MolNFT v2 · #212628 · protein
Crystal structure of APSK2 domain from human PAPSS2 in complex with exogenous APS and ADP
8I1O · Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase…: “Crystal structure of APSK2 domain from human PAPSS2 in complex with exogenous APS and ADP”. X-ray diffraction at 2.4, 2 ligands (ADP, ADX), 5 pockets (best druggability…
- 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
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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