6OKM: Human OX40R

Human OX40R (TNFRSF4) bound to Fab 3C8. Determined by X-ray diffraction at 2.1 Å resolution. Released 28 Aug 2019.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,432
Mol. weight: 64.81 kDa
Released: 28 Aug 2019

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

Secondary structure: helices and β-sheets

6OKM contains 24 α-helices and 58 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 H: 8 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	34-39	6	2
β-strand	46-51	6	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	103	1	3
β-strand	104	1	2
β-strand	108-112	5	2
β-strand	118	1	4
α-helix	119-120	2
β-strand	121-125	5	5
β-strand	133	1	5
β-strand	136-146	11	5
β-strand	147	1	4
β-strand	152-155	4	6
α-helix	156-158	3
β-strand	165-166	2	5
α-helix	167-169	3
β-strand	170-171	2	5
β-strand	177-186	10	5
α-helix	187-190	4
β-strand	195-201	7	6
α-helix	202-204	3
β-strand	206-212	7	6

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	3
β-strand	19-25	7	7
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	3
α-helix	96	1
β-strand	98	1	3
β-strand	102-106	5	3
β-strand	111	1	8
α-helix	112-113	2
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
α-helix	155	1
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 R: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	35-37	3	11
β-strand	42-44	3	11
β-strand	46	1	12
α-helix	47	1
β-strand	50-54	5	13
α-helix	61-62	2
β-strand	63-66	4	13
α-helix	67-68	2
β-strand	71-72	2	14
β-strand	77	1	12
α-helix	80-81	2
β-strand	82-83	2	14
α-helix	84-85	2
α-helix	89-91	3
β-strand	93-97	5	15
β-strand	100	1	16
β-strand	103	1	16
β-strand	106-109	4	15
β-strand	113-115	3	17
β-strand	125-127	3	17
α-helix	139-141	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 3C8 Heavy Chain	H	protein	222	Homo sapiens
Fab 3C8 light chain	L	protein	214	Homo sapiens
Tumor necrosis factor receptor superfamily member 4	R	protein	163	Homo sapiens	P43489 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6OKM_1 Fab 3C8 Heavy Chain (chains H)
EVQLVQSGAEVKKPGASVKVSCKASGYAFTNYLIEWVRQAPGQGLEWIGVINPGSGDTYY
SEKFKGRVTLTADTSTSTAYLELSSLRSEDTAVYYCARDRLDYWGQGTLVTVSSASTKGP
SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS
SVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHL

Sequence of entity 2 (L), FASTA

>6OKM_2 Fab 3C8 light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCHASQDISSYIVWYQQKPGKSFKGLIYHGTNLESGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCVHYAQFPYTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (R), FASTA

>6OKM_3 Tumor necrosis factor receptor superfamily member 4 (chains 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
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
8AG1 3.3 Å, Crystal structure of a novel OX40 antibody

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