Research workbench
Crystal structure of plasmodium yoelii adenosine deaminase (PY02076)
Analyse Crystal structure of plasmodium yoelii adenosine deaminase (PY02076) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AMX
- Type
- protein
- Length
- 720 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine deaminase
- EC
- 3.5.4.4
- UniProt
- Q7RMV2
- Ligands
- CO, UNX
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine deaminase (EC 3.5.4.4) | protein | 364 | 53% helix, 12% strand | Q7RMV2 |
| B | Adenosine deaminase (EC 3.5.4.4) | protein | 356 | 51% helix, 13% strand | Q7RMV2 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 5 copies · chains A, B
- UNX · Unknown atom or ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.83 | 0.85 | 78 | UNX |
| 2 | 183 | 0.66 | 0.86 | 33 | empty |
| 3 | 100 | 0.38 | 0.75 | 19 | empty |
| 4 | 71 | 0.36 | 0.77 | 19 | empty |
| 5 | 103 | 0.36 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 629 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2AMX · Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076) · the same entry in another collection · 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 Q7RMV2
- Elsewhere: RCSB PDB 2AMX · PDBe 2AMX · UniProt Q7RMV2
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