5B8C: Human PD-1

High resolution structure of the human PD-1 in complex with pembrolizumab Fv. Determined by X-ray diffraction at 2.15 Å resolution. Released 26 Oct 2016.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 12
Atoms: 10,858
Mol. weight: 168 kDa
Released: 26 Oct 2016

Explore 5B8C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B8C contains 33 α-helices and 140 β-strands across 12 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: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
α-helix	17-18	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
α-helix	59	1
β-strand	66-71	6	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	88-94	7	2
α-helix	100	1
β-strand	101	1	4
β-strand	102	1	2
β-strand	106-110	5	2

Chains B and H: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
β-strand	10-12	3	4
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	32-39	8	4
β-strand	45-51	7	4
β-strand	58-60	3	4
α-helix	62-64	3
β-strand	68-73	6	5
β-strand	78-83	6	5
α-helix	88-90	3
β-strand	92-100	9	4
β-strand	107-110	4	4
β-strand	114-118	5	4

Chains C and F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
β-strand	36-38	3	6
β-strand	41-45	5	7
β-strand	50-55	6	6
β-strand	60	1	7
β-strand	63-70	8	7
β-strand	76-82	7	7
β-strand	95-99	5	6
β-strand	105-110	6	6
α-helix	115-117	3
β-strand	119-127	9	7
β-strand	133-136	4	7
β-strand	140-145	6	7

Chain D: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
α-helix	17-18	2
β-strand	19-25	7	8
β-strand	30-31	2	10
β-strand	34-35	2	10
β-strand	37-42	6	9
β-strand	49-53	5	9
β-strand	57-58	2	9
α-helix	59	1
β-strand	66-71	6	8
β-strand	74-79	6	8
α-helix	84-86	3
β-strand	88-94	7	9
α-helix	100	1
β-strand	101-102	2	9
β-strand	106-110	5	9

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	11
β-strand	10-12	3	12
β-strand	18-23	6	11
β-strand	32-39	8	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-100	9	12
β-strand	107-110	4	12
β-strand	114-118	5	12

Chain G: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	15
β-strand	10-13	4	16
β-strand	19-25	7	15
β-strand	30-31	2	17
β-strand	34-35	2	17
β-strand	37-42	6	16
β-strand	49-53	5	16
β-strand	57-58	2	16
α-helix	59	1
β-strand	66-71	6	15
β-strand	74-79	6	15
α-helix	84-86	3
β-strand	89-94	6	16
α-helix	100	1
β-strand	101	1	18
β-strand	102	1	16
β-strand	106-110	5	16

Chains I and L: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
β-strand	36-38	3	20
β-strand	41-45	5	21
β-strand	50-55	6	20
β-strand	63-70	8	21
β-strand	76-82	7	21
β-strand	95-99	5	20
β-strand	105-110	6	20
α-helix	115-117	3
β-strand	119-127	9	21
β-strand	133-136	4	21
β-strand	140-145	6	21

Chain J: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	22
β-strand	10-13	4	23
β-strand	19-25	7	22
β-strand	30-31	2	24
β-strand	34-35	2	24
β-strand	37-42	6	23
β-strand	49-53	5	23
β-strand	57-58	2	23
α-helix	59	1
β-strand	66-71	6	22
β-strand	74-79	6	22
α-helix	84-86	3
β-strand	89-94	6	23
α-helix	100	1
β-strand	102	1	23
β-strand	106-110	5	23

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pembrolizumab light chain variable region (PemVL)	A, D, G, J	protein	119	Homo sapiens
Pembrolizumab heavy chain variable region (PemVH)	B, E, H, K	protein	120	Homo sapiens
Programmed cell death protein 1	C, F, I, L	protein	139	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>5B8C_1 Pembrolizumab light chain variable region (PemVL) (chains A, D, G, J)
EIVLTQSPATLSLSPGERATLSCRASKGVSTSGYSYLHWYQQKPGQAPRLLIYLASYLES
GVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDLPLTFGGGTKVEIKTSENLYFQ

Sequence of entity 2 (B, E, H, K), FASTA

>5B8C_2 Pembrolizumab heavy chain variable region (PemVH) (chains B, E, H, K)
QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYMYWVRQAPGQGLEWMGGINPSNGGTNF
NEKFKNRVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTTVTVSS

Sequence of entity 3 (C, F, I, L), FASTA

>5B8C_3 Programmed cell death protein 1 (chains C, F, I, L)
GSWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQP
GQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRA
EVPTAHPSPSPTSENLYFQ

Primary citation

High-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1. Horita, S., Nomura, Y., Sato, Y. et al. Sci Rep (2016) 6:35297-35297. DOI 10.1038/srep35297 · 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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