Research workbench
Lysobacter enzymogenes lysc endoproteinase K30R mutant covalently inhibited by tlck
Analyse Lysobacter enzymogenes lysc endoproteinase K30R mutant covalently inhibited by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NSV
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl endopeptidase
- EC
- 3.4.21.50
- UniProt
- Q7M135
- Ligands
- 2OY, SO4, CL
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysyl endopeptidase (EC 3.4.21.50) | protein | 264 | 15% helix, 33% strand | Q7M135 |
Ligands and binding sites
- 2OY · N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-4-methylbenzenesulfonamide (Bound Form) · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.76 | 0.79 | 101 | 2OY, CL |
| 2 | 149 | 0.47 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 386 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 4NSV · Lysobacter enzymogenes lysc endoproteinase K30R mutant covalently inhibited by TLCK · the same entry in another collection · chain A against A, TM-score 1.00
- Q7M135 · AlphaFold monomer V2.0 prediction for lysyl endopeptidase (Q7M135) · a predicted model of the same protein · chain B 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 Q7M135
- Elsewhere: RCSB PDB 4NSV · PDBe 4NSV · UniProt Q7M135
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.