MolNFT v1 · #176964 · protein
Crystal structure of deoxypodophyllotoxin synthase from sinopodophyllum hexandrum in complex with 2-oxoglutarate
7E37: “Crystal structure of deoxypodophyllotoxin synthase from sinopodophyllum hexandrum in complex with…”. X-ray diffraction, 2 ligands (AKG, FE), 13 pockets (best druggability 0.73). MolNFT v1 #176964 on GenesisL1: 3D structure, binding…
- PDB
- 7E37
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxypodophyllotoxin synthase
- EC
- 1.14.20.8
- UniProt
- A0A0N9HQ36
- Ligands
- AKG, FE
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxypodophyllotoxin synthase (EC 1.14.20.8) | protein | 305 | 36% helix, 23% strand | A0A0N9HQ36 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.73 | 0.85 | 36 | FE, AKG |
| 2 | 309 | 0.73 | 0.85 | 38 | FE, AKG |
| 3 | 251 | 0.54 | 0.77 | 32 | empty |
| 4 | 89 | 0.54 | 0.85 | 19 | empty |
| 5 | 93 | 0.52 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 771 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7E37 · Crystal structure of deoxypodophyllotoxin synthase from Sinopodophyllum hexandrum in… · the same entry in another collection · chain A 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 A0A0N9HQ36
- Elsewhere: RCSB PDB 7E37 · PDBe 7E37 · UniProt A0A0N9HQ36
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