Research workbench
Crystal structure of adenosine deaminase from plasmodium vivax in complex with pentostatin
Analyse Crystal structure of adenosine deaminase from plasmodium vivax 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
- 2PGR
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine deaminase
- EC
- 3.5.4.4
- UniProt
- A5KE01
- Ligands
- CCN, DCF, ZN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine deaminase (EC 3.5.4.4) | protein | 359 | 53% helix, 14% strand | A5KE01 |
Ligands and binding sites
- CCN · Acetonitrile · ligand · 2 copies · chains A
- DCF · 2'-deoxycoformycin · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.78 | 0.98 | 25 | DCF |
| 2 | 118 | 0.41 | 0.76 | 17 | CCN |
| 3 | 52 | 0.34 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2PGR · Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin · the same entry in another collection · chain A against A, TM-score 1.00
- A5KE01 · AlphaFold monomer V2.0 prediction for adenosine deaminase (A5KE01) · 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 A5KE01
- Elsewhere: RCSB PDB 2PGR · PDBe 2PGR · UniProt A5KE01
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