9EHT: PD-1/retifanlimab complex

Crystal Structure of PD-1/retifanlimab complex. Determined by X-ray diffraction at 1.54 Å resolution. Released 3 Dec 2025.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,868
Mol. weight: 125.53 kDa
Released: 3 Dec 2025

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

Secondary structure: helices and β-sheets

9EHT contains 43 α-helices and 111 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: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30-31	2	3
β-strand	34-35	2	3
β-strand	37-42	6	2
β-strand	49-53	5	2
β-strand	57-58	2	2
β-strand	66-71	6	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	89-94	6	2
α-helix	100	1
β-strand	101-102	2	2
β-strand	106-110	5	2
β-strand	115	1	4
α-helix	116-117	2
β-strand	118-122	5	5
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	5
β-strand	144	1	4
β-strand	149-154	6	6
β-strand	157-158	2	6
α-helix	159	1
β-strand	163-167	5	5
α-helix	168-171	4
β-strand	177-186	10	5
α-helix	187-190	4
β-strand	195-201	7	6
β-strand	209-214	6	6

Chain B: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
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	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-100	9	8
β-strand	104-109	6	8
β-strand	113-117	5	8
α-helix	120-122	3
β-strand	123	1	9
α-helix	124-125	2
β-strand	126-130	5	10
β-strand	137-138	2	10
β-strand	141-151	11	10
β-strand	152	1	9
β-strand	157-160	4	11
α-helix	161-163	3
β-strand	165	1	11
β-strand	169-171	3	10
α-helix	172-174	3
β-strand	175-176	2	10
β-strand	182-191	10	10
α-helix	192-194	3
β-strand	201-206	6	11
α-helix	207-209	3
β-strand	211-216	6	11

Chain D: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	30-31	2	14
β-strand	34-35	2	14
β-strand	37-42	6	13
β-strand	49-53	5	13
β-strand	57-58	2	13
α-helix	59	1
β-strand	66-71	6	12
β-strand	74-79	6	12
α-helix	84-86	3
β-strand	89-94	6	13
α-helix	100	1
β-strand	101-102	2	13
β-strand	106-110	5	13
β-strand	115	1	15
α-helix	116-117	2
β-strand	118-122	5	16
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	16
β-strand	144	1	15
β-strand	149-154	6	17
β-strand	157-158	2	17
α-helix	159	1
β-strand	163-167	5	16
α-helix	168-171	4
β-strand	177-186	10	16
α-helix	187-190	4
β-strand	195-201	7	17
β-strand	209-214	6	17

Chain E: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	18
α-helix	7-9	3
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	45-52	8	19
β-strand	57-60	4	19
α-helix	62-64	3
β-strand	68-73	6	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-100	9	19
β-strand	104-109	6	19
β-strand	113-117	5	19
β-strand	123	1	20
α-helix	124-125	2
β-strand	126-130	5	21
β-strand	137-138	2	21
β-strand	141-151	11	21
β-strand	152	1	20
β-strand	157-160	4	22
α-helix	161-163	3
β-strand	169-171	3	21
α-helix	172-174	3
β-strand	175-176	2	21
β-strand	182-191	10	21
α-helix	192-194	3
β-strand	201-206	6	22
α-helix	207-209	3
β-strand	211-216	6	22

Chain F: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	23
β-strand	41-45	5	24
β-strand	50-55	6	23
β-strand	64-70	7	24
β-strand	77-82	6	24
α-helix	84-87	4
β-strand	95-99	5	23
β-strand	105-110	6	23
α-helix	115-117	3
β-strand	119-128	10	24
β-strand	132-136	5	24
α-helix	137-139	3
β-strand	140-145	6	24

Chain J: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	25
β-strand	41-45	5	26
β-strand	50-55	6	25
β-strand	64-69	6	26
β-strand	77-82	6	26
α-helix	84-87	4
β-strand	95-99	5	25
β-strand	105-110	6	25
α-helix	115-117	3
β-strand	119-128	10	26
β-strand	132-136	5	26
α-helix	137-139	3
β-strand	140-145	6	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
light chain	A, D	protein	218	Homo sapiens
heavy chain	B, E	protein	231	Homo sapiens
Programmed cell death protein 1	F, J	protein	125	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9EHT_1 light chain (chains A, D)
EIVLTQSPATLSLSPGERATLSCRASESVDNYGMSFMNWFQQKPGQPPKLLIHAASNQGS
GVPSRFSGSGSGTDFTLTISSLEPEDFAVYFCQQSKEVPYTFGGGTKVEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, E), FASTA

>9EHT_2 heavy chain (chains B, E)
QVQLVQSGAEVKKPGASVKVSCKASGYSFTSYWMNWVRQAPGQGLEWIGVIHPSDSETWL
DQKFKDRVTITVDKSTSTAYMELSSLRSEDTAVYYCAREHYGTSPFAYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Sequence of entity 3 (F, J), FASTA

>9EHT_3 Programmed cell death protein 1 (chains F, J)
DSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPED
RSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVT
ERRAE

Primary citation

Crystal Structure of PD-1/retifanlimab complex. Heo, Y.-S. To be published.

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
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
5GGS 2.0 Å, PD-1 in complex with pembrolizumab Fab

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