8GY5: Cemiplimab Fab

High-resolution structure of the cemiplimab Fab in complex with PD-1. Determined by X-ray diffraction at 1.98 Å resolution. Released 4 Oct 2023.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,854
Mol. weight: 123.7 kDa
Released: 4 Oct 2023

Explore 8GY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GY5 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: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	107	1	3
β-strand	111-113	3	3
β-strand	114-115	2	2
α-helix	119-120	2
β-strand	121	1	4
α-helix	122-123	2
β-strand	124-128	5	5
β-strand	139-149	11	5
β-strand	150	1	4
β-strand	155-158	4	6
α-helix	159-161	3
β-strand	163	1	6
β-strand	167-169	3	5
α-helix	170-172	3
β-strand	173-174	2	5
β-strand	180-189	10	5
α-helix	190-192	3
β-strand	198-204	7	6
α-helix	205-207	3
β-strand	209-215	7	6

Chain B: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
β-strand	93	1	9
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-155	3	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-197	7	12
β-strand	205-210	6	12

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	46-51	6	17
β-strand	58-60	3	17
α-helix	62-64	3
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-99	8	17
β-strand	107	1	17
β-strand	111-113	3	17
β-strand	114-115	2	16
α-helix	118-120	3
β-strand	121	1	18
α-helix	122-123	2
β-strand	124-128	5	19
β-strand	139-149	11	19
β-strand	150	1	18
β-strand	155-158	4	20
α-helix	159-161	3
β-strand	163	1	20
β-strand	167-169	3	19
α-helix	170-172	3
β-strand	173-174	2	19
β-strand	180-189	10	19
α-helix	190-192	3
β-strand	199-204	6	20
α-helix	205-207	3
β-strand	209-214	6	20

Chain L: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	21
β-strand	10-13	4	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	44-49	6	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-66	5	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	85-90	6	22
β-strand	93	1	23
α-helix	96	1
β-strand	97-98	2	22
β-strand	102-106	5	22
β-strand	111	1	24
α-helix	112-113	2
β-strand	114-118	5	25
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	25
β-strand	140	1	24
β-strand	145-150	6	26
β-strand	153-154	2	26
α-helix	155	1
β-strand	159-163	5	25
α-helix	164-167	4
β-strand	173-182	10	25
α-helix	183-186	4
β-strand	191-197	7	26
β-strand	205-210	6	26

Chain P: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
β-strand	36-38	3	27
β-strand	41-45	5	28
β-strand	50-55	6	27
β-strand	63-70	8	28
β-strand	76-82	7	28
α-helix	84-85	2
β-strand	95-99	5	27
β-strand	105-110	6	27
α-helix	115-117	3
β-strand	119-127	9	28
β-strand	131	1	23
β-strand	133-136	4	28
β-strand	140-145	6	28

Chain Q: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
β-strand	36-38	3	13
β-strand	41-45	5	14
β-strand	50-55	6	13
β-strand	63-70	8	14
β-strand	76-82	7	14
β-strand	95-99	5	13
β-strand	105-110	6	13
α-helix	115-117	3
β-strand	119-127	9	14
β-strand	131	1	9
β-strand	133-136	4	14
α-helix	137-139	3
β-strand	140-145	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain	A, H	protein	229	Homo sapiens
light chain	B, L	protein	214	Homo sapiens
Programmed cell death protein 1	P, Q	protein	125	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>8GY5_1 heavy chain (chains A, H)
EVQLLESGGVLVQPGGSLRLSCAASGFTFSNFGMTWVRQAPGKGLEWVSGISGGGRDTYF
ADSVKGRFTISRDNSKNTLYLQMNSLKGEDTAVYYCVKWGNIYFDYWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Sequence of entity 2 (B, L), FASTA

>8GY5_2 light chain (chains B, L)
DIQMTQSPSSLSASVGDSITITCRASLSINTFLNWYQQKPGKAPNLLIYAASSLHGGVPS
RFSGSGSGTDFTLTIRTLQPEDFATYYCQQSSNTPFTFGPGTVVDFRRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (P, Q), FASTA

>8GY5_3 Programmed cell death protein 1 (chains P, Q)
DSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPED
RSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVT
ERRAE

Primary citation

High-resolution structure of the cemiplimab Fab in complex with PD-1. Heo, Y.-S., Jeong, T.J. 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
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
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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