Research workbench
The crystal structure of adenosine deaminase in complex with chloropurine from pseudomonas aeruginosa
Analyse The crystal structure of adenosine deaminase in complex with chloropurine from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PBM
- Type
- protein
- Length
- 627 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine deaminase
- EC
- 3.5.4.4
- UniProt
- Q9I6Y4
- Ligands
- ES4, ZN
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine deaminase (EC 3.5.4.4) | protein | 313 | 58% helix, 12% strand | Q9I6Y4 |
| B | Adenosine deaminase (EC 3.5.4.4) | protein | 314 | 54% helix, 13% strand | Q9I6Y4 |
Ligands and binding sites
- ES4 · 6-chloro-9H-purine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.46 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 789 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3PBM · The crystal structure of adenosine deaminase in complex with chloropurine from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I6Y4 · AlphaFold monomer V2.0 prediction for adenine deaminase (Q9I6Y4) · a predicted model of the same protein · chain B 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 Q9I6Y4
- Elsewhere: RCSB PDB 3PBM · PDBe 3PBM · UniProt Q9I6Y4
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