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Complex structure of PD-1 and nivolumab-Fab

Analyse Complex structure of PD-1 and nivolumab-Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WT9
Type: protein
Length: 533 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.401
Source: Homo sapiens
Molecule: Heavy Chain of Nivolumab; Light Chain of Nivolumab; Programmed cell death protein 1
UniProt: Q15116
Ligands: NAG, FUC
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · resolution 2.401 · 3 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Heavy Chain of Nivolumab	protein	208	8% helix, 52% strand	—
L	Light Chain of Nivolumab	protein	216	6% helix, 50% strand	—
G	Programmed cell death protein 1	protein	109	3% helix, 45% strand	Q15116

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains G
FUC · alpha-L-fucopyranose · sugar · chains G

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	276	0.65	0.82	41	empty
2	423	0.57	0.74	51	empty
3	182	0.46	0.75	32	empty
4	80	0.34	0.75	18	empty
5	81	0.31	0.73	18	empty

Interfaces

3 interfaces between chains.

H–L · 1642 Å² buried · 17 hydrogen bonds · protein-protein
H–G · 645 Å² buried · 14 hydrogen bonds · protein-protein
L–G · 333 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5WT9 · Complex structure of pd-1 and nivolumab-Fab · the same entry in another collection · chain G against G, 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 G 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 5WT9 · PDBe 5WT9 · UniProt Q15116

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