8F0L: ADI-26906 Fab Heavy Chain

Crystal Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed with ADI-26906 FAB. Determined by X-ray diffraction at 1.81 Å resolution. Released 29 Mar 2023.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,610
Mol. weight: 99.68 kDa
Released: 29 Mar 2023

Explore 8F0L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F0L contains 36 α-helices and 89 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: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-52	8	13
β-strand	57-59	3	13
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	103	1	13
β-strand	107-111	5	13
β-strand	121	1	14
α-helix	122-123	2
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	167-169	3	15
α-helix	170-172	3
β-strand	173-174	2	15
β-strand	180-189	10	15
α-helix	190-194	5
β-strand	199-204	6	16
α-helix	205-207	3
β-strand	209-214	6	16

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	30	1	19
β-strand	31	1	19
β-strand	33-38	6	18
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
β-strand	97-98	2	18
β-strand	102-106	5	18
β-strand	111	1	20
α-helix	112-113	2
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	153-154	2	22
α-helix	155	1
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	183-187	5
β-strand	191-197	7	22
β-strand	205-210	6	22

Chain H: 10 helices, 22 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	33-39	7	2
β-strand	45-52	8	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	103	1	2
β-strand	107-111	5	2
α-helix	118-120	3
β-strand	121	1	3
α-helix	122-123	2
β-strand	124-128	5	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	199-204	6	5
α-helix	205-207	3
β-strand	209-214	6	5

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	30-30A	2	8
β-strand	30F-31	2	8
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
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Chains P and Q: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADI-26906 Fab Heavy Chain	A, H	protein	223	Homo sapiens
ADI-26906 Fab Light Chain	B, L	protein	219	Homo sapiens
T-cell surface glycoprotein CD3 epsilon chain	P, Q	protein	13	Homo sapiens	P07766 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>8F0L_1 ADI-26906 Fab Heavy Chain (chains A, H)
QVQLVQSGAEVKKPGASVKVSCKASGFNIKDYYMHWVRQAPGQRLEWMGWIDLENANTIY
DAKFQGRVTITRDTSASTAYMELSSLRSEDTAVYYCARDAYGRYFYDVWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 2 (B, L), FASTA

>8F0L_2 ADI-26906 Fab Light Chain (chains B, L)
DIVMTQSPDSLAVSLGERATINCKSSQSLLNARTGKNYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCKQSYSRRTFGGGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (P, Q), FASTA

>8F0L_3 T-cell surface glycoprotein CD3 epsilon chain (chains P, Q)
QDGNEEMGGITQT

Primary citation

Structure-based engineering of a novel CD3 epsilon-targeting antibody for reduced polyreactivity. Liu, C.Y., Ahonen, C.L., Brown, M.E. et al. MAbs (2023) 15:2189974-2189974. DOI 10.1080/19420862.2023.2189974 · PubMed

Other PDB entries of the same protein (UniProt P07766 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5QU2 1.04 Å, Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY
9T46 1.65 Å, Crystal structure of the Fab 40G5c in complex with a CD3 epsilon peptide
8VY4 1.7 Å, Engineering a Tumor-Selective Prodrug T Cell Engager Bispecific Antibody for Safer…
1XIW 1.9 Å, Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody…
1SY6 2.1 Å, Crystal Structure of CD3gammaepsilon Heterodimer in Complex with OKT3 Fab Fragment
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
1A81 3.0 Å, Crystal structure of the tandem SH2 domain of the syk kinase bound to a dually…
7FJE 3.0 Å, Cryo-EM structure of a membrane protein(LL)
9CI8 3.01 Å, T cell receptor complex
8ES7 3.04 Å, CryoEM structure of PN45545 TCR-CD3 complex
7PHR 3.08 Å, Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
9JY1 3.08 Å, delta epsilon/delta epsilon Fab-TCR tetramer

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