Research workbench
Crystal structure of a lactonase double mutant
Analyse Crystal structure of a lactonase double mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z5J
- Type
- protein
- Length
- 2,102 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactonase for protein
- UniProt
- A0A0D2ILK1
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Lactonase for protein | protein | 263 | 48% helix, 18% strand | A0A0D2ILK1 |
| D | Lactonase for protein | protein | 264 | 48% helix, 19% strand | A0A0D2ILK1 |
| E, G, H | Lactonase for protein | protein | 262 | 46% helix, 18% strand | A0A0D2ILK1 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.76 | 0.88 | 32 | empty |
| 2 | 326 | 0.76 | 0.87 | 35 | empty |
| 3 | 379 | 0.75 | 0.85 | 40 | empty |
| 4 | 301 | 0.75 | 0.87 | 33 | empty |
| 5 | 333 | 0.74 | 0.85 | 34 | empty |
Interfaces
10 interfaces between chains.
- A–C · 682 Ų buried · 9 hydrogen bonds · protein-protein
- E–H · 665 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 656 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 655 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 352 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5Z5J · Crystal structure of a lactonase double mutant · 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 5Z5J · PDBe 5Z5J · UniProt A0A0D2ILK1
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