Research workbench
Crystal structure of human dimethylarginine dimethylaminohydrolase-1 (ddah-1) variant C274S bound with N5-(1-iminopentyl)-L-ornithine
Analyse Crystal structure of human dimethylarginine dimethylaminohydrolase-1 (ddah-1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P8P
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
- EC
- 3.5.3.18
- UniProt
- O94760
- Ligands
- LN6
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18) | protein | 275 | 31% helix, 26% strand | O94760 |
Ligands and binding sites
- LN6 · N~5~-[(1E)-pentanimidoyl]-L-ornithine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.81 | 0.92 | 34 | empty |
| 2 | 326 | 0.81 | 0.91 | 32 | empty |
| 3 | 386 | 0.65 | 0.79 | 54 | LN6 |
| 4 | 98 | 0.61 | 0.88 | 25 | LN6 |
| 5 | 219 | 0.52 | 0.77 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 393 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3P8P · Crystal Structure of Human Dimethylarginine Dimethylaminohydrolase-1 (DDAH-1) variant… · the same entry in another collection · chain A against A, TM-score 1.00
- O94760 · AlphaFold monomer V2.0 prediction for N(G),N(G)-dimethylarginine dimethylaminohydrolase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O94760
- Elsewhere: RCSB PDB 3P8P · PDBe 3P8P · UniProt O94760
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