Research workbench
Crystal structure of L1 protease of lysobacter sp. XL1
Analyse Crystal structure of L1 protease of lysobacter sp. XL1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MRR
- 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
- NA, CL, SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lytic endopeptidase preproenzyme | protein | 199 | 7% helix, 53% strand | D2K8B3 |
Ligands and binding sites
- NA · Sodium ion · metal · chains D
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, D, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.69 | 0.79 | 39 | empty |
| 2 | 154 | 0.62 | 0.85 | 23 | CL, GOL |
| 3 | 135 | 0.62 | 0.86 | 30 | GOL |
| 4 | 96 | 0.56 | 0.86 | 28 | empty |
| 5 | 85 | 0.53 | 0.85 | 20 | CL, NA |
Interfaces
5 interfaces between chains.
- A–D · 457 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 404 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 369 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 318 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 235 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5MRR · Crystal structure of L1 protease of Lysobacter sp. XL1 · 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 5MRR · PDBe 5MRR · UniProt D2K8B3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.