MolNFT v1 · #185394 · protein
C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to choline
7PTH · Choline sulfatase: “C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to choline”. X-ray diffraction, 2 ligands (CHT, CA), 20 pockets (best druggability 0.80). MolNFT v1 #185394 on GenesisL1: 3D structure, binding…
- PDB
- 7PTH
- Type
- protein
- Length
- 2,058 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline sulfatase
- EC
- 3.1.6.6
- UniProt
- A0A410NSD4
- Ligands
- CHT, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 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 | 510 | 0.80 | 0.87 | 54 | empty |
| 2 | 553 | 0.72 | 0.81 | 44 | empty |
| 3 | 153 | 0.68 | 0.88 | 32 | CHT |
| 4 | 213 | 0.65 | 0.84 | 44 | CHT |
| 5 | 123 | 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
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