MolNFT v1 · #173807 · protein

CD73 in complex with the humanized antagonistic antibody MAB19

7BBJ · 5'-nucleotidase: “CD73 in complex with the humanized antagonistic antibody MAB19”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #173807 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7BBJ
Type: protein
Length: 1,892 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-nucleotidase; Heavy chain MAB19; Light chain MAB19
EC: 3.1.3.5
UniProt: P21589
Ligands: ZN, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-nucleotidase (EC 3.1.3.5)	protein	524	30% helix, 28% strand	P21589
H	Heavy chain MAB19	protein	217	6% helix, 53% strand	—
L, N	Light chain MAB19	protein	211	6% helix, 50% strand	—
M	Heavy chain MAB19	protein	205	4% helix, 56% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1019	0.83	0.84	97	empty
2	258	0.64	0.82	34	empty
3	375	0.61	0.77	48	empty
4	386	0.60	0.77	45	empty
5	349	0.59	0.77	53	empty

Interfaces

7 interfaces between chains.

H–L · 1847 Å² buried · 10 hydrogen bonds · protein-protein
M–N · 1730 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1329 Å² buried · 20 hydrogen bonds · protein-protein
A–H · 532 Å² buried · 6 hydrogen bonds · protein-protein
B–N · 525 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

7BBJ · CD73 in complex with the humanized antagonistic antibody mAb19 · the same entry in another collection · chain N against N, TM-score 1.00
P21589 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase (P21589) · a predicted model of the same protein · chain B 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 7BBJ · PDBe 7BBJ · UniProt P21589

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