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N-glycosylation of pd-1 and glycosylation dependent binding of pd-1 specific monoclonal antibody camrelizumab

Analyse N-glycosylation of pd-1 and glycosylation dependent binding of pd-1 specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CU5
Type: protein
Length: 682 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camrelizumab-scfv; Programmed cell death protein 1
UniProt: Q15116
Ligands: NAG, MAN, FUC
Pockets: 7 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Camrelizumab-scfv	protein	230	4% helix, 49% strand	—
E, Q	Programmed cell death protein 1	protein	111	3% helix, 53% strand	Q15116

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains Q, A, E, B
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains Q, B
FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, Q, B, E

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

Pockets

7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.49	0.75	32	empty
2	200	0.48	0.75	30	empty
3	147	0.41	0.74	20	empty
4	75	0.41	0.79	19	FUC
5	76	0.40	0.79	16	FUC

Interfaces

5 interfaces between chains.

B–A · 1898 Å² buried · 15 hydrogen bonds · protein-protein
A–Q · 475 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 457 Å² buried · 5 hydrogen bonds · protein-protein
B–Q · 265 Å² buried · 3 hydrogen bonds · protein-protein
E–A · 249 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

7CU5 · N-Glycosylation of PD-1 and glycosylation dependent binding of PD-1 specific monoclonal… · the same entry in another collection · chain B against B, TM-score 1.00
Q15116 · AlphaFold monomer V2.0 prediction for programmed cell death protein 1 (Q15116) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 Q15116
Elsewhere: RCSB PDB 7CU5 · PDBe 7CU5 · UniProt Q15116

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