5DK3: Pembrolizumab, a full length IgG4 antibody

Crystal Structure of Pembrolizumab, a full length IgG4 antibody. Determined by X-ray diffraction at 2.28 Å resolution. Released 18 Nov 2015.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,749
Mol. weight: 149.95 kDa
Released: 18 Nov 2015

Explore 5DK3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DK3 contains 52 α-helices and 136 β-strands across 4 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
α-helix	18	1
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
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	187-191	5
β-strand	195-201	7	6
β-strand	209-214	6	6

Chain B: 19 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	32-39	8	8
β-strand	45-51	7	8
β-strand	58-60	3	8
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-100	9	8
β-strand	107-110	4	8
β-strand	114-118	5	8
α-helix	122-123	2
β-strand	124	1	9
α-helix	125-126	2
β-strand	127-131	5	10
β-strand	142-152	11	10
β-strand	153	1	9
β-strand	158-161	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-177	2	10
β-strand	183-192	10	10
α-helix	193-195	3
β-strand	196	1	12
β-strand	199	1	12
β-strand	201-207	7	11
α-helix	208-210	3
β-strand	212-219	8	11
β-strand	239-243	5	13
α-helix	244	1
β-strand	258-266	9	13
β-strand	273-279	7	14
β-strand	282-284	3	14
β-strand	288-289	2	13
α-helix	290-292	3
β-strand	293	1	15
β-strand	300	1	13
β-strand	301	1	15
β-strand	302-307	6	13
α-helix	312-315	4
α-helix	317-318	2
β-strand	319-325	7	14
β-strand	332-336	5	14
β-strand	344	1	16
α-helix	345-346	2
β-strand	347-351	5	17
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	17
β-strand	373	1	16
β-strand	378-383	6	18
β-strand	386-387	2	18
β-strand	391-393	3	17
α-helix	394-396	3
β-strand	397-398	2	17
β-strand	404-413	10	17
α-helix	414-418	5
α-helix	421-422	2
β-strand	423-428	6	18
α-helix	433-435	3
β-strand	437-441	5	18

Chain F: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	20
β-strand	15	1	21
β-strand	17	1	21
β-strand	19-25	7	19
β-strand	30-31	2	22
β-strand	34-35	2	22
β-strand	37-42	6	20
β-strand	49-53	5	20
β-strand	57-58	2	20
α-helix	59	1
β-strand	66-71	6	19
β-strand	74-79	6	19
α-helix	84-86	3
β-strand	89-94	6	20
α-helix	100	1
β-strand	101-102	2	20
β-strand	106-110	5	20
β-strand	115	1	23
β-strand	118-122	5	24
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	24
β-strand	144	1	23
β-strand	149-154	6	25
β-strand	157-158	2	25
β-strand	163-167	5	24
α-helix	168-171	4
β-strand	177-186	10	24
α-helix	187-192	6
β-strand	195-201	7	25
β-strand	209-214	6	25

Chain G: 17 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	26
β-strand	10-12	3	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	32-39	8	27
β-strand	45-52	8	27
β-strand	57-60	4	27
β-strand	68-73	6	26
β-strand	78-83	6	26
α-helix	88-90	3
β-strand	92-100	9	27
β-strand	110	1	27
β-strand	114-118	5	27
β-strand	124	1	28
α-helix	125-126	2
β-strand	127-131	5	29
β-strand	142-152	11	29
β-strand	153	1	28
β-strand	158-161	4	30
α-helix	162-164	3
β-strand	166	1	30
β-strand	170-172	3	29
α-helix	173-175	3
β-strand	176-177	2	29
β-strand	183-192	10	29
α-helix	193-195	3
β-strand	201-207	7	30
α-helix	208-210	3
β-strand	212-219	8	30
β-strand	239-243	5	31
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	31
β-strand	274-279	6	32
β-strand	282-284	3	32
β-strand	288-289	2	31
α-helix	290-292	3
β-strand	293-294	2	31
β-strand	300-307	8	31
α-helix	310-314	5
β-strand	319-324	6	32
β-strand	332-336	5	32
α-helix	338-340	3
β-strand	344	1	33
β-strand	347-351	5	34
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	34
β-strand	373	1	33
β-strand	378-383	6	35
β-strand	386-387	2	35
β-strand	391-393	3	34
α-helix	394-396	3
β-strand	397-398	2	34
β-strand	404-413	10	34
α-helix	414-418	5
β-strand	423-428	6	35
α-helix	433-435	3
β-strand	437-441	5	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light Chain	A, F	protein	218	Homo sapiens
Heavy Chain	B, G	protein	444	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>5DK3_1 Light Chain (chains A, F)
EIVLTQSPATLSLSPGERATLSCRASKGVSTSGYSYLHWYQQKPGQAPRLLIYLASYLES
GVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDLPLTFGGGTKVEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, G), FASTA

>5DK3_2 Heavy Chain (chains B, G)
QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYMYWVRQAPGQGLEWMGGINPSNGGTNF
NEKFKNRVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTTVTVSS
ASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCPPCPAPEFLGGPSV
FLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTY
RVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTK
NQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQQG
NVFSCSVMHEALHNHYTQKSLSLS

Primary citation

Structure of full-length human anti-PD1 therapeutic IgG4 antibody pembrolizumab. Scapin, G., Yang, X., Prosise, W.W. et al. Nat Struct Mol Biol (2015) 22:953-958. DOI 10.1038/nsmb.3129 · PubMed

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5DK3 is part of these collections:

Antibodies and the immune system

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