Research workbench
Crystal structure of dimethylglycine oxidase of arthrobacter globiformis in complex with acetate
Analyse Crystal structure of dimethylglycine oxidase of arthrobacter globiformis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJ5
- 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
- FAD, NA
- Pockets
- 9 · best druggability 0.87
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
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.87 | 0.91 | 95 | ACT, FAD |
| 2 | 458 | 0.81 | 0.88 | 80 | empty |
| 3 | 241 | 0.72 | 0.87 | 31 | empty |
| 4 | 397 | 0.72 | 0.83 | 42 | empty |
| 5 | 296 | 0.57 | 0.77 | 46 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 1PJ5 · Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with… · 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 1PJ5 · PDBe 1PJ5 · UniProt Q9AGP8
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