MolNFT v1 · #136335 · protein
Acyl-CoA synthetase PTMA2 from streptomyces platensis in complex with SBNP465 ligand
5UPQ: “Acyl-CoA synthetase PTMA2 from streptomyces platensis in complex with SBNP465 ligand”. X-ray diffraction, 3 ligands (8JJ, SO4, CL), 16 pockets (best druggability 0.79). MolNFT v1 #136335 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5UPQ
- Type
- protein
- Length
- 1,000 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA synthetase PTMA2
- UniProt
- A0A0A0V031
- Ligands
- 8JJ, SO4, CL
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA synthetase PTMA2 | protein | 512 | 33% helix, 24% strand | A0A0A0V031 |
| B | Acyl-CoA synthetase PTMA2 | protein | 488 | 34% helix, 22% strand | A0A0A0V031 |
Ligands and binding sites
- 8JJ · 5'-O-[(R)-{[(7beta,8alpha,9beta,10alpha,13alpha, 16beta)-7,16-dihydroxy-18-oxokauran-18-yl]oxy}(hydroxy)phosphoryl]adenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.79 | 0.94 | 24 | empty |
| 2 | 69 | 0.72 | 0.97 | 26 | empty |
| 3 | 63 | 0.71 | 0.97 | 23 | empty |
| 4 | 438 | 0.59 | 0.74 | 56 | 8JJ |
| 5 | 299 | 0.55 | 0.75 | 41 | 8JJ |
Interfaces
1 interface between chains.
- A–B · 2096 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5UPQ · Acyl-CoA synthetase PtmA2 from Streptomyces platensis in complex with SBNP465 ligand · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0A0V031
- Elsewhere: RCSB PDB 5UPQ · PDBe 5UPQ · UniProt A0A0A0V031
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