MolNFT v1 · #93413 · protein
Crystal structure of a truncated soluble form of human CD73 with ecto- 5'-nucleotidase activity
4H1S: “Crystal structure of a truncated soluble form of human CD73 with ecto- 5'-nucleotidase activity”. X-ray diffraction, 3 ligands (NAG, ZN, PO4), 8 pockets (best druggability 0.85). MolNFT v1 #93413 on GenesisL1: 3D structure, binding…
- PDB
- 4H1S
- Type
- protein
- Length
- 1,039 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-nucleotidase
- EC
- 3.1.3.5
- UniProt
- P21589
- Ligands
- NAG, ZN, PO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 521 | 30% helix, 27% strand | P21589 |
| B | 5'-nucleotidase (EC 3.1.3.5) | protein | 518 | 30% helix, 27% strand | P21589 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.85 | 0.86 | 104 | empty |
| 2 | 642 | 0.74 | 0.81 | 98 | ZN, PO4 |
| 3 | 239 | 0.70 | 0.86 | 48 | ZN, PO4 |
| 4 | 148 | 0.68 | 0.89 | 34 | empty |
| 5 | 121 | 0.65 | 0.88 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1315 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4H1S · Crystal Structure of a Truncated Soluble form of Human CD73 with Ecto-5'-Nucleotidase… · 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 B 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 4H1S · PDBe 4H1S · UniProt P21589
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