Research workbench
Pseudomonas serine-carboxyl proteinase (sedolisin) complexed with the inhibitor pseudotyrostatin
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
- 6M9C
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sedolisin; Pseudotyrostatin
- EC
- 3.4.21.100
- UniProt
- P42790
- Ligands
- IVA, CA, SO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 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 | Pseudotyrostatin | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · chains A, B
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- ACY · Acetic acid · additive · 5 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 | 128 | 0.40 | 0.74 | 22 | empty |
| 2 | 71 | 0.33 | 0.75 | 19 | IVA |
Interfaces
1 interface between chains.
- A–B · 354 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, nonstandard).
Compared structures
- 6M9C · 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 6M9C · PDBe 6M9C · UniProt P42790
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