Research workbench
Human CD73 (5'-nucleotidase) in complex with PSB12489 (an aopcp derivative) in the closed state
Analyse Human CD73 (5'-nucleotidase) in complex with PSB12489 (an aopcp derivative) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S7H
- Type
- protein
- Length
- 519 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
- KYW, ZN, CA
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 519 | 31% helix, 28% strand | P21589 |
Ligands and binding sites
- KYW · (N6,N6)-methyl,benzyl-C2-chloro-(alpha,beta)-methylene-ADP · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.75 | 0.79 | 95 | KYW |
| 2 | 73 | 0.68 | 0.95 | 24 | empty |
| 3 | 57 | 0.27 | 0.73 | 17 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6S7H · Human CD73 (5'-nucleotidase) in complex with PSB12489 (an AOPCP derivative) in the closed… · 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 0.98
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 6S7H · PDBe 6S7H · UniProt P21589
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