Research workbench
Human Ecto-5'-nucleotidase (CD73) in complex with A2396 (compound 74 in publication) in the closed form in crystal form IV
Analyse Human Ecto-5'-nucleotidase (CD73) in complex with A2396 (compound 74 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XUE
- Type
- protein
- Length
- 1,030 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Homo sapiens
- Molecule
- 5'-nucleotidase
- EC
- 3.1.3.5
- UniProt
- P21589
- Ligands
- O1H, ZN, CA, PO4
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.94 · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 516 | 30% helix, 26% strand | P21589 |
| B | 5'-nucleotidase (EC 3.1.3.5) | protein | 514 | 29% helix, 27% strand | P21589 |
Ligands and binding sites
- O1H · 4-[[5-[7-chloranyl-3-(1~{H}-indazol-6-yl)benzotriazol-5-yl]pyrazol-1-yl]methyl]benzenecarbonitrile · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.85 | 0.87 | 84 | empty |
| 2 | 739 | 0.76 | 0.81 | 103 | PO4, O1H |
| 3 | 626 | 0.74 | 0.81 | 98 | ZN, PO4, O1H |
| 4 | 183 | 0.67 | 0.86 | 42 | empty |
| 5 | 168 | 0.64 | 0.86 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1268 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6XUE · Human ecto-5'-nucleotidase (CD73) in complex with A2396 (compound 74 in publication) in… · the same entry in another collection · chain A against A, TM-score 1.00
- P21589 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase (P21589) · 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 P21589
- Elsewhere: RCSB PDB 6XUE · PDBe 6XUE · UniProt P21589
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