MolNFT v1 · #14383 · protein
Crystal structure of aps kinase from penicillium chrysogenum: structure with aps soaked out of one dimer
1M7H · Adenylylsulfate kinase: “Crystal structure of aps kinase from penicillium chrysogenum: structure with aps soaked out of one dimer”. X-ray diffraction, 3 ligands (ADP, ADX, SO4), 7 pockets (best druggability 0.63). MolNFT v1 #14383…
- PDB
- 1M7H
- Type
- protein
- Length
- 805 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
- ADP, ADX, SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylylsulfate kinase (EC 2.7.1.25) | protein | 203 | 42% helix, 14% strand | Q12657 |
| B | Adenylylsulfate kinase (EC 2.7.1.25) | protein | 200 | 45% helix, 14% strand | Q12657 |
| C | Adenylylsulfate kinase (EC 2.7.1.25) | protein | 204 | 42% helix, 14% strand | Q12657 |
| D | Adenylylsulfate kinase (EC 2.7.1.25) | protein | 198 | 45% helix, 14% strand | Q12657 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- ADX · Adenosine-5'-phosphosulfate · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.63 | 0.77 | 44 | SO4, ADP |
| 2 | 513 | 0.63 | 0.76 | 47 | SO4, ADP |
| 3 | 350 | 0.61 | 0.77 | 36 | ADX |
| 4 | 178 | 0.59 | 0.82 | 30 | empty |
| 5 | 288 | 0.58 | 0.78 | 32 | ADX |
Interfaces
2 interfaces between chains.
- A–B · 2010 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1971 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1M7H · Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked… · 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 0.96
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 1M7H · PDBe 1M7H · UniProt Q12657
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