Research workbench
Pikromycin thioesterase in complex with product 10-deoxymethynolide
Analyse Pikromycin thioesterase in complex with product 10-deoxymethynolide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HFK
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I polyketide synthase pikaiv
- UniProt
- Q9ZGI2
- Ligands
- E4H, MG, SO4
- Pockets
- 6 · best druggability 0.78
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 | 280 | 42% helix, 15% strand | Q9ZGI2 |
| B | Type I polyketide synthase pikaiv | protein | 277 | 42% helix, 14% strand | Q9ZGI2 |
Ligands and binding sites
- E4H · (3R,4S,5S,7R,9E,11R,12R)-12-ethyl-4-hydroxy-3,5,7,11-tetramethyloxacyclododec-9-ene-2,8-dione · 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 · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.78 | 0.84 | 44 | DMS, E4H |
| 2 | 653 | 0.78 | 0.83 | 47 | DMS, E4H |
| 3 | 96 | 0.48 | 0.81 | 22 | empty |
| 4 | 105 | 0.44 | 0.78 | 15 | DMS |
| 5 | 86 | 0.42 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 790 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2HFK · Pikromycin thioesterase in complex with product 10-deoxymethynolide · the same entry in another collection · chain B against B, TM-score 1.00
- Q9ZGI2 · AlphaFold monomer V2.0 prediction for NARBONOLIDE/10-deoxymethynolide synthase PIKA4… · a predicted model of the same protein · chain B 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 2HFK · PDBe 2HFK · UniProt Q9ZGI2
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