MolNFT v1 · #153881 · protein
Crystal structure of dipeptidyl peptidase 11 (DPP11) with sh-5 from porphyromonas gingivalis (space)
6JTC · ASP/GLU-specific dipeptidyl-peptidase: “Crystal structure of dipeptidyl peptidase 11 (DPP11) with sh-5 from porphyromonas gingivalis (space)”. X-ray diffraction, 1 ligand (C8O), 13 pockets (best druggability 0.73). MolNFT v1 #153881…
- PDB
- 6JTC
- Type
- protein
- Length
- 1,398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASP/GLU-specific dipeptidyl-peptidase
- EC
- 3.4.14.-
- UniProt
- B2RID1
- Ligands
- C8O
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 699 | 51% helix, 16% strand | B2RID1 |
Ligands and binding sites
- C8O · 2-(2-azanylethylamino)-5-nitro-benzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.73 | 0.77 | 94 | GOL, C8O |
| 2 | 834 | 0.71 | 0.77 | 85 | C8O |
| 3 | 301 | 0.52 | 0.74 | 48 | empty |
| 4 | 52 | 0.48 | 0.85 | 12 | empty |
| 5 | 134 | 0.42 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 765 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6JTC · Crystal structure of dipeptidyl peptidase 11 (DPP11) with SH-5 from Porphyromonas… · 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 0.91
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 6JTC · PDBe 6JTC · UniProt B2RID1
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