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Crystal Structure of Adenosine Deaminase from Vibrio cholerae Complexed with Pentostatin (Deoxycoformycin)
Analyse Crystal Structure of Adenosine Deaminase from Vibrio cholerae Complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N91
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Vibrio cholerae O1 biovar El Tor str. N16961
- Molecule
- Adenosine deaminase
- EC
- 3.5.4.4
- UniProt
- Q9KNI7
- Ligands
- DCF, ZN, NA, PO4, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.05 · 1 distinct chain · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosine deaminase (EC 3.5.4.4) | protein | 334 | 57% helix, 13% strand | Q9KNI7 |
Ligands and binding sites
- DCF · 2'-deoxycoformycin · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.71 | 0.86 | 45 | empty |
| 2 | 117 | 0.68 | 0.90 | 25 | DCF |
| 3 | 121 | 0.67 | 0.89 | 25 | DCF |
| 4 | 227 | 0.46 | 0.73 | 40 | empty |
| 5 | 51 | 0.28 | 0.74 | 10 | CXS, SO4 |
Interfaces
1 interface between chains.
- A–B · 1140 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6N91 · Crystal structure of adenosine deaminase from vibrio cholerae complexed with pentostatin… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KNI7 · AlphaFold monomer V2.0 prediction for adenosine deaminase (Q9KNI7) · 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 Q9KNI7
- Elsewhere: RCSB PDB 6N91 · PDBe 6N91 · UniProt Q9KNI7
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