6O8D: Anti-CD28xCD3 CODV Fab

Anti-CD28xCD3 CODV Fab bound to CD28. Determined by X-ray diffraction at 3.55 Å resolution. Released 20 Nov 2019.

Method: X-ray diffraction
Resolution: 3.55 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,183
Mol. weight: 91.25 kDa
Ligands: NAG
Released: 20 Nov 2019

Explore 6O8D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O8D contains 18 α-helices and 93 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 C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	1
β-strand	29	1	2
α-helix	32-34	3
β-strand	35-42	8	1
β-strand	53-57	5	3
β-strand	63-69	7	3
β-strand	77-79	3	3
β-strand	85	1	1
β-strand	88-90	3	1
β-strand	94-100	7	1
β-strand	109-112	4	3
β-strand	131-132	2	3
β-strand	133	1	2

Chain H: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	18
β-strand	10-11	2	19
β-strand	18-25	8	18
β-strand	34	1	20
β-strand	35	1	21
β-strand	37-39	3	19
β-strand	41	1	22
β-strand	43	1	22
β-strand	49	1	23
β-strand	50	1	21
α-helix	53-55	3
β-strand	60	1	23
α-helix	62-64	3
β-strand	70-73	4	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-95	4	19
β-strand	97-99	3	24
α-helix	100	1
β-strand	107-110	4	24
β-strand	114-117	4	19
β-strand	125	1	25
β-strand	126-128	3	26
β-strand	131-133	3	27
β-strand	139-140	2	26
β-strand	142-144	3	26
α-helix	150-152	3
β-strand	154-160	7	27
β-strand	166-172	7	27
β-strand	181-183	3	27
α-helix	185-187	3
β-strand	192-196	5	26
α-helix	197-199	3
β-strand	201-206	6	26
α-helix	211-213	3
β-strand	215-223	9	27
β-strand	229-231	3	27
β-strand	233	1	25
β-strand	236-240	5	27
β-strand	248	1	28
α-helix	249-250	2
β-strand	251-255	5	29
β-strand	266-276	11	29
β-strand	277	1	28
β-strand	282-285	4	30
β-strand	294-296	3	29
α-helix	297-299	3
β-strand	300-301	2	29
β-strand	307-316	10	29
β-strand	326-331	6	30
β-strand	336-341	6	30

Chain L: 7 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	4
β-strand	10-12	3	5
β-strand	19-24	6	4
β-strand	30	1	6
β-strand	36	1	6
β-strand	40-43	4	7
β-strand	49-53	5	7
β-strand	59	1	7
α-helix	60	1
β-strand	67-72	6	4
β-strand	75-80	6	4
α-helix	85-87	3
β-strand	90-93	4	7
β-strand	94-95	2	8
α-helix	101	1
β-strand	102-103	2	8
β-strand	107	1	7
β-strand	108-110	3	5
β-strand	123-124	2	9
β-strand	129-131	3	10
β-strand	138-141	4	11
β-strand	143-144	2	9
β-strand	153-156	4	12
β-strand	164-167	4	12
β-strand	173	1	12
β-strand	181-184	4	11
β-strand	191-194	4	11
α-helix	199-201	3
β-strand	204-205	2	10
β-strand	206-208	3	12
β-strand	221-224	4	10
β-strand	235	1	13
β-strand	240-242	3	14
α-helix	246-249	4
β-strand	253-259	7	14
β-strand	263	1	15
β-strand	264	1	13
β-strand	269-272	4	16
β-strand	273-274	2	17
β-strand	277-278	2	17
β-strand	283-287	5	14
α-helix	289-291	3
β-strand	297	1	15
β-strand	299-306	8	14
α-helix	307-310	4
β-strand	315-321	7	16
β-strand	329-334	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell-specific surface glycoprotein CD28	C	protein	126	Homo sapiens	P10747 (AlphaFold model)
Anti-CD28xCD3 CODV Fab Light chain	L	protein	338	Homo sapiens
Anti-CD28xCD3 CODV Fab Heavy chain	H	protein	358	Homo sapiens

Sequence of entity 1 (C), FASTA

>6O8D_1 T-cell-specific surface glycoprotein CD28 (chains C)
NKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQV
YSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKHH
HHHHHH

Sequence of entity 2 (L), FASTA

>6O8D_2 Anti-CD28xCD3 CODV Fab Light chain (chains L)
DIVMTQTPLSLSVTPGQPASISCKSSQSLVHNNANTYLSWYLQKPGQSPQSLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCGQGTQYPFTFGSGTKVEIKGQPKAAPD
IQMTQSPSSLSASVGDRVTITCQASQNIYVWLNWYQQKPGKAPKLLIYKASNLHTGVPSR
FSGSGSGTDFTLTISSLQPEDIATYYCQQGQTYPYTFGQGTKLEIKTKGPSRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>6O8D_3 Anti-CD28xCD3 CODV Fab Heavy chain (chains H)
QVQLVQSGAEVVKPGASVKVSCKASGYTFTSYYIHWVRQAPGQGLEWIGSIYPGNVNTNY
AQKFQGRATLTVDTSISTAYMELSRLRSDDTAVYYCTRSHYGLDWNFDVWGKGTTVTVSS
SQVQLVESGGGVVQPGRSLRLSCAASGFTFTKAWMHWVRQAPGKQLEWVAQIKDKSNSYA
TYYADSVKGRFTISRDDSKNTLYLQMNSLRAEDTAVYYCRGVYYALSPFDYWGQGTLVTV
SSRTASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTHHHHHH

Ligands and cofactors

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

Primary citation

Trispecific antibodies enhance the therapeutic efficacy of tumor-directed T cells through T cell receptor co-stimulation. Wu, L., Seung, E., Xu, L. et al. To be published. DOI 10.1038/s43018-019-0004-z

Other PDB entries of the same protein (UniProt P10747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GJI 0.9 Å, PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex
5AUL 1.1 Å, PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex
5GJH 1.2 Å, Gads SH2 domain/CD28-derived peptide complex
3WA4 1.35 Å, Grb2 SH2 domain/CD28-derived peptide complex
7PPN 1.9 Å, SHP2 catalytic domain in complex with CD28 (183-198) phosphopeptide (pTyr-191, p-Thr-195)
1YJD 2.7 Å, Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody…
8S6Z 3.05 Å, CD28 in complex with the antibody Fab fragment AI3
7VU5 Structure of the transmembrane domain of the CD28 dimer
8W2V Solution Structure of the CD28 hinge used in chimeric antigen receptor (CAR) T-cells

Browse structure collections

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