9T46: Fab 40G5c

Crystal structure of the Fab 40G5c in complex with a CD3 epsilon peptide. Determined by X-ray diffraction at 1.65 Å resolution. Released 13 May 2026.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,919
Mol. weight: 50.02 kDa
Released: 13 May 2026

Explore 9T46 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9T46 contains 18 α-helices and 47 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: 9 helices, 24 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	45-51	7	2
β-strand	58-60	3	2
β-strand	65	1	1
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	108-109	2	2
β-strand	113-117	5	2
β-strand	123	1	3
α-helix	124-125	2
β-strand	126-130	5	4
α-helix	134-136	3
β-strand	137-138	2	4
β-strand	141-151	11	4
β-strand	152	1	3
β-strand	157-160	4	5
α-helix	161-163	3
β-strand	165	1	5
β-strand	169-171	3	4
α-helix	172-174	3
β-strand	175-176	2	4
β-strand	182-191	10	4
α-helix	192-194	3
β-strand	201-206	6	5
α-helix	207-209	3
β-strand	211-216	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	1	8
β-strand	37	1	8
β-strand	39-44	6	7
β-strand	51-55	5	7
β-strand	59-60	2	7
α-helix	61	1
β-strand	68-73	6	6
β-strand	76-81	6	6
α-helix	86-88	3
β-strand	90-96	7	7
β-strand	102-103	2	7
β-strand	107-111	5	7
β-strand	116	1	9
α-helix	117-118	2
β-strand	119-123	5	10
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	10
β-strand	145	1	9
β-strand	150-155	6	11
β-strand	158-159	2	11
α-helix	160	1
β-strand	164-168	5	10
α-helix	169-172	4
β-strand	178-187	10	10
α-helix	188-192	5
β-strand	196-202	7	11
β-strand	210-215	6	11

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin Fab fragment 40G5c, Heavy Chain	H	protein	224	Homo sapiens
Immunoglobulin Fab fragment 40G5c, Light Chain	L	protein	219	Homo sapiens
T-cell surface glycoprotein CD3 epsilon chain	P	protein	10	Homo sapiens	P07766 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9T46_1 Immunoglobulin Fab fragment 40G5c, Heavy Chain (chains H)
EVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYIHWVRQAPGQGLEWIGWIYPGDGNTKY
NEKFKGRATLTADTSTSTAYLELSSLRSEDTAVYYCARDSYSNYYFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 2 (L), FASTA

>9T46_2 Immunoglobulin Fab fragment 40G5c, Light Chain (chains L)
DIVMTQSPDSLAVSLGERATINCKSSQSLLNSRTRKNYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCTQSFILRTFGQGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (P), FASTA

>9T46_3 T-cell surface glycoprotein CD3 epsilon chain (chains P)
QDGNEEMGGX

Primary citation

Engineering of acidic pH-responsive anti-CD3 binding antibodies. La Sala, G., Kroell, K.B., Pincha, M. et al. MAbs (2026) 18:2658902-2658902. DOI 10.1080/19420862.2026.2658902 · 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
8VY4 1.7 Å, Engineering a Tumor-Selective Prodrug T Cell Engager Bispecific Antibody for Safer…
8F0L 1.81 Å, Crystal Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed…
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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