MolNFT v1 · #174946 · protein
Crystal structure of benzophenone synthase from garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis
7CBF · 2,4,6-trihydroxybenzophenone synthase: “Crystal structure of benzophenone synthase from garcinia mangostana L. pericarps reveals basis for substrate…”. X-ray diffraction, 1 ligand (IOD), 6 pockets (best druggability 0.76). MolNFT v1…
- 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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