MolNFT v1 · #156600 · protein
Pseudomonas serine-carboxyl proteinase (sedolisin) complexed with the inhibitor tyrostatin
6M9F: “Pseudomonas serine-carboxyl proteinase (sedolisin) complexed with the inhibitor tyrostatin”. X-ray diffraction, 3 ligands (IVA, CA, SO4), 2 pockets (best druggability 0.41). MolNFT v1 #156600 on GenesisL1: 3D structure, binding…
- PDB
- 6M9F
- Type
- protein
- Length
- 371 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sedolisin; Tyrostatin
- EC
- 3.4.21.100
- UniProt
- P42790
- Ligands
- IVA, CA, SO4
- Pockets
- 2 · best druggability 0.41
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 | 368 | 33% helix, 28% strand | P42790 |
| B | Tyrostatin | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · chains A, B
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 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 | 145 | 0.41 | 0.74 | 21 | empty |
| 2 | 79 | 0.34 | 0.75 | 15 | IVA |
Interfaces
1 interface between chains.
- A–B · 396 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, nonstandard).
Compared structures
- 6M9F · PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR Tyrostatin · 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 6M9F · PDBe 6M9F · UniProt P42790
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.