MolNFT v1 · #185007 · protein
Crystal structure of CD73 in complex with caffeine in the open form
7PBB · 5'-nucleotidase: “Crystal structure of CD73 in complex with caffeine in the open form”. X-ray diffraction, 3 ligands (CFF, ZN, CA), 5 pockets (best druggability 0.67). MolNFT v1 #185007 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7PBB
- Type
- protein
- Length
- 524 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
- CFF, ZN, CA
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 524 | 31% helix, 26% strand | P21589 |
Ligands and binding sites
- CFF · Caffeine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 293 | 0.67 | 0.82 | 35 | GOL |
| 2 | 495 | 0.66 | 0.78 | 59 | CFF |
| 3 | 122 | 0.43 | 0.77 | 23 | GOL |
| 4 | 59 | 0.33 | 0.77 | 20 | empty |
| 5 | 50 | 0.24 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 7PBB · PDBe 7PBB · UniProt P21589
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