6OKN: OX40R

OX40R (TNFRSF4) bound to Fab 1A7. Determined by X-ray diffraction at 3.25 Å resolution. Released 10 Jul 2019.

Method: X-ray diffraction
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,927
Mol. weight: 131.59 kDa
Released: 10 Jul 2019

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

Secondary structure: helices and β-sheets

6OKN contains 40 α-helices and 102 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
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
α-helix	108	1
β-strand	111-115	5	2
α-helix	119-120	2
β-strand	121	1	3
β-strand	124-128	5	4
α-helix	131-134	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 B: 7 helices, 23 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
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	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	145-150	6	11
β-strand	153-154	2	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain C: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-51	7	13
β-strand	60	1	13
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-98	7	13
β-strand	106-107	2	13
α-helix	108	1
β-strand	111-115	5	13
α-helix	119-120	2
β-strand	121	1	14
β-strand	124-128	5	15
β-strand	139-149	11	15
β-strand	150	1	14
β-strand	155-158	4	16
α-helix	159-161	3
β-strand	163	1	16
β-strand	167-169	3	15
α-helix	170-172	3
β-strand	173-174	2	15
β-strand	180-189	10	15
α-helix	190-192	3
β-strand	198-204	7	16
α-helix	205-207	3
β-strand	209-215	7	16

Chain D: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-14	5	18
β-strand	19-25	7	17
β-strand	33-38	6	18
α-helix	43-44	2
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-90	7	18
α-helix	96	1
β-strand	98	1	18
β-strand	102-107	6	18
β-strand	111	1	19
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	145-150	6	21
β-strand	153-154	2	21
β-strand	159-163	5	20
β-strand	173-182	10	20
α-helix	183-187	5
β-strand	191-197	7	21
β-strand	205-210	6	21

Chain E: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	93-97	5	22
β-strand	106-109	4	22
β-strand	113-115	3	23
β-strand	125-127	3	23
α-helix	128-129	2
β-strand	132-133	2	24
β-strand	142-143	2	24
α-helix	144-145	2
α-helix	148-150	3
α-helix	153-154	2

Chain R: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	71-72	2	25
β-strand	82-83	2	25
α-helix	84-85	2
β-strand	93-97	5	26
α-helix	104-105	2
β-strand	106-109	4	26
α-helix	110	1
β-strand	113-115	3	27
β-strand	125-127	3	27
α-helix	128-129	2
β-strand	132-133	2	28
β-strand	142-143	2	28
α-helix	144	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 1A7 heavy chain	A, C	protein	225	Homo sapiens
Fab 1A7 light chain	B, D	protein	214	Homo sapiens
Tumor necrosis factor receptor superfamily member 4	E, R	protein	163	Homo sapiens	P43489 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6OKN_1 Fab 1A7 heavy chain (chains A, C)
EVQLVQSGAEVKKPGASVKVSCKASGYTFTDSYMSWVRQAPGQGLEWIGDMYPDNGDSSY
NQKFRERVTITRDTSTSTAYLELSSLRSEDTAVYYCVLAPRWYFSVWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHL

Sequence of entity 2 (B, D), FASTA

>6OKN_2 Fab 1A7 light chain (chains B, D)
DIQMTQSPSSLSASVGDRVTITCRASQDISNYLNWYQQKPGKAPKLLIYYTSRLRSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQGHTLPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E, R), FASTA

>6OKN_3 Tumor necrosis factor receptor superfamily member 4 (chains E, R)
MGSSHHHHHHSSGLVPRGSHMLHCVGDTYPSNDRCCHECRPGNGMVSRCSRSQNTVCRPC
GPGFYNDVVSSKPCKPCTWCNLRSGSERKQLCTATQDTVCRCRAGTQPLDSYKPGVDCAP
CPPGHFSPGDNQACKPWTNCTLAGKHTLQPASNSSDAICEDRD

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
6OGX 2.77 Å, Ternary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2
8AG1 3.3 Å, Crystal structure of a novel OX40 antibody

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