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Human ecto-5'-nucleotidase (CD73): crystal form II (open) in complex with PSB11552
Analyse Human ecto-5'-nucleotidase (CD73): crystal form II (open) 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
- 4H1Y
- Type
- protein
- Length
- 524 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-nucleotidase
- EC
- 3.1.3.5
- UniProt
- P21589
- Ligands
- 0YQ, ZN, CA, CL
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | 5'-nucleotidase (EC 3.1.3.5) | protein | 524 | 30% helix, 27% strand | P21589 |
Ligands and binding sites
- 0YQ · 2,2'-[(2-{[2-({[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)ethyl]amino}-2-oxoethyl)imino]diacetic acid (non-preferred name) · ligand · chains P
- ZN · Zinc ion · metal · 2 copies · chains P
- CA · Calcium ion · metal · chains P
- CL · Chloride ion · ion · chains P
- GOL · Glycerol · additive · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.66 | 0.81 | 34 | empty |
| 2 | 451 | 0.64 | 0.78 | 55 | CL |
| 3 | 135 | 0.43 | 0.76 | 22 | empty |
| 4 | 57 | 0.32 | 0.77 | 17 | empty |
| 5 | 61 | 0.28 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4H1Y · Human ecto-5'-nucleotidase (CD73): crystal form II (open) in complex with PSB11552 · the same entry in another collection · chain P against P, TM-score 1.00
- P21589 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase (P21589) · a predicted model of the same protein · chain P against A, TM-score 0.69
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 4H1Y · PDBe 4H1Y · UniProt P21589
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