Research workbench
Crystal structure of aps kinase from penicillium chrysogenum: ternary structure with ADP and aps
Analyse Crystal structure of aps kinase from penicillium chrysogenum: ternary structure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M7G
- Type
- protein
- Length
- 782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylylsulfate kinase
- EC
- 2.7.1.25
- UniProt
- Q12657
- Ligands
- ADX, AV2, ADP, SO4
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylylsulfate kinase (EC 2.7.1.25) | protein | 208 | 43% helix, 13% strand | Q12657 |
| B | Adenylylsulfate kinase (EC 2.7.1.25) | protein | 182 | 45% helix, 16% strand | Q12657 |
| C | Adenylylsulfate kinase (EC 2.7.1.25) | protein | 209 | 41% helix, 13% strand | Q12657 |
| D | Adenylylsulfate kinase (EC 2.7.1.25) | protein | 183 | 43% helix, 16% strand | Q12657 |
Ligands and binding sites
- ADX · Adenosine-5'-phosphosulfate · ligand · 4 copies · chains A, B, C, D
- AV2 · Adenosine-5'-diphosphate-2',3'-vanadate · ligand · 2 copies · chains A, C
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.62 | 0.79 | 32 | ADX |
| 2 | 362 | 0.60 | 0.77 | 51 | SO4, GOL |
| 3 | 252 | 0.56 | 0.77 | 29 | ADX |
| 4 | 249 | 0.56 | 0.77 | 33 | ADX |
| 5 | 242 | 0.56 | 0.77 | 34 | ADX |
Interfaces
3 interfaces between chains.
- C–D · 806 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 768 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 211 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1M7G · Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP… · the same entry in another collection · chain D against D, TM-score 1.00
- Q12657 · AlphaFold monomer V2.0 prediction for adenylyl-sulfate kinase (Q12657) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q12657
- Elsewhere: RCSB PDB 1M7G · PDBe 1M7G · UniProt Q12657
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.