Research workbench
Pseudomonas serine-carboxyl proteinase (sedolisin) complexed with the inhibitor aipf
Analyse Pseudomonas serine-carboxyl proteinase (sedolisin) complexed with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M8Y
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sedolisin; Aipf peptide inhibitor
- EC
- 3.4.21.100
- UniProt
- P42790
- Ligands
- ACE, CA, CL
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sedolisin (EC 3.4.21.100) | protein | 369 | 33% helix, 28% strand | P42790 |
| B | Aipf peptide inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.37 | 0.73 | 27 | empty |
| 2 | 60 | 0.32 | 0.76 | 15 | ACE |
Interfaces
1 interface between chains.
- A–B · 332 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, nonstandard).
Compared structures
- 6M8Y · Pseudomonas serine-carboxyl proteinase (sedolisin) complexed with the inhibitor aipf · the same entry in another collection · chain A against A, TM-score 1.00
- P42790 · AlphaFold monomer V2.0 prediction for pseudomonalisin (P42790) · a predicted model of the same protein · 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 P42790
- Elsewhere: RCSB PDB 6M8Y · PDBe 6M8Y · UniProt P42790
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