MolNFT v1 · #93434 · protein
Human ecto-5'-nucleotidase (CD73): crystal form I (open) in complex with adenosine
4H2F: “Human ecto-5'-nucleotidase (CD73): crystal form I (open) in complex with adenosine”. X-ray diffraction, 4 ligands (ADN, ZN, CA), 5 pockets (best druggability 0.57). MolNFT v1 #93434 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4H2F
- 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
- ADN, ZN, CA, CL
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 524 | 31% helix, 27% strand | P21589 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.57 | 0.82 | 33 | empty |
| 2 | 135 | 0.48 | 0.78 | 27 | ADN |
| 3 | 189 | 0.46 | 0.75 | 25 | empty |
| 4 | 111 | 0.38 | 0.75 | 21 | empty |
| 5 | 86 | 0.38 | 0.77 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4H2F · Human ecto-5'-nucleotidase (CD73): crystal form I (open) in complex with adenosine · 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 0.67
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 4H2F · PDBe 4H2F · UniProt P21589
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