MolNFT v1 · #138701 · protein
Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with pap and gastrin peptide
5WRJ · Protein-tyrosine sulfotransferase 1: “Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with pap and gastrin peptide”. X-ray diffraction, 2 ligands (A3P, MG), 15 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5WRJ
- Type
- protein
- Length
- 1,118 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine sulfotransferase 1; Gastrin peptide
- EC
- 2.8.2.20
- UniProt
- O60507
- Ligands
- A3P, MG
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Protein-tyrosine sulfotransferase 1 (EC 2.8.2.20) | protein | 275 | 50% helix, 9% strand | O60507 |
| C | Protein-tyrosine sulfotransferase 1 (EC 2.8.2.20) | protein | 273 | 49% helix, 9% strand | O60507 |
| F, H, J, L | Gastrin peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 4 copies · chains A, F, B, H, C, D, L
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.72 | 0.90 | 32 | A3P |
| 2 | 149 | 0.71 | 0.90 | 28 | A3P |
| 3 | 222 | 0.69 | 0.86 | 38 | A3P |
| 4 | 158 | 0.69 | 0.88 | 31 | A3P |
| 5 | 153 | 0.61 | 0.84 | 30 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1520 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1519 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 723 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 404 Ų buried · 10 hydrogen bonds · protein-protein
- C–J · 392 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5WRJ · Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and… · the same entry in another collection · chain L against L, TM-score 1.00
- O60507 · AlphaFold monomer V2.0 prediction for protein-tyrosine sulfotransferase 1 (O60507) · a predicted model of the same protein · 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 O60507
- Elsewhere: RCSB PDB 5WRJ · PDBe 5WRJ · UniProt O60507
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