MolNFT v1 · #185001 · protein

Crystal structure of CD73 in complex with ump in the open form

7PB5 · 5'-nucleotidase: “Crystal structure of CD73 in complex with ump in the open form”. X-ray diffraction, 3 ligands (U, ZN, CA), 5 pockets (best druggability 0.66). MolNFT v1 #185001 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7PB5
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: U, ZN, CA
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-nucleotidase (EC 3.1.3.5)	protein	524	30% helix, 26% strand	P21589

Ligands and binding sites

U · Uridine-5'-monophosphate · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
CA · Calcium ion · metal · chains A
GOL · Glycerol · additive · 2 copies · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	286	0.66	0.82	35	empty
2	457	0.65	0.78	57	U
3	110	0.42	0.77	20	empty
4	63	0.33	0.76	20	empty
5	57	0.26	0.73	15	empty

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7PB5 · Crystal structure of CD73 in complex with UMP in the open form · 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 0.69

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 7PB5 · PDBe 7PB5 · UniProt P21589

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