Research workbench
Crystal structure of D552A dimethylglycine oxidase mutant of arthrobacter globiformis in complex with tetrahydrofolate
Analyse Crystal structure of D552A dimethylglycine oxidase mutant of arthrobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GSI
- 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
- THG, FAD, MG
- 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
- THG · (6S)-5,6,7,8-tetrahydrofolate · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- MG · Magnesium ion · metal · 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 | 664 | 0.87 | 0.91 | 97 | FAD |
| 2 | 379 | 0.78 | 0.87 | 53 | THG |
| 3 | 187 | 0.72 | 0.89 | 29 | empty |
| 4 | 375 | 0.71 | 0.83 | 38 | empty |
| 5 | 80 | 0.54 | 0.85 | 20 | empty |
Compared structures
- 3GSI · Crystal structure of D552A dimethylglycine oxidase mutant of Arthrobacter globiformis in… · 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 3GSI · PDBe 3GSI · UniProt Q9AGP8
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