MolNFT v1 · #66894 · protein
Crystal structure of dimethylarginine dimethylaminohydrolase-1 (ddah- 1) in complex with N5-(1-iminopropyl)-L-ornithine
3I4A · N(G),N(G)-dimethylarginine dimethylaminohydrolase 1: “Crystal structure of dimethylarginine dimethylaminohydrolase-1 (ddah- 1) in complex with…”. X-ray diffraction, 1 ligand (LN5), 6 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 3I4A
- 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
- LN5
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% 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 | 32% helix, 26% strand | O94760 |
Ligands and binding sites
- LN5 · N5-(1-iminopropyl)-L-ornithine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.82 | 0.91 | 34 | empty |
| 2 | 362 | 0.81 | 0.90 | 32 | empty |
| 3 | 338 | 0.67 | 0.81 | 53 | LN5 |
| 4 | 112 | 0.56 | 0.84 | 22 | LN5 |
| 5 | 256 | 0.55 | 0.77 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3I4A · Crystal structure of dimethylarginine dimethylaminohydrolase-1 (DDAH-1) in complex with… · 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 3I4A · PDBe 3I4A · UniProt O94760
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