Research workbench
Pikromycin thioesterase adduct with reduced triketide affinity label
Analyse Pikromycin thioesterase adduct with reduced triketide affinity label in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H7X
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I polyketide synthase pikaiv
- UniProt
- Q9ZGI2
- Ligands
- PSX, MG, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type I polyketide synthase pikaiv | protein | 279 | 42% helix, 15% strand | Q9ZGI2 |
| B | Type I polyketide synthase pikaiv | protein | 276 | 42% helix, 14% strand | Q9ZGI2 |
Ligands and binding sites
- PSX · [(2S,3R,4S)-2,4-dihydroxy-3-methylhexyl]phosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.77 | 0.83 | 50 | PSX |
| 2 | 608 | 0.77 | 0.83 | 46 | PSX |
| 3 | 96 | 0.46 | 0.80 | 23 | empty |
| 4 | 105 | 0.45 | 0.79 | 16 | DMS |
| 5 | 92 | 0.42 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 797 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2H7X · Pikromycin Thioesterase adduct with reduced triketide affinity label · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZGI2 · AlphaFold monomer V2.0 prediction for NARBONOLIDE/10-deoxymethynolide synthase PIKA4… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9ZGI2
- Elsewhere: RCSB PDB 2H7X · PDBe 2H7X · UniProt Q9ZGI2
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