Research workbench
Human ecto-5'-nucleotidase (CD73) in complex with the ampcp derivative A894 (compound 2N in publication) in the closed form (crystal form IV)
Analyse Human ecto-5'-nucleotidase (CD73) in complex with the ampcp derivative A894… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YE1
- Type
- protein
- Length
- 1,045 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
- OO2, ZN
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 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 |
| B | 5'-nucleotidase (EC 3.1.3.5) | protein | 521 | 31% helix, 27% strand | P21589 |
Ligands and binding sites
- OO2 · [(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-(cyclopentylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxymethylphosphonic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 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 | 728 | 0.76 | 0.81 | 83 | ZN, OO2 |
| 2 | 541 | 0.74 | 0.82 | 67 | OO2 |
| 3 | 313 | 0.66 | 0.81 | 48 | empty |
| 4 | 133 | 0.66 | 0.88 | 31 | empty |
| 5 | 122 | 0.52 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6YE1 · Human Ecto-5'-nucleotidase (CD73) in complex with the AMPCP derivative A894 (compound 2n… · 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 6YE1 · PDBe 6YE1 · UniProt P21589
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