Research workbench
Structure of dimethylglycine oxidase of arthrobacter globiformis in complex with folinic acid
Analyse Structure of dimethylglycine oxidase of arthrobacter globiformis in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJ7
- Type
- protein
- Length
- 827 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N,N-dimethylglycine oxidase
- EC
- 1.5.3.10
- UniProt
- Q9AGP8
- Ligands
- FFO, FAD, NA
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N,N-dimethylglycine oxidase (EC 1.5.3.10) | protein | 827 | 30% helix, 29% strand | Q9AGP8 |
Ligands and binding sites
- FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.86 | 0.91 | 86 | FAD |
| 2 | 406 | 0.79 | 0.88 | 53 | FFO |
| 3 | 175 | 0.71 | 0.89 | 30 | empty |
| 4 | 356 | 0.71 | 0.83 | 37 | empty |
| 5 | 73 | 0.53 | 0.86 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 1PJ7 · Structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folinic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AGP8 · AlphaFold monomer V2.0 prediction for dimethylglycine oxidase (Q9AGP8) · 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 Q9AGP8
- Elsewhere: RCSB PDB 1PJ7 · PDBe 1PJ7 · UniProt Q9AGP8
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