Research workbench
Structure of the protease domain of degs (degs-deltapdz) at 1.65 a
Analyse Structure of the protease domain of degs (degs-deltapdz) at 1.65 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LGI
- Type
- protein
- Length
- 663 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease degs
- EC
- 3.4.21.-
- UniProt
- P0AEE3
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease degs (EC 3.4.21.-) | protein | 220 | 14% helix, 35% strand | P0AEE3 |
| B | Protease degs (EC 3.4.21.-) | protein | 228 | 14% helix, 36% strand | P0AEE3 |
| C | Protease degs (EC 3.4.21.-) | protein | 215 | 14% helix, 40% strand | P0AEE3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.69 | 0.98 | 21 | empty |
| 2 | 222 | 0.62 | 0.82 | 66 | empty |
| 3 | 185 | 0.43 | 0.73 | 32 | empty |
| 4 | 119 | 0.42 | 0.76 | 21 | PO4 |
| 5 | 149 | 0.41 | 0.74 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1311 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1238 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1134 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3LGI · Structure of the protease domain of DegS (DegS-deltaPDZ) at 1.65 A · the same entry in another collection · chain A against A, TM-score 1.00
- P0AEE3 · AlphaFold monomer V2.0 prediction for serine endoprotease degs (P0AEE3) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P0AEE3
- Elsewhere: RCSB PDB 3LGI · PDBe 3LGI · UniProt P0AEE3
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