Research workbench
Crystal structure of the protease domain of degq from escherichia COLI
Analyse Crystal structure of the protease domain of degq from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3STI
- Type
- protein
- Length
- 551 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease degq
- EC
- 3.4.21.-
- UniProt
- P39099
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease degq (EC 3.4.21.-) | protein | 184 | 20% helix, 37% strand | P39099 |
| B | Protease degq (EC 3.4.21.-) | protein | 184 | 16% helix, 40% strand | P39099 |
| C | Protease degq (EC 3.4.21.-) | protein | 183 | 14% helix, 39% strand | P39099 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.74 | 0.81 | 72 | empty |
| 2 | 59 | 0.44 | 0.83 | 19 | empty |
| 3 | 86 | 0.41 | 0.78 | 18 | empty |
| 4 | 75 | 0.38 | 0.77 | 16 | empty |
| 5 | 62 | 0.36 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 882 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 849 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 741 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3STI · Crystal structure of the protease domain of DegQ from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P39099 · AlphaFold monomer V2.0 prediction for periplasmic pH-dependent serine endoprotease degq… · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P39099
- Elsewhere: RCSB PDB 3STI · PDBe 3STI · UniProt P39099
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