Research workbench
Crystal structure of adenosine 5'-phosphosulfate kinase from arabidopsis thaliana in complex with sulfate and aps
Analyse Crystal structure of adenosine 5'-phosphosulfate kinase from arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FXP
- Type
- protein
- Length
- 583 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylyl-sulfate kinase 1, chloroplastic
- EC
- 2.7.1.25
- UniProt
- Q43295
- Ligands
- ADX, SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylyl-sulfate kinase 1, chloroplastic (EC 2.7.1.25) | protein | 192 | 43% helix, 14% strand | Q43295 |
| B | Adenylyl-sulfate kinase 1, chloroplastic (EC 2.7.1.25) | protein | 200 | 42% helix, 14% strand | Q43295 |
| C | Adenylyl-sulfate kinase 1, chloroplastic (EC 2.7.1.25) | protein | 191 | 43% helix, 14% strand | Q43295 |
Ligands and binding sites
- ADX · Adenosine-5'-phosphosulfate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.71 | 0.86 | 53 | ADX, SO4 |
| 2 | 202 | 0.60 | 0.81 | 32 | ADX, SO4 |
| 3 | 239 | 0.59 | 0.80 | 30 | ADX, SO4 |
| 4 | 208 | 0.58 | 0.80 | 31 | empty |
| 5 | 149 | 0.46 | 0.77 | 22 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2110 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 176 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4FXP · Crystal structure of adenosine 5'-phosphosulfate kinase from Arabidopsis thaliana in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q43295 · AlphaFold monomer V2.0 prediction for adenylyl-sulfate kinase 1, chloroplastic (Q43295) · a predicted model of the same protein · chain C 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 Q43295
- Elsewhere: RCSB PDB 4FXP · PDBe 4FXP · UniProt Q43295
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