MolNFT v1 · #127896 · protein
Structure of dpp III from bacteroides thetaiotaomicron in closed form
5NA8 · Putative dipeptidyl-peptidase III: “Structure of dpp III from bacteroides thetaiotaomicron in closed form”. X-ray diffraction, 2 ligands (ZN, SO4), 13 pockets (best druggability 0.86). MolNFT v1 #127896 on GenesisL1: 3D structure…
- PDB
- 5NA8
- Type
- protein
- Length
- 1,300 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dipeptidyl-peptidase III
- EC
- 3.4.14.4
- UniProt
- Q8A6N1
- Ligands
- ZN, SO4
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dipeptidyl-peptidase III (EC 3.4.14.4) | protein | 651 | 48% helix, 14% strand | Q8A6N1 |
| B | Putative dipeptidyl-peptidase III (EC 3.4.14.4) | protein | 649 | 48% helix, 14% strand | Q8A6N1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.86 | 0.87 | 76 | empty |
| 2 | 628 | 0.84 | 0.89 | 64 | SO4 |
| 3 | 67 | 0.69 | 0.95 | 19 | empty |
| 4 | 110 | 0.69 | 0.91 | 27 | empty |
| 5 | 94 | 0.64 | 0.90 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 494 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5NA8 · Structure of DPP III from Bacteroides thetaiotaomicron in closed form · the same entry in another collection · chain A 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 Q8A6N1
- Elsewhere: RCSB PDB 5NA8 · PDBe 5NA8 · UniProt Q8A6N1
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