Research workbench
Crystal structure of L1 protease lysobacter sp. XL1 in complex with aebsf
Analyse Crystal structure of L1 protease lysobacter sp. XL1 in complex with aebsf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MRS
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lytic endopeptidase preproenzyme
- UniProt
- D2K8B3
- Ligands
- AES, SO4, CL
- Pockets
- 11 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lytic endopeptidase preproenzyme | protein | 199 | 7% helix, 54% strand | D2K8B3 |
Ligands and binding sites
- AES · 4-(2-aminoethyl)benzenesulfonyl fluoride · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · 4 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, C
- PGE · Triethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.58 | 0.79 | 45 | SO4 |
| 2 | 206 | 0.49 | 0.76 | 35 | empty |
| 3 | 125 | 0.42 | 0.76 | 26 | empty |
| 4 | 82 | 0.39 | 0.77 | 20 | AES |
| 5 | 90 | 0.38 | 0.76 | 19 | AES |
Interfaces
4 interfaces between chains.
- A–C · 434 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 419 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 214 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 72 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5MRS · Crystal structure of L1 protease Lysobacter sp. XL1 in complex with AEBSF · the same entry in another collection · 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 D2K8B3
- Elsewhere: RCSB PDB 5MRS · PDBe 5MRS · UniProt D2K8B3
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