MolNFT v1 · #127273 · protein
Crystal structure of L1 protease lysobacter sp. XL1 in complex with aebsf
5MRS · Lytic endopeptidase preproenzyme: “Crystal structure of L1 protease lysobacter sp. XL1 in complex with aebsf”. X-ray diffraction, 3 ligands (AES, SO4, CL), 11 pockets (best druggability 0.58). MolNFT v1 #127273 on GenesisL1: 3D…
- 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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