Research workbench
Choline sulfatase from ensifer (sinorhizobium) meliloti cocrystalized with choline
Analyse Choline sulfatase from ensifer (sinorhizobium) meliloti cocrystalized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G60
- Type
- protein
- Length
- 2,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline-sulfatase
- EC
- 3.1.6.6
- UniProt
- O69787
- Ligands
- CHT, MG, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline-sulfatase (EC 3.1.6.6) | protein | 508 | 38% helix, 15% strand | O69787 |
| B | Choline-sulfatase (EC 3.1.6.6) | protein | 506 | 38% helix, 15% strand | O69787 |
| C, D | Choline-sulfatase (EC 3.1.6.6) | protein | 505 | 39% helix, 15% strand | O69787 |
Ligands and binding sites
- CHT · Choline ion · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.76 | 0.79 | 107 | empty |
| 2 | 210 | 0.61 | 0.82 | 29 | SO4 |
| 3 | 292 | 0.59 | 0.78 | 37 | empty |
| 4 | 218 | 0.59 | 0.81 | 26 | SO4 |
| 5 | 161 | 0.53 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1668 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1666 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 506 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6G60 · Choline sulfatase from Ensifer (Sinorhizobium) meliloti cocrystalized with choline · the same entry in another collection · chain D against D, TM-score 1.00
- O69787 · AlphaFold monomer V2.0 prediction for choline-sulfatase (O69787) · a predicted model of the same protein · chain D 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 O69787
- Elsewhere: RCSB PDB 6G60 · PDBe 6G60 · UniProt O69787
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