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 360 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7R51 · Structure of P. gingivalis DPP11 in complex with the dipeptide Arg-Asp · the same entry in another collection · chain A against A, TM-score 1.00
- B2RID1 · AlphaFold monomer V2.0 prediction for ASP/GLU-specific dipeptidyl- peptidase (B2RID1) · 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 B2RID1
- Elsewhere: RCSB PDB 7R51 · PDBe 7R51 · UniProt B2RID1
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