Research workbench
Crystal structure of adenosine-5'-phosphosulfate kinase in complex with aps and sulfate
Analyse Crystal structure of adenosine-5'-phosphosulfate kinase in complex with aps and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CB8
- Type
- protein
- Length
- 350 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable adenylyl-sulfate kinase
- EC
- 2.7.1.25
- UniProt
- P72940
- Ligands
- ADX, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable adenylyl-sulfate kinase (EC 2.7.1.25) | protein | 174 | 44% helix, 16% strand | P72940 |
| B | Probable adenylyl-sulfate kinase (EC 2.7.1.25) | protein | 176 | 43% helix, 15% strand | P72940 |
Ligands and binding sites
- ADX · Adenosine-5'-phosphosulfate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.63 | 0.83 | 34 | ADX, SO4 |
| 2 | 219 | 0.62 | 0.82 | 34 | ADX, SO4 |
| 3 | 67 | 0.30 | 0.74 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 689 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5CB8 · Crystal structure of Adenosine-5'-phosphosulfate kinase in complex with APS and sulfate · the same entry in another collection · chain A against A, TM-score 1.00
- P72940 · AlphaFold monomer V2.0 prediction for probable adenylyl-sulfate kinase (P72940) · 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 P72940
- Elsewhere: RCSB PDB 5CB8 · PDBe 5CB8 · UniProt P72940
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.