MolNFT v1 · #170599 · protein
Crystal structure of gcoa T296A bound to P-vanillin
6YCK · Aromatic O-demethylase, cytochrome P450 subunit: “Crystal structure of gcoa T296A bound to P-vanillin”. X-ray diffraction, 2 ligands (HEM, V55), 4 pockets (best druggability 0.86). MolNFT v1 #170599 on GenesisL1: 3D structure…
- PDB
- 6YCK
- Type
- protein
- Length
- 403 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic O-demethylase, cytochrome P450 subunit
- EC
- 1.14.14.-
- UniProt
- P0DPQ7
- Ligands
- HEM, V55
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic O-demethylase, cytochrome P450 subunit (EC 1.14.14.-) | protein | 403 | 56% helix, 11% strand | P0DPQ7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- V55 · 4-hydroxy-3-methoxybenzaldehyde · ligand · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.86 | 0.94 | 43 | HEM, V55 |
| 2 | 98 | 0.40 | 0.77 | 17 | empty |
| 3 | 50 | 0.31 | 0.77 | 17 | EPE |
| 4 | 73 | 0.30 | 0.73 | 13 | empty |
Compared structures
- 6YCK · Crystal structure of GcoA T296A bound to p-vanillin · the same entry in another collection · chain A against A, TM-score 1.00
- P0DPQ7 · AlphaFold monomer V2.0 prediction for aromatic O-demethylase, cytochrome P450 subunit… · a predicted model of the same protein · 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 P0DPQ7
- Elsewhere: RCSB PDB 6YCK · PDBe 6YCK · UniProt P0DPQ7
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