8VY4: Fab Heavy Chain

Engineering a Tumor-Selective Prodrug T Cell Engager Bispecific Antibody for Safer Immunotherapy. Determined by X-ray diffraction at 1.7 Å resolution. Released 24 Jul 2024.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,876
Mol. weight: 47.68 kDa
Released: 24 Jul 2024

Explore 8VY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VY4 contains 18 α-helices and 43 β-strands across 2 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	2-5	4	1
β-strand	9-11	3	2
α-helix	15-16	2
β-strand	17-24	8	1
α-helix	28-30	3
β-strand	33-38	6	2
β-strand	44-50	7	2
β-strand	56-58	3	2
β-strand	66-71	6	1
β-strand	76-81	6	1
α-helix	86-88	3
β-strand	90-96	7	2
β-strand	105-106	2	2
β-strand	110-114	5	2
α-helix	118-119	2
β-strand	120	1	3
α-helix	121-122	2
β-strand	123-127	5	4
α-helix	128-129	2
β-strand	138-148	11	4
β-strand	149	1	3
β-strand	154-157	4	5
α-helix	158-160	3
β-strand	162	1	5
β-strand	166-168	3	4
α-helix	169-171	3
β-strand	172-174	3	4
β-strand	177-187	11	4
β-strand	197-202	6	5
α-helix	203-205	3
β-strand	207-212	6	5

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	18-25	8	6
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	7
β-strand	47-51	5	7
β-strand	55-56	2	7
α-helix	57	1
β-strand	64-69	6	6
β-strand	72-78	7	6
α-helix	82-84	3
β-strand	86-94	9	7
β-strand	100-103	4	7
β-strand	107-112	6	7
β-strand	116	1	8
α-helix	117-118	2
β-strand	119-123	5	9
α-helix	124-126	3
α-helix	130-132	3
β-strand	134-144	11	9
β-strand	145	1	8
β-strand	149-154	6	10
β-strand	157-159	3	10
β-strand	163-167	5	9
α-helix	168-171	4
β-strand	177-186	10	9
α-helix	187-190	4
β-strand	195-202	8	10
β-strand	205-212	8	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab Heavy Chain	A	protein	224	Mus musculus
Fab Light Chain	B	protein	216	Homo sapiens
Pca-asp-gly-asn-glu-glu-met	C	protein	7	Homo sapiens	P07766 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8VY4_1 Fab Heavy Chain (chains A)
QSVEESEGGLFKPTDTLTLTCTVSGFSLSSNAISWVRQAPGKGLEWIGFVAVTGYSYYAS
WAKSRSTITRNTGLNTVTLKMTSLTAADTATYFCARIGIGIDFNIWGPGTLVTVSSAKTT
APSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGSHHHHHH

Sequence of entity 2 (B), FASTA

>8VY4_2 Fab Light Chain (chains B)
AIDMTQTPSSKSVAVGDTVTINCQASETVYKNNYLAWYQQKPGQPPKRLIYSVSTLDSGV
PSRFSGSGSGTQFTLTISGVQCDDAATYYCAGYRTTPIYHIRFGGGTEVVVEGDPVAPTV
LIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLS
STLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC

Sequence of entity 3 (C), FASTA

>8VY4_3 PCA-ASP-GLY-ASN-GLU-GLU-MET (chains C)
QDGNEEM

Primary citation

Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy. McCue, A.C., Demarest, S.J., Froning, K.J. et al. MAbs (2024) 16:2373325-2373325. DOI 10.1080/19420862.2024.2373325 · 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
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

Browse structure collections

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