MolNFT v1 · #123854 · protein

Human pd-1 ectodomain complexed with pembrolizumab Fab

5JXE · Programmed cell death protein 1: “Human pd-1 ectodomain complexed with pembrolizumab Fab”. X-ray diffraction, 9 pockets (best druggability 0.54). MolNFT v1 #123854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JXE
Type: protein
Length: 1,043 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death protein 1; Pembrolizumab Fab light chain; Pembrolizumab Fab heavy…
UniProt: Q15116
Pockets: 9 · best druggability 0.54

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death protein 1	protein	97	3% helix, 48% strand	Q15116
B	Programmed cell death protein 1	protein	101	0% helix, 44% strand	Q15116
C, F	Pembrolizumab Fab light chain	protein	215	4% helix, 50% strand	—
D	Pembrolizumab Fab heavy chain	protein	197	6% helix, 51% strand	—
G	Pembrolizumab Fab heavy chain	protein	218	6% helix, 48% strand	—

Pockets

9 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	311	0.54	0.75	43	empty
2	337	0.52	0.73	47	empty
3	125	0.48	0.79	20	empty
4	84	0.40	0.78	18	empty
5	92	0.38	0.76	20	empty

Interfaces

7 interfaces between chains.

F–G · 1811 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1746 Å² buried · 12 hydrogen bonds · protein-protein
A–G · 640 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 602 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 406 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

5JXE · Human PD-1 ectodomain complexed with Pembrolizumab 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 A against A, TM-score 0.95

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 5JXE · PDBe 5JXE · UniProt Q15116

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