MolNFT v1 · #103214 · protein
Crystal structure of the mature form of rat dmgdh
4P9S · Dimethylglycine dehydrogenase: “Crystal structure of the mature form of rat dmgdh”. X-ray diffraction, 1 ligand (FAD), 19 pockets (best druggability 0.87). MolNFT v1 #103214 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4P9S
- Type
- protein
- Length
- 1,632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethylglycine dehydrogenase
- EC
- 1.5.8.4
- UniProt
- Q5RKL4
- Ligands
- FAD
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dimethylglycine dehydrogenase (EC 1.5.8.4) | protein | 816 | 30% helix, 28% strand | Q5RKL4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.87 | 0.90 | 105 | FAD |
| 2 | 479 | 0.86 | 0.93 | 80 | FAD |
| 3 | 547 | 0.83 | 0.89 | 84 | empty |
| 4 | 160 | 0.79 | 0.95 | 38 | empty |
| 5 | 215 | 0.74 | 0.89 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 1147 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 4P9S · Crystal structure of the mature form of rat DMGDH · the same entry in another collection · 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 Q5RKL4
- Elsewhere: RCSB PDB 4P9S · PDBe 4P9S · UniProt Q5RKL4
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