Research workbench
Crystal structure of CD73 in complex with caffeine in the open form
Analyse Crystal structure of CD73 in complex with caffeine in the open form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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