Research workbench
PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR Chymostatin
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
- 6M9D
- Type
- protein
- Length
- 371 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Pseudomonas sp. (strain 101); SYNTHETIC CONSTRUCT
- Molecule
- Sedolisin; Chymostatin A
- EC
- 3.4.21.100
- UniProt
- P42790
- Ligands
- CA
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sedolisin (EC 3.4.21.100) | protein | 368 | 33% helix, 27% strand | P42790 |
| B | Chymostatin A | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.37 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 402 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (nonstandard, disulfide).
Compared structures
- 6M9D · Pseudomonas serine-carboxyl proteinase (sedolisin) complexed with the inhibitor… · 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 6M9D · PDBe 6M9D · UniProt P42790
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