8AG1: Novel OX40 antibody

Crystal structure of a novel OX40 antibody. Determined by X-ray diffraction at 3.3 Å resolution. Released 19 Jul 2023.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,038
Mol. weight: 133.86 kDa
Ligands: NAG
Released: 19 Jul 2023

Explore 8AG1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AG1 contains 34 α-helices and 121 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: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	48	1	38
β-strand	50	1	38
β-strand	66	1	38
β-strand	72	1	39
β-strand	82	1	39
β-strand	95	1	40
β-strand	107	1	40
α-helix	127-128	2

Chain A: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	35-37	3	31
β-strand	42-44	3	31
α-helix	45	1
β-strand	46	1	32
α-helix	47	1
β-strand	50-54	5	33
β-strand	63-66	4	33
β-strand	71-72	2	34
β-strand	77	1	32
α-helix	81	1
β-strand	82-83	2	34
α-helix	84-85	2
β-strand	93-97	5	35
α-helix	104-105	2
β-strand	106-109	4	35
β-strand	113-115	3	36
β-strand	125-127	3	36
α-helix	128-129	2
β-strand	132-133	2	37
α-helix	139-141	3
β-strand	142-143	2	37
α-helix	144-145	2
α-helix	147-150	4

Chain h: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	18-25	8	11
β-strand	35-41	7	13
β-strand	48-56	9	13
β-strand	58-63	6	13
α-helix	65-67	3
β-strand	71-72	2	11
β-strand	75-76	2	11
β-strand	81-86	6	11
α-helix	91-93	3
β-strand	95-103	9	13
β-strand	105-109	5	13
β-strand	113-115	3	13
β-strand	116-117	2	12
α-helix	121-122	2
β-strand	123	1	14
β-strand	126-130	5	15
β-strand	141-151	11	15
β-strand	152	1	14
β-strand	157-160	4	16
β-strand	170-171	2	15
α-helix	172-174	3
β-strand	175-176	2	15
β-strand	182-191	10	15
β-strand	200-206	7	16
β-strand	211-217	7	16

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	17-25	9	6
β-strand	35-42	8	3
β-strand	46-56	11	3
β-strand	58-63	6	3
α-helix	65-67	3
β-strand	71-72	2	6
β-strand	75-76	2	6
β-strand	81-87	7	6
α-helix	91-93	3
β-strand	95-102	8	3
β-strand	106-109	4	3
β-strand	113-115	3	3
β-strand	116-117	2	7
β-strand	123	1	8
β-strand	126-130	5	9
α-helix	131-133	3
β-strand	141-151	11	9
β-strand	152	1	8
β-strand	157-160	4	10
β-strand	169-171	3	9
α-helix	172-174	3
β-strand	175-176	2	9
β-strand	182-191	10	9
α-helix	193-196	4
β-strand	200-206	7	10
α-helix	207-209	3
β-strand	211-217	7	10

Chain l: 5 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	17
β-strand	12-13	2	18
β-strand	19-22	4	19
β-strand	24-25	2	17
β-strand	30	1	20
β-strand	35	1	21
β-strand	36-37	2	22
β-strand	38	1	23
β-strand	45-46	2	22
β-strand	48-49	2	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-65	4	19
β-strand	68	1	20
β-strand	72-75	4	19
α-helix	80-82	3
β-strand	85	1	23
β-strand	86	1	25
β-strand	88	1	21
β-strand	89	1	26
β-strand	100	1	26
β-strand	104	1	25
β-strand	107-108	2	18
β-strand	113	1	27
β-strand	116-120	5	28
α-helix	121-123	3
α-helix	126-129	4
β-strand	132-141	10	28
β-strand	142	1	27
β-strand	147-148	2	29
β-strand	151	1	30
β-strand	156	1	30
β-strand	161-162	2	28
β-strand	165	1	28
β-strand	175-183	9	28
α-helix	185-190	6
β-strand	193-199	7	29
β-strand	207-212	6	29

Chain L: 9 helices, 21 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	33-38	6	2
α-helix	43-44	2
β-strand	45-48	4	2
β-strand	54	1	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
β-strand	99	1	3
β-strand	104-108	5	2
α-helix	113-115	3
β-strand	116-120	5	4
α-helix	121-123	3
α-helix	124-129	6
β-strand	131-141	11	4
β-strand	149-152	4	5
β-strand	156	1	5
β-strand	161-162	2	4
β-strand	165	1	4
α-helix	166-169	4
β-strand	175-177	3	4
β-strand	180-184	5	4
α-helix	185-190	6
β-strand	193-198	6	5
β-strand	207-212	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Novel OX40 antibody light chain	L, l	protein	216	Homo sapiens
Novel OX40 antibody heavy chain	H, h	protein	240	Homo sapiens
Tumor necrosis factor receptor superfamily member 4	A, a	protein	156	Homo sapiens	P43489 (AlphaFold model)

Sequence of entity 1 (L, l), FASTA

>8AG1_1 Novel OX40 antibody light chain (chains L, l)
EIVLTQSPATLSLSPGERATLSCRASQSVGSYLAWYQQKPGQAPRLLIYDASNRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPGYTFGQGTKLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H, h), FASTA

>8AG1_2 Novel OX40 antibody heavy chain (chains H, h)
QVQLQQSGPGLVKPSQTLSLTCAISGDSVSSNSVSWDWIRQSPSRGLEWLGRTYYRSKWY
NEYAVSVESRITINPDTSKNQFSLQLNSVTPEDTAIYFCVRNDYFFDLWGRGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHMDPGGSHHHHHHHH

Sequence of entity 3 (A, a), FASTA

>8AG1_3 Tumor necrosis factor receptor superfamily member 4 (chains A, a)
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
7YK4 2.7 Å, ox40-antibody
6OGX 2.77 Å, Ternary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2
6OKN 3.25 Å, OX40R (TNFRSF4) bound to Fab 1A7

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