Research workbench
Crystal structure of a lactonase double mutant in complex with ligand L
Analyse Crystal structure of a lactonase double mutant in complex with ligand L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z7J
- Type
- protein
- Length
- 2,106 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactonase for protein
- UniProt
- A0A0D2ILK1
- Ligands
- 36J
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, H | Lactonase for protein | protein | 263 | 48% helix, 18% strand | A0A0D2ILK1 |
| C, D | Lactonase for protein | protein | 264 | 47% helix, 18% strand | A0A0D2ILK1 |
| E, G | Lactonase for protein | protein | 263 | 46% helix, 19% strand | A0A0D2ILK1 |
Ligands and binding sites
- 36J · (3S,7R,11E)-7,14,16-trihydroxy-3-methyl-3,4,5,6,7,8,9, 10-octahydro-1H-2-benzoxacyclotetradecin-1-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.77 | 0.90 | 30 | 36J |
| 2 | 229 | 0.76 | 0.90 | 30 | 36J |
| 3 | 228 | 0.75 | 0.89 | 31 | 36J |
| 4 | 225 | 0.75 | 0.89 | 31 | 36J |
| 5 | 222 | 0.75 | 0.89 | 30 | 36J |
Interfaces
10 interfaces between chains.
- B–D · 683 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 677 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 673 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 673 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 344 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5Z7J · Crystal structure of a lactonase double mutant in complex with ligand l · 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 A0A0D2ILK1
- Elsewhere: RCSB PDB 5Z7J · PDBe 5Z7J · UniProt A0A0D2ILK1
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