Research workbench
Pentaketide chromone synthase (M207G mutant complexed with CoA)
Analyse Pentaketide chromone synthase (M207G mutant complexed with CoA) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D52
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentaketide chromone synthase
- UniProt
- Q58VP7
- Ligands
- COA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentaketide chromone synthase | protein | 405 | 40% helix, 23% strand | Q58VP7 |
| B | Pentaketide chromone synthase | protein | 395 | 42% helix, 24% strand | Q58VP7 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.78 | 0.99 | 25 | empty |
| 2 | 95 | 0.77 | 0.98 | 24 | empty |
| 3 | 215 | 0.61 | 0.81 | 29 | COA |
| 4 | 263 | 0.60 | 0.80 | 29 | empty |
| 5 | 220 | 0.60 | 0.81 | 31 | COA |
Interfaces
1 interface between chains.
- A–B · 3478 Ų buried · 83 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2D52 · Pentaketide chromone synthase (M207G mutant complexed with Coa) · the same entry in another collection · chain A against A, TM-score 1.00
- Q58VP7 · AlphaFold monomer V2.0 prediction for 5,7-dihydroxy-2-methylchromone synthase (Q58VP7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q58VP7
- Elsewhere: RCSB PDB 2D52 · PDBe 2D52 · UniProt Q58VP7
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