MolNFT v1 · #163584 · protein
Human CD73 (5'-nucleotidase) in complex with PSB12379 (an aopcp derivative) in the closed state
6S7F: “Human CD73 (5'-nucleotidase) in complex with PSB12379 (an aopcp derivative) in the closed state”. X-ray diffraction, 3 ligands (KYK, ZN, CA), 3 pockets (best druggability 0.74). MolNFT v1 #163584 on GenesisL1: 3D structure, binding…
- PDB
- 6S7F
- 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
- KYK, ZN, CA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 519 | 30% helix, 27% strand | P21589 |
Ligands and binding sites
- KYK · N6-benzyl-(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 | 755 | 0.74 | 0.80 | 84 | ZN, KYK |
| 2 | 117 | 0.66 | 0.89 | 32 | empty |
| 3 | 51 | 0.26 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6S7F · Human CD73 (5'-nucleotidase) in complex with PSB12379 (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 6S7F · PDBe 6S7F · UniProt P21589
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