8EQ6: PD1 signaling receptor

PD1 signaling receptor bound to FAB Complex. Determined by X-ray diffraction at 1.65 Å resolution. Released 11 Oct 2023.

Method: X-ray diffraction
Resolution: 1.65 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 4,117
Mol. weight: 62.3 kDa
Released: 11 Oct 2023

Explore 8EQ6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EQ6 contains 22 α-helices and 53 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	1
β-strand	22-26	5	2
β-strand	31-36	6	1
β-strand	47-50	4	2
β-strand	76-80	5	1
β-strand	86-91	6	1
α-helix	96-98	3
β-strand	100-105	6	2
β-strand	117	1	2
α-helix	118-120	3
β-strand	121-126	6	2
β-strand	127	1	3

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
α-helix	7-9	3
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-40	7	10
β-strand	44-52	9	10
β-strand	57-60	4	10
α-helix	62-64	3
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	109-110	2	10
β-strand	114-118	5	10
β-strand	124	1	11
α-helix	125-126	2
β-strand	127-131	5	12
β-strand	142-152	11	12
β-strand	153	1	11
β-strand	158-161	4	13
α-helix	162-164	3
β-strand	166	1	13
β-strand	170-172	3	12
α-helix	173-175	3
β-strand	176-177	2	12
β-strand	183-192	10	12
α-helix	193-195	3
β-strand	202-207	6	13
α-helix	208-210	3
β-strand	212-217	6	13

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	19-29	11	4
α-helix	31-33	3
β-strand	34-39	6	5
β-strand	46-50	5	5
β-strand	54-55	2	5
α-helix	56	1
β-strand	63-76	14	4
α-helix	81-83	3
β-strand	86-91	6	5
β-strand	94	1	3
α-helix	97	1
β-strand	98-99	2	5
β-strand	103-107	5	5
β-strand	112	1	6
α-helix	113-114	2
β-strand	115-119	5	7
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	7
β-strand	141	1	6
β-strand	146-151	6	8
β-strand	154-155	2	8
α-helix	156	1
β-strand	160-164	5	7
α-helix	165-168	4
β-strand	174-183	10	7
α-helix	184-189	6
β-strand	192-198	7	8
β-strand	206-211	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death protein 1	A	protein	129	Homo sapiens	Q15116 (AlphaFold model)
Antibody FAB light chain	L	protein	215	Mus musculus
Antibody FAB heavy chain	H	protein	227	Mus musculus

Sequence of entity 1 (A), FASTA

>8EQ6_1 Programmed cell death protein 1 (chains A)
GPSGALDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKL
AAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLR
AELRVTERR

Sequence of entity 2 (L), FASTA

>8EQ6_2 Antibody FAB light chain (chains L)
ENQLTQSPSSLSASVGDRVTITCRASSSVISSYLHWYQQKPGKAPKLLIYSTSNLASGVP
SRFSGSGSGTDYTLTISSLQPEDFATYYCQQYNSYPLTFGGGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>8EQ6_3 Antibody FAB heavy chain (chains H)
QVQLVQSGAEVKKPGASVKVSCKAFGYTFTTYPIEWMRQAPGKGLEWIGNFHPYNDDTKY
NEKFQGRVTLTVDKSSTTVYMELSSLRSEDTAVYYCARENYGSHGGFVYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Primary citation

Antibody agonists trigger immune receptor signaling through local exclusion of receptor-type protein tyrosine phosphatases. Lippert, A.H., Paluch, C., Gaglioni, M. et al. Immunity (2024) 57:256-270.e10. DOI 10.1016/j.immuni.2024.01.007 · PubMed

Other PDB entries of the same protein (UniProt Q15116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UMU 1.18 Å, Human apo PD-1 triple mutant
6J14 1.4 Å, Complex structure of GY-14 and PD-1
6UMV 1.42 Å, Human apo PD-1 double mutant
7WSL 1.53 Å, PD-1 in complex with Dostarlimab
9EHT 1.54 Å, Crystal Structure of PD-1/retifanlimab complex
7VUX 1.64 Å, Complex structure of PD1 and 609A-Fab
6K0Y 1.7 Å, Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor
7E9B 1.78 Å, Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody…
9Q8L 1.85 Å, Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution
8GY5 1.98 Å, High-resolution structure of the cemiplimab Fab in complex with PD-1
6UMT 1.99 Å, High-affinity human PD-1 PD-L2 complex
5GGS 2.0 Å, PD-1 in complex with pembrolizumab Fab

Browse structure collections

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