Research workbench

The complex structure of pd-1 and cemiplimab

Analyse The complex structure of pd-1 and cemiplimab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WVM
Type: protein
Length: 670 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain of cemiplimab; Light chain of cemiplimab; Programmed cell death protein 1
UniProt: Q15116
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heavy chain of cemiplimab	protein	117	5% helix, 46% strand	—
B, D	Light chain of cemiplimab	protein	107	3% helix, 49% strand	—
E	Programmed cell death protein 1	protein	113	3% helix, 51% strand	Q15116
C	Heavy chain of cemiplimab	protein	116	5% helix, 47% strand	—
F	Programmed cell death protein 1	protein	110	3% helix, 52% strand	Q15116

Pockets

8 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	676	0.71	0.78	70	empty
2	234	0.52	0.76	41	empty
3	94	0.41	0.77	16	empty
4	73	0.33	0.75	16	empty
5	87	0.32	0.73	22	empty

Interfaces

8 interfaces between chains.

A–B · 844 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 831 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 618 Å² buried · 7 hydrogen bonds · protein-protein
C–F · 581 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 250 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7WVM · The complex structure of PD-1 and cemiplimab · the same entry in another collection · chain F against F, 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 F 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 7WVM · PDBe 7WVM · UniProt Q15116

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.