Research workbench
Crystal structure of the dimethylarginine dimethylaminohydrolase adduct with 4-chloro-2-hydroxymethylpyridine
Analyse Crystal structure of the dimethylarginine dimethylaminohydrolase adduct with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RHY
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N(G),N(G)-dimethylarginine dimethylaminohydrolase
- EC
- 3.5.3.18
- UniProt
- Q9I4E3
- Ligands
- HM3
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N(G),N(G)-dimethylarginine dimethylaminohydrolase (EC 3.5.3.18) | protein | 248 | 31% helix, 25% strand | Q9I4E3 |
Ligands and binding sites
- HM3 · (4-chloropyridin-2-yl)methanol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.78 | 0.96 | 24 | empty |
| 2 | 112 | 0.77 | 0.96 | 23 | empty |
| 3 | 218 | 0.57 | 0.80 | 26 | HM3 |
| 4 | 148 | 0.48 | 0.78 | 29 | HM3 |
| 5 | 55 | 0.34 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 900 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3RHY · Crystal structure of the dimethylarginine dimethylaminohydrolase adduct with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I4E3 · AlphaFold monomer V2.0 prediction for N(G),N(G)-dimethylarginine dimethylaminohydrolase… · 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 Q9I4E3
- Elsewhere: RCSB PDB 3RHY · PDBe 3RHY · UniProt Q9I4E3
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