5GGS: PD-1

PD-1 in complex with pembrolizumab Fab. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,239
Mol. weight: 125.78 kDa
Released: 9 Nov 2016

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

Secondary structure: helices and β-sheets

5GGS contains 43 α-helices and 114 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: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	10-12	3	2
β-strand	18-23	6	1
α-helix	26-31	6
β-strand	32-39	8	2
β-strand	46-51	6	2
β-strand	58-60	3	2
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	107-110	4	2
β-strand	114-118	5	2
α-helix	121-123	3
β-strand	124	1	3
α-helix	125-126	2
β-strand	127-131	5	4
α-helix	135-137	3
β-strand	138-139	2	4
β-strand	142-152	11	4
β-strand	153	1	3
β-strand	158-161	4	5
α-helix	162-164	3
β-strand	166	1	5
β-strand	170-172	3	4
α-helix	173-175	3
β-strand	176-177	2	4
β-strand	183-192	10	4
α-helix	193-197	5
β-strand	202-207	6	5
α-helix	208-210	3
β-strand	212-217	6	5

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	30-31	2	8
β-strand	34-35	2	8
β-strand	37-42	6	7
β-strand	49-53	5	7
β-strand	57-58	2	7
α-helix	59	1
β-strand	66-71	6	6
β-strand	74-79	6	6
α-helix	84-86	3
β-strand	89-94	6	7
α-helix	100	1
β-strand	101-102	2	7
β-strand	106-110	5	7
β-strand	115	1	9
α-helix	116-117	2
β-strand	118-122	5	10
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	10
β-strand	144	1	9
β-strand	149-154	6	11
β-strand	157-158	2	11
α-helix	159	1
β-strand	163-167	5	10
α-helix	168-171	4
β-strand	177-186	10	10
α-helix	187-190	4
β-strand	195-201	7	11
β-strand	209-214	6	11

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	32-39	8	13
β-strand	46-51	6	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-100	9	13
β-strand	109-110	2	13
β-strand	114-118	5	13
β-strand	124	1	14
α-helix	125-126	2
β-strand	127-131	5	15
α-helix	135-137	3
β-strand	138-139	2	15
β-strand	142-152	11	15
β-strand	153	1	14
β-strand	158-161	4	16
α-helix	162-164	3
β-strand	166	1	16
β-strand	170-172	3	15
α-helix	173-175	3
β-strand	176-177	2	15
β-strand	183-192	10	15
α-helix	193-196	4
β-strand	202-207	6	16
α-helix	208-210	3
β-strand	212-217	6	16

Chain D: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	30-31	2	19
β-strand	34-35	2	19
β-strand	37-42	6	18
β-strand	49-53	5	18
β-strand	57-58	2	18
α-helix	59	1
β-strand	66-71	6	17
β-strand	74-79	6	17
α-helix	84-86	3
β-strand	89-94	6	18
α-helix	100	1
β-strand	101-102	2	18
β-strand	106-110	5	18
β-strand	115	1	20
α-helix	116-117	2
β-strand	118-122	5	21
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	21
β-strand	144	1	20
β-strand	149-154	6	22
β-strand	157-158	2	22
α-helix	159	1
β-strand	163-167	5	21
α-helix	168-171	4
β-strand	177-186	10	21
α-helix	187-190	4
β-strand	195-201	7	22
β-strand	209-214	6	22

Chain Y: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	36-38	3	23
β-strand	41-45	5	24
β-strand	46	1	25
β-strand	48	1	25
β-strand	50-55	6	23
β-strand	63-70	8	24
β-strand	76-82	7	24
β-strand	95-99	5	23
β-strand	105-110	6	23
α-helix	115-117	3
β-strand	119-127	9	24
β-strand	134-136	3	24
β-strand	140-145	6	24

Chain Z: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	36-38	3	26
β-strand	41-42	2	27
β-strand	49-55	7	26
β-strand	63-70	8	27
β-strand	76-82	7	27
β-strand	95-99	5	26
β-strand	105-111	7	26
α-helix	115-117	3
β-strand	119-127	9	27
β-strand	134-136	3	27
α-helix	137-139	3
β-strand	140-142	3	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain	A, C	protein	232	Homo sapiens
light chain	B, D	protein	218	Homo sapiens
Programmed cell death protein 1	Y, Z	protein	123	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5GGS_1 heavy chain (chains A, C)
QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYMYWVRQAPGQGLEWMGGINPSNGGTNF
NEKFKNRVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTTVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Sequence of entity 2 (B, D), FASTA

>5GGS_2 light chain (chains B, D)
EIVLTQSPATLSLSPGERATLSCRASKGVSTSGYSYLHWYQQKPGQAPRLLIYLASYLES
GVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDLPLTFGGGTKVEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (Y, Z), FASTA

>5GGS_3 Programmed cell death protein 1 (chains Y, Z)
DSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPED
RSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVT
ERR

Primary citation

Structural basis of checkpoint blockade by monoclonal antibodies in cancer immunotherapy. Lee, J.Y., Lee, H.T., Shin, W. et al. Nat Commun (2016) 7:13354-13354. DOI 10.1038/ncomms13354 · 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 more

5GGS is part of these collections:

Antibodies and the immune system

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