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Pd-1 in complex with dostarlimab

Analyse Pd-1 in complex with dostarlimab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WSL
Type: protein
Length: 534 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain; Programmed cell death protein 1; Heavy chain
UniProt: Q15116
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Light chain	protein	212	6% helix, 51% strand	—
D	Programmed cell death protein 1	protein	113	3% helix, 53% strand	Q15116
H	Heavy chain	protein	209	10% helix, 53% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	332	0.55	0.75	46	empty
2	59	0.43	0.82	16	empty
3	121	0.39	0.74	26	empty
4	77	0.31	0.73	15	empty

Interfaces

3 interfaces between chains.

L–H · 1720 Å² buried · 14 hydrogen bonds · protein-protein
D–H · 709 Å² buried · 17 hydrogen bonds · protein-protein
L–D · 326 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7WSL · PD-1 in complex with Dostarlimab · the same entry in another collection · chain L against L, 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 D against A, TM-score 0.96

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 7WSL · PDBe 7WSL · UniProt Q15116

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