Research workbench
Crystal structure of benzophenone synthase from garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis
Analyse Crystal structure of benzophenone synthase from garcinia mangostana L.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CBF
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,4,6-trihydroxybenzophenone synthase
- EC
- 2.3.1.220
- UniProt
- L7NCQ3
- Ligands
- IOD
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,4,6-trihydroxybenzophenone synthase (EC 2.3.1.220) | protein | 383 | 44% helix, 24% strand | L7NCQ3 |
| B | 2,4,6-trihydroxybenzophenone synthase (EC 2.3.1.220) | protein | 377 | 44% helix, 24% strand | L7NCQ3 |
Ligands and binding sites
- IOD · Iodide ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- IMD · Imidazole · additive · 2 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 | 343 | 0.76 | 0.87 | 45 | IMD, GOL |
| 2 | 343 | 0.76 | 0.86 | 46 | empty |
| 3 | 125 | 0.41 | 0.76 | 34 | IOD |
| 4 | 94 | 0.36 | 0.75 | 27 | IOD |
| 5 | 52 | 0.34 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2406 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 7CBF · Crystal structure of benzophe synthase from Garcinia mangostana L. pericarps reveals… · the same entry in another collection · chain A against A, TM-score 1.00
- L7NCQ3 · AlphaFold monomer V2.0 prediction for 2,4,6-trihydroxybenzophenone synthase (L7NCQ3) · a predicted model of the same protein · chain B 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 L7NCQ3
- Elsewhere: RCSB PDB 7CBF · PDBe 7CBF · UniProt L7NCQ3
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