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Crystal structure of APSK2 domain from human PAPSS2 in complex with exogenous APS and ADP
Analyse Crystal structure of APSK2 domain from human PAPSS2 in complex with exogenous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8I1O
- Type
- protein
- Length
- 781 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens
- Molecule
- Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
- EC
- 2.7.7.4, 2.7.1.25
- UniProt
- O95340
- Ligands
- ADP, ADX
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (EC 2.7.7.4, 2.7.1.25) | protein | 195 | 44% helix, 14% strand | O95340 |
| C | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (EC 2.7.7.4, 2.7.1.25) | protein | 196 | 45% helix, 14% strand | O95340 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- ADX · Adenosine-5'-phosphosulfate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.84 | 0.85 | 118 | ADX |
| 2 | 356 | 0.66 | 0.80 | 46 | ADP, ADX |
| 3 | 305 | 0.63 | 0.79 | 39 | ADP, ADX |
| 4 | 138 | 0.51 | 0.80 | 20 | empty |
| 5 | 63 | 0.29 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1602 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1539 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 281 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 233 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 181 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- O95340 · AlphaFold monomer V2.0 prediction for bifunctional 3'-phosphoadenosine 5'-phosphosulfate… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O95340
- Elsewhere: RCSB PDB 8I1O · PDBe 8I1O · UniProt O95340
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