Research workbench
Thebaine 6-O-demethylase (T6ODM) from papaver somniferum in complex with succinate
Analyse Thebaine 6-O-demethylase (T6ODM) from papaver somniferum in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O7Y
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thebaine 6-O-demethylase
- EC
- 1.14.11.31
- UniProt
- D4N500
- Ligands
- NI
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thebaine 6-O-demethylase (EC 1.14.11.31) | protein | 358 | 34% helix, 20% strand | D4N500 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.72 | 0.78 | 78 | NI, SIN, EDO, PEG |
| 2 | 68 | 0.38 | 0.78 | 20 | empty |
| 3 | 83 | 0.30 | 0.72 | 18 | empty |
Compared structures
- 5O7Y · Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum in complex with succinate · the same entry in another collection · chain A against A, TM-score 1.00
- D4N500 · AlphaFold monomer V2.0 prediction for thebaine 6-O-demethylase (D4N500) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 D4N500
- Elsewhere: RCSB PDB 5O7Y · PDBe 5O7Y · UniProt D4N500
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