6OGX: Ternary complex of OX40R

Ternary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2. Determined by X-ray diffraction at 2.77 Å resolution. Released 10 Jul 2019.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,763
Mol. weight: 112.76 kDa
Ligands: NAG
Released: 10 Jul 2019

Explore 6OGX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OGX contains 43 α-helices and 108 β-strands across 5 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 C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-40	7	2
β-strand	44-52	9	2
β-strand	57-60	4	2
α-helix	65-67	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
β-strand	124-128	5	4
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	190-194	5
β-strand	198-204	7	5
α-helix	205-207	3
β-strand	209-215	7	5

Chain D: 7 helices, 21 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
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
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	98	1	7
β-strand	102-107	6	7
β-strand	111	1	8
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-154	2	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-197	7	10
β-strand	205-210	6	10

Chain G: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	36-37	2	11
β-strand	42-43	2	11
α-helix	44-45	2
β-strand	46	1	12
α-helix	47	1
β-strand	50-54	5	13
β-strand	57	1	14
β-strand	60	1	14
β-strand	63-66	4	13
α-helix	67-68	2
β-strand	71-72	2	15
β-strand	77	1	12
α-helix	80-81	2
β-strand	82-83	2	15
α-helix	84-85	2
α-helix	89-91	3
β-strand	93-97	5	16
β-strand	106-109	4	16
β-strand	110	1	17
β-strand	113-115	3	18
β-strand	125-127	3	18
α-helix	128-129	2
β-strand	132-133	2	19
β-strand	136	1	17
α-helix	139-141	3
β-strand	142-143	2	19
α-helix	144-145	2
α-helix	148-150	3
β-strand	153-156	4	20
β-strand	165-167	3	20

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	21
α-helix	7-9	3
β-strand	10-12	3	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	34-39	6	22
β-strand	45-51	7	22
β-strand	58-60	3	22
α-helix	62-64	3
β-strand	68-73	6	21
β-strand	78-83	6	21
α-helix	88-90	3
β-strand	92-98	7	22
β-strand	103	1	23
β-strand	104	1	22
β-strand	108-112	5	22
α-helix	116-117	2
β-strand	118	1	24
α-helix	119-120	2
β-strand	121-125	5	25
β-strand	137-146	10	25
β-strand	147	1	24
β-strand	152-155	4	26
α-helix	156-158	3
β-strand	164-166	3	25
α-helix	167-169	3
β-strand	170-171	2	25
β-strand	177-185	9	25
β-strand	196-201	6	26
α-helix	202-204	3
β-strand	206-211	6	26

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10-14	5	23
β-strand	19-25	7	27
β-strand	33-38	6	23
β-strand	45-49	5	23
β-strand	53-54	2	23
α-helix	55	1
β-strand	62-66	5	27
β-strand	70-75	6	27
α-helix	80-82	3
β-strand	84-90	7	23
α-helix	96	1
β-strand	97	1	22
β-strand	98	1	23
β-strand	102-107	6	23
β-strand	111	1	28
β-strand	114-118	5	29
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	29
β-strand	140	1	28
β-strand	145-150	6	30
β-strand	153-154	2	30
α-helix	155	1
β-strand	159-163	5	29
α-helix	164-167	4
β-strand	173-182	10	29
α-helix	183-187	5
β-strand	192-197	6	30
β-strand	205-209	5	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 1 Heavy Chain	C	protein	225	Homo sapiens
Fab1 Light Chain	D	protein	214	Homo sapiens
Tumor necrosis factor receptor superfamily member 4	G	protein	163	Homo sapiens	P43489 (AlphaFold model)
Fab2 heavy chain	H	protein	222	Homo sapiens
Fab2 light chain	L	protein	214	Homo sapiens

Sequence of entity 1 (C), FASTA

>6OGX_1 Fab 1 Heavy Chain (chains C)
EVQLVQSGAEVKKPGASVKVSCKASGYTFTDSYMSWVRQAPGQGLEWIGDMYPDNGDSSY
NQKFRERVTITRDTSTSTAYLELSSLRSEDTAVYYCVLAPRWYFSVWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHL

Sequence of entity 2 (D), FASTA

>6OGX_2 Fab1 Light Chain (chains D)
DIQMTQSPSSLSASVGDRVTITCRASQDISNYLNWYQQKPGKAPKLLIYYTSRLRSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQGHTLPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (G), FASTA

>6OGX_3 Tumor necrosis factor receptor superfamily member 4 (chains G)
MGSSHHHHHHSSGLVPRGSHMLHCVGDTYPSNDRCCHECRPGNGMVSRCSRSQNTVCRPC
GPGFYNDVVSSKPCKPCTWCNLRSGSERKQLCTATQDTVCRCRAGTQPLDSYKPGVDCAP
CPPGHFSPGDNQACKPWTNCTLAGKHTLQPASNSSDAICEDRD

Sequence of entity 4 (H), FASTA

>6OGX_4 Fab2 heavy chain (chains H)
EVQLVQSGAEVKKPGASVKVSCKASGYAFTNYLIEWVRQAPGQGLEWIGVINPGSGDTYY
SEKFKGRVTLTADTSTSTAYLELSSLRSEDTAVYYCARDRLDYWGQGTLVTVSSASTKGP
SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS
SVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHL

Sequence of entity 5 (L), FASTA

>6OGX_5 Fab2 light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCHASQDISSYIVWYQQKPGKSFKGLIYHGTNLESGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCVHYAQFPYTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Tetravalent biepitopic targeting enables intrinsic antibody agonism of tumor necrosis factor receptor superfamily members. Yang, Y., Yeh, S.H., Madireddi, S. et al. MAbs (2019) 11:996-1011. DOI 10.1080/19420862.2019.1625662 · 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
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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