MolNFT v1 · #46818 · protein
Crystal structure of the apsk domain of human PAPSS1 in complex with adpmg and paps
2OFX · Bifunctional 3'-phosphoadenosine 5'- phosphosulfate…: “Crystal structure of the apsk domain of human PAPSS1 in complex with adpmg and paps”. X-ray diffraction, 4 ligands (PPS, ADP, MG), 5 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 2OFX
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1
- EC
- 2.7.1.25
- UniProt
- O43252
- Ligands
- PPS, ADP, MG, PO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (EC 2.7.1.25) | protein | 205 | 42% helix, 14% strand | O43252 |
Ligands and binding sites
- PPS · 3'-phosphate-adenosine-5'-phosphate sulfate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
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 | 190 | 0.73 | 0.90 | 36 | MG, PPS, ADP |
| 2 | 227 | 0.69 | 0.86 | 44 | MG, PPS, ADP |
| 3 | 94 | 0.46 | 0.80 | 21 | empty |
| 4 | 82 | 0.41 | 0.79 | 22 | empty |
| 5 | 61 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2756 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 2OFX · crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS · the same entry in another collection · chain A against A, TM-score 1.00
- O43252 · AlphaFold monomer V2.0 prediction for bifunctional 3'-phosphoadenosine 5'-phosphosulfate… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O43252
- Elsewhere: RCSB PDB 2OFX · PDBe 2OFX · UniProt O43252
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