7YK4: Ox40-antibody

ox40-antibody. Determined by X-ray diffraction at 2.7 Å resolution. Released 9 Aug 2023.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,418
Mol. weight: 132.82 kDa
Ligands: NAG
Released: 9 Aug 2023

Explore 7YK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YK4 contains 39 α-helices and 99 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: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	83-85	3
β-strand	113-115	3	12
β-strand	125-127	3	12
α-helix	128-129	2
β-strand	132-133	2	13
β-strand	142-143	2	13

Chain B: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	113-114	2	23
α-helix	125	1
β-strand	126-127	2	23
α-helix	128-129	2
β-strand	132-133	2	24
α-helix	139-141	3
β-strand	142-143	2	24

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	45-52	8	2
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	106-107	2	2
β-strand	111-115	5	2
α-helix	119-120	2
β-strand	121	1	3
α-helix	122-123	2
β-strand	124-128	5	4
α-helix	132-134	3
β-strand	135	1	4
β-strand	139-149	11	4
β-strand	150	1	3
β-strand	155-158	4	5
α-helix	159-161	3
β-strand	163	1	5
β-strand	167-169	3	4
α-helix	170-172	3
β-strand	173-174	2	4
β-strand	180-189	10	4
α-helix	190-192	3
β-strand	198-204	7	5
α-helix	205-207	3
β-strand	209-215	7	5

Chain I: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	14
β-strand	10-12	3	15
β-strand	18-20	3	14
β-strand	22-24	3	14
β-strand	34-39	6	15
β-strand	45-51	7	15
β-strand	58-60	3	15
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-98	7	15
β-strand	106-107	2	15
β-strand	111-115	5	15
α-helix	119-120	2
β-strand	121	1	16
α-helix	122-123	2
β-strand	124-128	5	17
α-helix	132-134	3
β-strand	135-136	2	17
β-strand	139-149	11	17
β-strand	150	1	16
β-strand	155-158	4	18
β-strand	167-169	3	17
α-helix	170-172	3
β-strand	173-174	2	17
β-strand	180-189	10	17
α-helix	190-192	3
β-strand	198-204	7	18
α-helix	205-207	3
β-strand	209-215	7	18

Chain L: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	33-38	6	7
α-helix	43-44	2
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	56	1	8
β-strand	58	1	8
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96	1
β-strand	97	1	2
β-strand	98	1	7
β-strand	102-107	6	7
β-strand	111	1	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	144-150	7	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-188	6
β-strand	191-198	8	11
β-strand	205-210	6	11

Chain M: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-14	5	7
β-strand	19-25	7	19
β-strand	33-38	6	7
α-helix	43	1
β-strand	44-49	6	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96-97	2
β-strand	98	1	7
β-strand	102-107	6	7
β-strand	111	1	20
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	154	1	22
α-helix	155	1
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	183-186	4
β-strand	191-197	7	22
β-strand	205-210	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody-H	H, I	protein	238	Homo sapiens
antibody-L	L, M	protein	214	Homo sapiens
Tumor necrosis factor receptor superfamily member 4	A, B	protein	156	Homo sapiens	P43489 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>7YK4_1 antibody-H (chains H, I)
EVQLVQSGAEVKKPGASVKVSCKASGYTFTDSYMSWVRQAPGQGLEWIGDMYPDNGDSSY
NQKFRERVTITRDTSTSTAYLELSSLRSEDTAVYYCVLAPRWYFSVWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHMDPGGSHHHHHHHH

Sequence of entity 2 (L, M), FASTA

>7YK4_2 antibody-L (chains L, M)
DIQMTQSPSSLSASVGDRVTITCRASQDISNYLNWYQQKPGKAPKLLIYYTSRLRSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQGHTLPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, B), FASTA

>7YK4_3 Tumor necrosis factor receptor superfamily member 4 (chains A, B)
LHCVGDTYPSNDRCCHECRPGNGLVSRCSRSQNTVCRPCGPGFYNDVVSSKPCKPCTWCN
LRSGSERKQLCTATQDTVCRCRAGTQPLDSYKPGVDCAPCPPGHFSPGDNQACKPWTNCT
LAGKHTLQPASNSSDAICEDRDMDPGGSHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Structural Basis of a Novel Agonistic Anti-OX40 Antibody. Zhang, J., Jiang, X., Gao, H. et al. Biomolecules (2022) 12. DOI 10.3390/biom12091209 · PubMed

Other PDB entries of the same protein (UniProt P43489 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1D0A 2.0 Å, Structure of tnf receptor associated factor 2 (TRAF2) in complex with a human OX40 peptide
2HEY 2.0 Å, Crystal structure of murine OX40L bound to human OX40
6OKM 2.1 Å, Human OX40R (TNFRSF4) bound to Fab 3C8
2HEV 2.41 Å, Crystal structure of the complex between OX40L and OX40
6OGX 2.77 Å, Ternary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2
6OKN 3.25 Å, OX40R (TNFRSF4) bound to Fab 1A7
8AG1 3.3 Å, Crystal structure of a novel OX40 antibody

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