MolNFT v1 · #136338 · protein
Acyl-CoA synthetase PTMA2 from streptomyces platensis in complex with SBNP468 ligand
5UPT: “Acyl-CoA synthetase PTMA2 from streptomyces platensis in complex with SBNP468 ligand”. X-ray diffraction, 3 ligands (8JG, SO4, CL), 4 pockets (best druggability 0.67). MolNFT v1 #136338 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5UPT
- Type
- protein
- Length
- 515 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA synthetase PTMA2
- UniProt
- A0A0A0V031
- Ligands
- 8JG, SO4, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA synthetase PTMA2 | protein | 515 | 34% helix, 25% strand | A0A0A0V031 |
Ligands and binding sites
- 8JG · (7alpha,8alpha,10alpha,13alpha)-7,16-dihydroxykauran-18-oic acid · ligand · 3 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.67 | 0.76 | 70 | 8JG |
| 2 | 103 | 0.40 | 0.76 | 19 | 8JG |
| 3 | 114 | 0.38 | 0.74 | 23 | empty |
| 4 | 65 | 0.30 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 5UPT · Acyl-CoA synthetase PtmA2 from Streptomyces platensis in complex with SBNP468 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 5UPT · PDBe 5UPT · UniProt A0A0A0V031
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