9HK1: PD1 signaling receptor

PD1 signaling receptor bound to FAB Complex. Determined by X-ray diffraction at 2.03 Å resolution. Released 15 Jan 2025.

Method: X-ray diffraction
Resolution: 2.03 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,487
Mol. weight: 125.05 kDa
Ligands: NAG
Released: 15 Jan 2025

Explore 9HK1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HK1 contains 44 α-helices and 112 β-strands across 6 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, 11 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	45-51	7	2
β-strand	57-63	7	2
β-strand	76-80	5	1
β-strand	86-91	6	1
α-helix	96-98	3
β-strand	100-107	8	2
β-strand	116-117	2	2
α-helix	118-120	3
β-strand	121-126	6	2
β-strand	127	1	3

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	4
β-strand	22-26	5	5
β-strand	31-36	6	4
β-strand	46-51	6	5
β-strand	57-63	7	5
β-strand	76-80	5	4
β-strand	86-91	6	4
α-helix	96-98	3
β-strand	100-106	7	5
β-strand	116-117	2	5
α-helix	118-120	3
β-strand	121-126	6	5
β-strand	127	1	6

Chain H: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	12
α-helix	29-31	3
α-helix	33	1
β-strand	34-39	6	8
β-strand	45-52	8	8
β-strand	57-60	4	8
α-helix	62-64	3
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-98	7	8
β-strand	109-110	2	8
β-strand	114-118	5	8
β-strand	124	1	13
α-helix	125-126	2
β-strand	127-131	5	14
β-strand	142-152	11	14
β-strand	153	1	13
β-strand	158-161	4	15
β-strand	166	1	15
β-strand	171-172	2	14
α-helix	173-175	3
β-strand	176-177	2	14
β-strand	183-192	10	14
α-helix	193-195	3
β-strand	196	1	16
β-strand	199	1	16
β-strand	202-207	6	15
α-helix	208-210	3
β-strand	212-217	6	15

Chain I: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
α-helix	7-9	3
β-strand	10-12	3	18
β-strand	18-25	8	22
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	58-60	3	18
α-helix	62-65	4
β-strand	68-73	6	22
α-helix	74-76	3
β-strand	78-83	6	22
α-helix	88-90	3
β-strand	92-98	7	18
β-strand	109-110	2	18
β-strand	114-118	5	18
β-strand	124	1	23
α-helix	125-126	2
β-strand	127-131	5	24
β-strand	142-152	11	24
β-strand	153	1	23
β-strand	158-161	4	25
α-helix	162-164	3
β-strand	166	1	25
β-strand	170-172	3	24
α-helix	173-175	3
β-strand	176-177	2	24
β-strand	183-192	10	24
α-helix	193-195	3
β-strand	202-207	6	25
α-helix	208-210	3
β-strand	212-217	6	25

Chain L: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
α-helix	31-33	3
β-strand	34-39	6	8
α-helix	44-45	2
β-strand	46-50	5	8
β-strand	54-55	2	8
α-helix	56	1
β-strand	63-68	6	7
β-strand	71-76	6	7
α-helix	81-83	3
β-strand	86-91	6	8
β-strand	94	1	3
α-helix	97	1
β-strand	98-99	2	8
β-strand	103-107	5	8
β-strand	112	1	9
α-helix	113-114	2
β-strand	115-119	5	10
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	10
β-strand	141	1	9
β-strand	146-151	6	11
β-strand	154-155	2	11
β-strand	160-164	5	10
α-helix	165-168	4
β-strand	174-183	10	10
α-helix	184-188	5
β-strand	192-198	7	11
β-strand	206-211	6	11

Chain M: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
α-helix	31-33	3
β-strand	34-39	6	18
β-strand	46-50	5	18
β-strand	54-55	2	18
α-helix	56	1
β-strand	63-68	6	17
β-strand	71-76	6	17
α-helix	81-83	3
β-strand	86-91	6	18
β-strand	94	1	6
α-helix	97	1
β-strand	98-99	2	18
β-strand	103-107	5	18
β-strand	112	1	19
α-helix	113-114	2
β-strand	115-119	5	20
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	20
β-strand	141	1	19
β-strand	146-151	6	21
β-strand	154-155	2	21
α-helix	156	1
β-strand	160-164	5	20
α-helix	165-168	4
β-strand	174-183	10	20
α-helix	184-188	5
β-strand	192-198	7	21
β-strand	206-211	6	21

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>9HK1_1 Programmed cell death protein 1 (chains A, B)
GPSGALDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKL
AAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLR
AELRVTERR

Sequence of entity 2 (L, M), FASTA

>9HK1_2 Antibody FAB light chain (chains L, M)
ENQLTQSPSSLSASVGDRVTITCRASSSVISSYLHWYQQKPGKAPKLLIYSTSNLASGVP
SRFSGSGSGTDYTLTISSLQPEDFATYYCQQYNSYPLTFGGGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H, I), FASTA

>9HK1_3 Antibody FAB heavy chain (chains H, I)
QVQLVQSGAEVKKPGASVKVSCKAFGYTFTTYPIEWMRQAPGKGLEWIGNFHPYNDDTKY
NEKFQGRVTLTVDKSSTTVYMELSSLRSEDTAVYYCARENYGSHGGFVYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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
8EQ6 1.65 Å, PD1 signaling receptor bound to FAB Complex
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

Browse structure collections

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