MolNFT v1 · #139721 · protein
Crystal structure of a novel zen lactonase mutant
5XO6 · Lactonase for protein: “Crystal structure of a novel zen lactonase mutant”. X-ray diffraction, 12 pockets (best druggability 0.81). MolNFT v1 #139721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XO6
- Type
- protein
- Length
- 2,093 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactonase for protein
- UniProt
- A0A0D2ILK1
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, H | Lactonase for protein | protein | 263 | 47% helix, 18% strand | A0A0D2ILK1 |
| E | Lactonase for protein | protein | 262 | 43% helix, 19% strand | A0A0D2ILK1 |
| F | Lactonase for protein | protein | 259 | 45% helix, 19% strand | A0A0D2ILK1 |
| G | Lactonase for protein | protein | 257 | 47% helix, 19% strand | A0A0D2ILK1 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.81 | 0.92 | 32 | empty |
| 2 | 289 | 0.80 | 0.91 | 35 | 1PE |
| 3 | 255 | 0.79 | 0.92 | 36 | empty |
| 4 | 335 | 0.79 | 0.89 | 37 | empty |
| 5 | 322 | 0.78 | 0.89 | 37 | empty |
Interfaces
10 interfaces between chains.
- G–H · 683 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 672 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 670 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 645 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 364 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5XO6 · Crystal structure of a novel ZEN lactonase mutant · the same entry in another collection · chain D against D, 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 5XO6 · PDBe 5XO6 · UniProt A0A0D2ILK1
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