Research workbench
Structure of cys-null se-met dpp III from bacteroides thetaiotaomicron
Analyse Structure of cys-null se-met dpp III from bacteroides thetaiotaomicron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NA6
- Type
- protein
- Length
- 648 residues
- Chains
- 1
- 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, NA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dipeptidyl-peptidase III (EC 3.4.14.4) | protein | 648 | 50% helix, 14% strand | Q8A6N1 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · 4 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.75 | 0.78 | 65 | PE3 |
| 2 | 147 | 0.55 | 0.81 | 29 | empty |
| 3 | 101 | 0.53 | 0.83 | 24 | ACT |
| 4 | 196 | 0.50 | 0.76 | 29 | empty |
| 5 | 50 | 0.32 | 0.77 | 14 | empty |
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5NA6 · Structure of Cys-null Se-Met DPP III from Bacteroides thetaiotaomicron · 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 5NA6 · PDBe 5NA6 · UniProt Q8A6N1
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