Research workbench
Acyl-CoA synthetase PTMA2 from streptomyces platensis in complex with SBNP663 ligand
Analyse Acyl-CoA synthetase PTMA2 from streptomyces platensis in complex with SBNP663… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UPS
- Type
- protein
- Length
- 1,040 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA synthetase PTMA2
- UniProt
- A0A0A0V031
- Ligands
- 8K1, NA
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acyl-CoA synthetase PTMA2 | protein | 520 | 33% helix, 24% strand | A0A0A0V031 |
Ligands and binding sites
- 8K1 · 5'-O-[(R)-hydroxy{[(7beta,8alpha,9beta,10alpha,11beta, 13alpha)-7-hydroxy-19-oxo-11,16-epoxykauran-19-yl]oxy}phosphoryl]adenosine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.86 | 0.94 | 55 | 8K1 |
| 2 | 933 | 0.85 | 0.86 | 85 | 8K1 |
| 3 | 252 | 0.82 | 0.94 | 36 | empty |
| 4 | 67 | 0.71 | 0.97 | 22 | empty |
| 5 | 67 | 0.71 | 0.97 | 24 | FMT |
Interfaces
1 interface between chains.
- A–B · 1768 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 5UPS · Acyl-CoA synthetase PtmA2 from Streptomyces platensis in complex with SBNP663 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 5UPS · PDBe 5UPS · UniProt A0A0A0V031
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