6B9Z: Trastuzumab Fab v3

Trastuzumab Fab v3. Determined by X-ray diffraction at 1.82 Å resolution. Released 5 Sept 2018.

Method: X-ray diffraction
Resolution: 1.82 Å
Organisms: Mus musculus, Homo sapiens, Finegoldia magna
Chains: 4
Atoms: 4,915
Mol. weight: 60.29 kDa
Released: 5 Sept 2018

Explore 6B9Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B9Z contains 24 α-helices and 52 β-strands across 4 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain B: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-52	8	8
β-strand	57-60	4	8
β-strand	65	1	6
β-strand	68-73	6	6
α-helix	74-76	3
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-99	8	8
α-helix	101-103	3
β-strand	110	1	8
β-strand	114-116	3	8
β-strand	117-118	2	7
α-helix	122-123	2
β-strand	124	1	9
β-strand	127-131	5	10
β-strand	138-139	2	10
β-strand	142-152	11	10
β-strand	153	1	9
β-strand	158-161	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-177	2	10
β-strand	183-192	10	10
α-helix	193-195	3
β-strand	196	1	12
β-strand	199	1	12
β-strand	202-207	6	11
α-helix	208-210	3
β-strand	212-217	6	11

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	5-16	12
α-helix	22-34	13
α-helix	36-38	3
α-helix	39-52	14

Chain E: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	21-28	8	2
β-strand	34-41	8	2
α-helix	43-61	19
β-strand	64-69	6	2
α-helix	70-72	3
β-strand	74-79	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Trastuzumab Fab light chain	A	protein	214	Mus musculus, Homo sapiens	P01834 (AlphaFold model)
Trastuzumab Fab heavy chain	B	protein	223	Mus musculus, Homo sapiens	S6B291 (AlphaFold model)
Protein L	E	protein	64	Finegoldia magna	Q51918 (AlphaFold model)
Immunoglobulin G binding protein A	C	protein	54	Staphylococcus aureus	P02976 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6B9Z_1 Trastuzumab Fab light chain (chains A)
DIQMTQSPILLSASVGDRVTITCRASQDVNTAVAWYQQRTNGSPRLLIYSASFLYSGVPS
RFSGSRSGTDFTLTISSLQPEDEADYYCQQHYTTPPTFGAGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>6B9Z_2 Trastuzumab Fab heavy chain (chains B)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQSPGKGLEWVARIYPTNGYTRY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAIYYCSRWGGDGFYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPCVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (E), FASTA

>6B9Z_3 Protein L (chains E)
GSEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALLAKVNGEYTADLEDGGNHMNI
KFAG

Sequence of entity 4 (C), FASTA

>6B9Z_4 Immunoglobulin G binding protein A (chains C)
GSYNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQA

Primary citation

Template-Catalyzed, Disulfide Conjugation of Monoclonal Antibodies Using a Natural Amino Acid Tag. King, J.D., Ma, Y., Kuo, Y.C. et al. Bioconjug Chem (2018) 29:2074-2081. DOI 10.1021/acs.bioconjchem.8b00284 · PubMed

Other PDB entries of the same protein (UniProt P01834 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
1NGZ 1.6 Å, Chimeric Germline Fab 7g12-apo
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement
4XMP 1.78 Å, Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with…
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
3VH8 1.8 Å, KIR3DL1 in complex with HLA-B*5701
3X12 1.8 Å, Crystal structure of HLA-B*57:01.I80N
2VXQ 1.9 Å, Crystal structure of the major grass pollen allergen Phl p 2 in complex with its…
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
6DCV 1.9 Å, Crystal structure of human anti-tau antibody CBTAU-27.1
1GAF 1.95 Å, 48G7 hybridoma line FAB complexed with hapten 5-(para-nitrophenyl phosphonate)-pentanoic…

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