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Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with pap and C4 peptide
Analyse Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with pap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WRI
- Type
- protein
- Length
- 563 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine sulfotransferase 1; Asp-phe-glu-asp-tyr-glu-phe-asp
- EC
- 2.8.2.20
- UniProt
- O60507
- Ligands
- A3P, MG, ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-tyrosine sulfotransferase 1 (EC 2.8.2.20) | protein | 274 | 51% helix, 10% strand | O60507 |
| B | Protein-tyrosine sulfotransferase 1 (EC 2.8.2.20) | protein | 273 | 51% helix, 10% strand | O60507 |
| D, E | Asp-phe-glu-asp-tyr-glu-phe-asp | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.71 | 0.90 | 33 | A3P |
| 2 | 151 | 0.71 | 0.90 | 34 | A3P |
| 3 | 162 | 0.48 | 0.77 | 27 | empty |
| 4 | 67 | 0.31 | 0.75 | 14 | empty |
| 5 | 52 | 0.30 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1543 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 718 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 679 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 210 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 201 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WRI · Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and C4… · the same entry in another collection · chain A against A, TM-score 1.00
- O60507 · AlphaFold monomer V2.0 prediction for protein-tyrosine sulfotransferase 1 (O60507) · a predicted model of the same protein · chain B 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 5WRI · PDBe 5WRI · UniProt O60507
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