Research workbench
C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to choline
Analyse C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to choline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PTH
- Type
- protein
- Length
- 2,058 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Rhizobium meliloti
- Molecule
- Choline sulfatase
- EC
- 3.1.6.6
- UniProt
- A0A410NSD4
- Ligands
- CHT, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.85 · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Choline sulfatase (EC 3.1.6.6) | protein | 517 | 37% helix, 14% strand | A0A410NSD4 |
| B, D | Choline sulfatase (EC 3.1.6.6) | protein | 512 | 38% helix, 15% strand | A0A410NSD4 |
Ligands and binding sites
- CHT · Choline ion · ligand · 4 copies · chains A, B, D, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 509 | 0.80 | 0.87 | 54 | empty |
| 2 | 554 | 0.72 | 0.81 | 44 | empty |
| 3 | 153 | 0.68 | 0.88 | 32 | CHT |
| 4 | 212 | 0.65 | 0.84 | 44 | CHT |
| 5 | 124 | 0.53 | 0.82 | 30 | CHT |
Interfaces
5 interfaces between chains.
- B–D · 3333 Ų buried · 72 hydrogen bonds · protein-protein
- A–C · 201 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 72 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7PTH · C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to choline · 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 A0A410NSD4
- Elsewhere: RCSB PDB 7PTH · PDBe 7PTH · UniProt A0A410NSD4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.