Research workbench
X-ray structure of adenosine 5'-monophosphate deaminase from arabidopsis thaliana in complex with coformycin 5'-phosphate
Analyse X-ray structure of adenosine 5'-monophosphate deaminase from arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A3L
- Type
- protein
- Length
- 616 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMP deaminase
- UniProt
- O80452
- Ligands
- CF5, ZN, PO4
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMP deaminase | protein | 616 | 42% helix, 8% strand | O80452 |
Ligands and binding sites
- CF5 · Coformycin 5'-phosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.84 | 0.85 | 92 | empty |
| 2 | 264 | 0.75 | 0.88 | 45 | CF5 |
| 3 | 166 | 0.69 | 0.88 | 28 | empty |
| 4 | 216 | 0.67 | 0.85 | 23 | empty |
| 5 | 106 | 0.56 | 0.84 | 22 | empty |
Compared structures
- 2A3L · X-Ray Structure of Adenosine 5'-Monophosphate Deaminase from Arabidopsis Thaliana in… · the same entry in another collection · chain A against A, TM-score 1.00
- O80452 · AlphaFold monomer V2.0 prediction for AMP deaminase (O80452) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O80452
- Elsewhere: RCSB PDB 2A3L · PDBe 2A3L · UniProt O80452
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