Research workbench
Crystal structure of a lactonase double mutant in complex with ligand N
Analyse Crystal structure of a lactonase double mutant in complex with ligand N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z97
- Type
- protein
- Length
- 1,050 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactonase for protein
- UniProt
- A0A0D2ILK1
- Ligands
- ZER, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lactonase for protein | protein | 263 | 48% helix, 19% strand | A0A0D2ILK1 |
| D | Lactonase for protein | protein | 261 | 44% helix, 17% strand | A0A0D2ILK1 |
Ligands and binding sites
- ZER · (3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.78 | 0.91 | 29 | ZER |
| 2 | 238 | 0.77 | 0.90 | 31 | ZER |
| 3 | 220 | 0.76 | 0.90 | 30 | empty |
| 4 | 282 | 0.73 | 0.86 | 39 | ZER |
| 5 | 62 | 0.47 | 0.84 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 674 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 670 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 522 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5Z97 · Crystal structure of a lactonase double mutant in complex with ligand N · 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 5Z97 · PDBe 5Z97 · UniProt A0A0D2ILK1
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