Research workbench
Human CD73 (ecto 5'-nucleotidase) in complex with PSB12604 (an aopcp derivative, compound 21 in publication) in the closed state
Analyse Human CD73 (ecto 5'-nucleotidase) in complex with PSB12604 (an aopcp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TWF
- Type
- protein
- Length
- 521 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
- O05, ZN, CA
- Pockets
- 5 · best druggability 0.75
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 | 521 | 31% helix, 27% strand | P21589 |
Ligands and binding sites
- O05 · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · 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 | 744 | 0.75 | 0.80 | 79 | O05 |
| 2 | 122 | 0.71 | 0.92 | 27 | empty |
| 3 | 72 | 0.43 | 0.81 | 17 | empty |
| 4 | 53 | 0.36 | 0.79 | 15 | empty |
| 5 | 53 | 0.27 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6TWF · Human CD73 (ecto 5'-nucleotidase) in complex with PSB12604 (an AOPCP derivative, compound… · 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 0.97
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 6TWF · PDBe 6TWF · UniProt P21589
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