Research workbench
Crystal structure of dimethylarginine dimethylaminohydrolase I in complex with L-homocysteine
Analyse Crystal structure of dimethylarginine dimethylaminohydrolase I in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CI5
- Type
- protein
- Length
- 545 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ng, ng-dimethylarginine dimethylaminohydrolase 1
- EC
- 3.5.3.18
- UniProt
- P56965
- Ligands
- HCS
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ng, ng-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18) | protein | 272 | 32% helix, 24% strand | P56965 |
| B | Ng, ng-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18) | protein | 273 | 32% helix, 25% strand | P56965 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.81 | 0.90 | 32 | empty |
| 2 | 326 | 0.81 | 0.90 | 30 | empty |
| 3 | 371 | 0.64 | 0.79 | 42 | empty |
| 4 | 159 | 0.54 | 0.80 | 25 | empty |
| 5 | 105 | 0.38 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2CI5 · Crystal structure of Dimethylarginine Dimethylaminohydrolase I in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P56965 · AlphaFold monomer V2.0 prediction for N(G),N(G)-dimethylarginine dimethylaminohydrolase 1… · a predicted model of the same protein · chain B 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 P56965
- Elsewhere: RCSB PDB 2CI5 · PDBe 2CI5 · UniProt P56965
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