Research workbench
Human CD73 (ecto 5'-nucleotidase) in complex with ampcp in the open state
Analyse Human CD73 (ecto 5'-nucleotidase) in complex with ampcp in the open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TVG
- Type
- protein
- Length
- 524 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-nucleotidase, ecto (CD73), isoform CRA_A
- EC
- 3.1.3.5
- UniProt
- Q53Z63
- Ligands
- AP2, ZN, NA, CA
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase, ecto (CD73), isoform CRA_A (EC 3.1.3.5) | protein | 524 | 31% helix, 27% strand | Q53Z63 |
Ligands and binding sites
- AP2 · Phosphomethylphosphonic acid adenosyl ester · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- CA · Calcium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.66 | 0.83 | 34 | empty |
| 2 | 442 | 0.64 | 0.77 | 56 | AP2, NA |
| 3 | 109 | 0.40 | 0.76 | 20 | empty |
| 4 | 66 | 0.33 | 0.76 | 20 | empty |
| 5 | 50 | 0.25 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6TVG · Human CD73 (ecto 5'-nucleotidase) in complex with AMPCP in the open state · the same entry in another collection · chain A 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 Q53Z63
- Elsewhere: RCSB PDB 6TVG · PDBe 6TVG · UniProt Q53Z63
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