Research workbench
Crystal structure of arabidopsis thaliana agmatine deiminase from cell free expression
Analyse Crystal structure of arabidopsis thaliana agmatine deiminase from cell free… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H7C
- Type
- protein
- Length
- 369 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agmatine deiminase
- EC
- 3.5.3.12
- UniProt
- Q8GWW7
- Ligands
- 211, NA, MG, K, CL
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Agmatine deiminase (EC 3.5.3.12) | protein | 369 | 31% helix, 24% strand | Q8GWW7 |
Ligands and binding sites
- 211 · 2,2',2''-nitrilotriethanol · ligand · chains X
- NA · Sodium ion · metal · 2 copies · chains X
- MG · Magnesium ion · metal · chains X
- K · Potassium ion · metal · chains X
- CL · Chloride ion · ion · 2 copies · chains X
- 1PE · Pentaethylene glycol · additive · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.65 | 0.89 | 32 | 211 |
| 2 | 55 | 0.28 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3H7C · Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression · the same entry in another collection · chain X against X, TM-score 1.00
- Q8GWW7 · AlphaFold monomer V2.0 prediction for agmatine deiminase (Q8GWW7) · a predicted model of the same protein · chain X 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 3H7C · PDBe 3H7C · UniProt Q8GWW7
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