7R58: GPVI-glenzocimab complex

Crystal structure of the GPVI-glenzocimab complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 16 Nov 2022.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 5,638
Mol. weight: 71.61 kDa
Ligands: SCN
Released: 16 Nov 2022

Explore 7R58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R58 contains 27 α-helices and 65 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	4	1
β-strand	5	1	1
α-helix	6-8	3
β-strand	9-13	5	2
β-strand	17-19	3	3
β-strand	24-29	6	2
β-strand	36-41	6	4
β-strand	47-48	2	4
β-strand	52-55	4	2
α-helix	60-62	3
β-strand	64-72	9	4
β-strand	75-76	2	4
β-strand	77	1	1
α-helix	78-82	5
β-strand	83-85	3	4
β-strand	86-88	3	3
α-helix	92-94	3
β-strand	95-99	5	5
β-strand	103-104	2	6
β-strand	110-115	6	5
β-strand	122-127	6	7
β-strand	134	1	7
β-strand	142-147	6	5
α-helix	152-154	3
β-strand	156-164	9	7
β-strand	167-171	5	7
α-helix	172-177	6
β-strand	178-180	3	7
β-strand	181-182	2	6

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
α-helix	7-9	3
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	32-39	8	9
β-strand	45-51	7	9
β-strand	58-60	3	9
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-100	9	9
β-strand	110	1	9
β-strand	114-118	5	9
α-helix	122-123	2
β-strand	124	1	10
α-helix	125-126	2
β-strand	127-131	5	11
β-strand	144-153	10	11
β-strand	154	1	10
β-strand	159-162	4	12
α-helix	163-165	3
β-strand	167	1	12
β-strand	171-173	3	11
α-helix	174-176	3
β-strand	177-178	2	11
β-strand	184-192	9	11
α-helix	194-196	3
β-strand	203-208	6	12
α-helix	209-211	3
β-strand	213-218	6	12
α-helix	221-223	3

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	38-43	6	14
β-strand	50-54	5	14
β-strand	58-59	2	14
α-helix	60	1
β-strand	67-72	6	13
β-strand	75-80	6	13
α-helix	85-87	3
β-strand	89-95	7	14
α-helix	101	1
β-strand	102-103	2	14
β-strand	107-112	6	14
β-strand	116	1	15
α-helix	117-118	2
β-strand	119-123	5	16
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	16
β-strand	145	1	15
β-strand	150-155	6	17
β-strand	158-159	2	17
α-helix	160	1
β-strand	164-168	5	16
α-helix	169-172	4
β-strand	178-187	10	16
α-helix	188-192	5
β-strand	196-202	7	17
β-strand	210-215	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet glycoprotein VI	A	protein	204	Homo sapiens	Q9HCN6 (AlphaFold model)
Fab heavy chain	H	protein	227	Mus musculus
Fab light chain	L	protein	219	Mus musculus

Sequence of entity 1 (A), FASTA

>7R58_1 Platelet glycoprotein VI (chains A)
HHHHHHSSGVDLGTENLYFQSQSGPLPKPSLQALPSSLVPLEKPVTLRCQGPPGVDLYRL
EKLSSSRYQDQAVLFIPAMKRSLAGRYRCSYQNGSLWSLPSDQLELVATGVFAKPSLSAQ
PGPAVSSGGDVTLQCQTRYGFDQFALYKEGDPAPYKNPERWYRASFPIITVTAAHSGTYR
CYSFSSRDPYLWSAPSDPLELVVT

Sequence of entity 2 (H), FASTA

>7R58_2 Fab heavy chain (chains H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYNMHWVRQAPGQGLEWMGGIYPGNGDTSY
NQKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARGTVVGDWYFDVWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 3 (L), FASTA

>7R58_3 Fab light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRSSQSLENSNGNTYLNWYQQKPGKAPKLLIYRVSNRF
SGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCLQLTHVPWTFGQGTKVEITRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
SCN	Thiocyanate ion	C N S	1

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

Primary citation

Targeting platelet GPVI with glenzocimab: a novel mechanism for inhibition. Billiald, P., Slater, A., Welin, M. et al. Blood Adv (2023) 7:1258-1268. DOI 10.1182/bloodadvances.2022007863 · PubMed

Other PDB entries of the same protein (UniProt Q9HCN6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5OU7 1.9 Å, Crystal structure of the Glycoprotein VI loop truncation mutant PAVS-PAPYKN
2GI7 2.4 Å, Crystal structure of human platelet Glycoprotein VI (GPVI)
5OU8 2.5 Å, Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)5
5OU9 2.5 Å, Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3
7NMU 2.5 Å, Crystal structure of human platelet glycoprotein VI in complex with an inhibitory…

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