Research workbench
X-ray structure of gene product from arabidopsis thaliana AT5G08170, agmatine iminohydrolase
Analyse X-ray structure of gene product from arabidopsis thaliana AT5G08170, agmatine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VKP
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agmatine iminohydrolase
- EC
- 3.5.3.12
- UniProt
- Q8GWW7
- Ligands
- MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agmatine iminohydrolase (EC 3.5.3.12) | protein | 365 | 30% helix, 24% strand | Q8GWW7 |
| B | Agmatine iminohydrolase (EC 3.5.3.12) | protein | 363 | 32% helix, 24% 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.70 | 0.91 | 30 | EDO |
| 2 | 78 | 0.45 | 0.81 | 18 | empty |
| 3 | 107 | 0.36 | 0.74 | 16 | empty |
| 4 | 68 | 0.36 | 0.78 | 13 | empty |
| 5 | 61 | 0.29 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 891 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1VKP · X-ray structure of gene product from arabidopsis thaliana AT5G08170, agmatine… · 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 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 Q8GWW7
- Elsewhere: RCSB PDB 1VKP · PDBe 1VKP · UniProt Q8GWW7
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