MolNFT v1 · #151780 · protein

Structure of human CD73 in complex with antibody IPH53

6HXW · 5'-nucleotidase: “Structure of human CD73 in complex with antibody IPH53”. X-ray diffraction, 2 ligands (NAG, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #151780 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HXW
Type: protein
Length: 1,894 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-nucleotidase; IPH53 heavy chain; IPH53 light chain
EC: 3.1.3.5
UniProt: P21589
Ligands: NAG, ZN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-nucleotidase (EC 3.1.3.5)	protein	523	31% helix, 26% strand	P21589
C, H	IPH53 heavy chain	protein	215	7% helix, 48% strand	—
D, L	IPH53 light chain	protein	209	5% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
ZN · Zinc ion · metal · 4 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	887	0.85	0.86	81	empty
2	637	0.74	0.81	92	ZN
3	572	0.73	0.81	91	ZN
4	141	0.66	0.88	35	empty
5	101	0.66	0.90	30	empty

Interfaces

7 interfaces between chains.

H–L · 1930 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1919 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1352 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 628 Å² buried · 8 hydrogen bonds · protein-protein
A–H · 622 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6HXW · structure of human CD73 in complex with antibody IPH53 · the same entry in another collection · chain L against L, 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 0.99

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 6HXW · PDBe 6HXW · UniProt P21589

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