Research workbench
The crystal structure of the first half of the periplasmic protease pqql from escherichia COLI
Analyse The crystal structure of the first half of the periplasmic protease pqql from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OFT
- Type
- protein
- Length
- 937 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable zinc protease pqql
- EC
- 3.4.24.-
- UniProt
- P31828
- Ligands
- PO4, CL
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable zinc protease pqql (EC 3.4.24.-) | protein | 469 | 48% helix, 19% strand | P31828 |
| B | Probable zinc protease pqql (EC 3.4.24.-) | protein | 468 | 49% helix, 19% strand | P31828 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.73 | 0.84 | 54 | CL |
| 2 | 579 | 0.66 | 0.76 | 45 | empty |
| 3 | 529 | 0.65 | 0.76 | 45 | empty |
| 4 | 306 | 0.64 | 0.81 | 41 | empty |
| 5 | 234 | 0.55 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1456 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6OFT · The crystal structure of the first half of the periplasmic protease PqqL from Escherichia… · the same entry in another collection · chain A against A, TM-score 1.00
- P31828 · AlphaFold monomer V2.0 prediction for probable zinc protease pqql (P31828) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P31828
- Elsewhere: RCSB PDB 6OFT · PDBe 6OFT · UniProt P31828
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