Research workbench
Choline sulfatase from ensifer (sinorhizobium) meliloti
Analyse Choline sulfatase from ensifer (sinorhizobium) meliloti in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G5Z
- Type
- protein
- Length
- 2,022 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline-sulfatase
- EC
- 3.1.6.6
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 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 | — |
| B | Choline-sulfatase (EC 3.1.6.6) | protein | 503 | 38% helix, 15% strand | — |
| C | Choline-sulfatase (EC 3.1.6.6) | protein | 506 | 38% helix, 15% strand | — |
| D | Choline-sulfatase (EC 3.1.6.6) | protein | 505 | 38% helix, 15% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.79 | 0.81 | 123 | empty |
| 2 | 263 | 0.62 | 0.80 | 42 | SO4 |
| 3 | 197 | 0.60 | 0.82 | 29 | empty |
| 4 | 144 | 0.54 | 0.81 | 20 | empty |
| 5 | 155 | 0.53 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1685 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1675 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 553 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6G5Z · Choline sulfatase from Ensifer (Sinorhizobium) meliloti · 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
- Elsewhere: RCSB PDB 6G5Z · PDBe 6G5Z
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