7VUX: Complex structure of PD1 and 609A-Fab

Complex structure of PD1 and 609A-Fab. Determined by X-ray diffraction at 1.64 Å resolution. Released 17 Nov 2021.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,410
Mol. weight: 63.18 kDa
Ligands: MG, THR
Released: 17 Nov 2021

Explore 7VUX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VUX contains 21 α-helices and 56 β-strands across 3 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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	1
β-strand	41-45	5	2
β-strand	50-55	6	1
β-strand	63-70	8	2
β-strand	76-82	7	2
β-strand	95-99	5	1
β-strand	105-110	6	1
α-helix	115-117	3
β-strand	119-127	9	2
β-strand	131	1	3
β-strand	133-136	4	2
α-helix	137-139	3
β-strand	140-145	6	2
α-helix	146-151	6

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-12	2	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	34-39	6	6
β-strand	46-51	6	6
β-strand	58-59	2	6
β-strand	68-73	6	4
α-helix	74-76	3
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-100	9	6
β-strand	103-107	5	6
β-strand	111-113	3	6
β-strand	114-115	2	5
β-strand	121	1	7
α-helix	122-123	2
β-strand	124-128	5	8
β-strand	139-149	11	8
β-strand	150	1	7
β-strand	155-158	4	9
α-helix	159-161	3
β-strand	163	1	9
β-strand	167-169	3	8
α-helix	170-172	3
β-strand	173-174	2	8
β-strand	180-189	10	8
α-helix	190-193	4
β-strand	199-204	6	9
α-helix	205-207	3
β-strand	209-214	6	9

Chain L: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	10
β-strand	10-13	4	6
β-strand	19-25	7	10
β-strand	33-38	6	6
β-strand	45-49	5	6
β-strand	53-54	2	6
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	84-90	7	6
β-strand	93	1	3
α-helix	96	1
β-strand	97-98	2	6
β-strand	102-106	5	6
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	153-154	2	13
α-helix	155	1
β-strand	159-163	5	12
α-helix	164-167	4
β-strand	173-182	10	12
α-helix	183-186	4
β-strand	191-197	7	13
β-strand	205-210	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death protein 1	A	protein	136	Homo sapiens	Q15116 (AlphaFold model)
Heavy chain of Fab fragment	H	protein	216	Homo sapiens
Light chain of Fab fragment	L	protein	214	Homo sapiens

Sequence of entity 1 (A), FASTA

>7VUX_1 Programmed cell death protein 1 (chains A)
MWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPG
QDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAE
VPTAHPSPSPENLYFQ

Sequence of entity 2 (H), FASTA

>7VUX_2 Heavy chain of Fab fragment (chains H)
EVKLVESGGGLVQPGGSLRLSCAASGFAFSSYDMSWVRQAPGKRLEWVATISGGGRYTYY
PDTVKGRFTISRDNAKNSHYLQMNSLRAEDTAVYFCASPYGGYFDVWGQGTLVTVSSAST
KGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE

Sequence of entity 3 (L), FASTA

>7VUX_3 Light chain of Fab fragment (chains L)
EIVLTQSPATLSLSPGERATLSCRASQSISNFLHWYQQKPGQAPRLLIKYASQSISGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYFCQQSNSWPHTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
THR	Threonine	C4 H9 N O3	1

Water and common crystallization additives (CL, PEG, EDO, GOL) are not listed.

Primary citation

A strategy for the efficient construction of anti-PD1-based bispecific antibodies with desired IgG-like properties. Zhao, J., Jiang, L., Yang, H. et al. MAbs (2022) 14:2044435-2044435. DOI 10.1080/19420862.2022.2044435 · 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
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

Browse structure collections

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