Research workbench
Ensemble refinement of the protein crystal structure of gene product from arabidopsis thaliana AT5G08170, agmatine iminohydrolase
Analyse Ensemble refinement of the protein crystal structure of gene product from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q3U
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agmatine deiminase
- EC
- 3.5.3.12
- UniProt
- Q8GWW7
- Ligands
- MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agmatine deiminase (EC 3.5.3.12) | protein | 365 | 29% helix, 25% strand | Q8GWW7 |
| B | Agmatine deiminase (EC 3.5.3.12) | protein | 363 | 30% helix, 23% strand | Q8GWW7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.98 | 22 | EDO |
| 2 | 125 | 0.69 | 0.91 | 36 | EDO |
| 3 | 91 | 0.46 | 0.80 | 17 | empty |
| 4 | 107 | 0.39 | 0.76 | 15 | empty |
| 5 | 62 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 864 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2Q3U · Ensemble refinement of the protein crystal structure of gene product from Arabidopsis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8GWW7 · AlphaFold monomer V2.0 prediction for agmatine deiminase (Q8GWW7) · 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 Q8GWW7
- Elsewhere: RCSB PDB 2Q3U · PDBe 2Q3U · UniProt Q8GWW7
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