6BGT: Trastuzumab Fab mutant

Structure of Trastuzumab Fab mutant in complex with Her2 extracellular domain. Determined by X-ray diffraction at 2.7 Å resolution. Released 31 Oct 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,806
Mol. weight: 120.92 kDa
Ligands: NAG
Released: 31 Oct 2018

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

Secondary structure: helices and β-sheets

6BGT contains 42 α-helices and 109 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 A: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-14	5	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	45-49	5	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	84-90	7	22
α-helix	96	1
β-strand	97-98	2	22
β-strand	102-107	6	22
β-strand	111	1	23
α-helix	112-113	2
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	24
β-strand	140	1	23
β-strand	144-150	7	25
β-strand	154	1	25
β-strand	159-163	5	24
α-helix	164-167	4
β-strand	173-182	10	24
α-helix	183-187	5
β-strand	191-198	8	25
β-strand	205-210	6	25

Chain B: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	10-12	3	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	34-39	6	27
β-strand	46-52	7	27
β-strand	57-60	4	27
α-helix	62-64	3
β-strand	68-73	6	26
β-strand	78-83	6	26
α-helix	88-90	3
β-strand	92-98	7	27
β-strand	101	1	28
β-strand	104	1	28
β-strand	109-110	2	27
β-strand	114-118	5	27
β-strand	124	1	29
α-helix	125-126	2
β-strand	127-131	5	30
β-strand	143-152	10	30
β-strand	153	1	29
β-strand	158-161	4	31
α-helix	162-164	3
β-strand	166	1	31
β-strand	170-172	3	30
α-helix	173-175	3
β-strand	176-177	2	30
β-strand	183-191	9	30
β-strand	202-207	6	31
β-strand	212-217	6	31

Chain C: 28 helices, 64 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	7	1	2
α-helix	12-14	3
α-helix	17-19	3
α-helix	20-28	9
β-strand	33-35	3	1
β-strand	37	1	2
β-strand	38-41	4	3
α-helix	50-52	3
β-strand	57-58	2	1
β-strand	62-65	4	3
β-strand	79-80	2	1
β-strand	86	1	3
β-strand	90-95	6	3
β-strand	125-126	2	1
β-strand	130-134	5	3
α-helix	142-144	3
α-helix	147-150	4
β-strand	151	1	1
α-helix	153-155	3
β-strand	160-162	3	3
α-helix	171-174	4
β-strand	182	1	4
α-helix	187-189	3
β-strand	190	1	4
α-helix	191-193	3
β-strand	205	1	5
α-helix	210-212	3
β-strand	213	1	5
α-helix	214-215	2
β-strand	218-222	5	6
β-strand	230-233	4	6
β-strand	236-238	3	7
β-strand	241-243	3	7
α-helix	246-248	3
β-strand	250-252	3	8
β-strand	259-261	3	8
β-strand	267-269	3	7
β-strand	272-274	3	7
α-helix	277-278	2
α-helix	281	1
β-strand	282-284	3	9
β-strand	288	1	7
β-strand	289-290	2	9
β-strand	297-301	5	9
β-strand	307-311	5	9
α-helix	316-318	3
β-strand	320-321	2	10
β-strand	323	1	11
α-helix	326-328	3
α-helix	339-342	4
β-strand	347-349	3	10
β-strand	351	1	11
β-strand	352-354	3	12
α-helix	356-359	4
β-strand	362	1	13
α-helix	363-365	3
β-strand	367	1	13
α-helix	368-371	4
α-helix	374-380	7
β-strand	383-384	2	10
β-strand	388-390	3	12
α-helix	401-403	3
β-strand	408-409	2	10
β-strand	415	1	12
β-strand	419-424	6	12
β-strand	438-439	2	10
β-strand	443-447	5	12
α-helix	460-463	4
β-strand	464	1	10
β-strand	471-474	4	12
α-helix	479-484	6
β-strand	493	1	14
α-helix	494-496	3
β-strand	498	1	15
β-strand	506	1	15
β-strand	509	1	14
β-strand	512-514	3	16
β-strand	517-519	3	16
β-strand	531-534	4	16
β-strand	537-540	4	16
α-helix	541-542	2
β-strand	545	1	17
α-helix	546-547	2
β-strand	554	1	18
β-strand	562	1	18
β-strand	565	1	17
β-strand	568-570	3	19
β-strand	573-575	3	19
β-strand	593-595	3	20
β-strand	600	1	19
β-strand	601-603	3	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor tyrosine-protein kinase erbB-2	C	protein	658	Homo sapiens	P04626 (AlphaFold model)
Herceptin light chain mutant	A	protein	214	Homo sapiens	Q7Z3Y4 (AlphaFold model)
Herceptin heavy chain Fab fragment mutant	B	protein	231	Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6BGT_1 Receptor tyrosine-protein kinase erbB-2 (chains C)
MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNL
ELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNG
DPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLA
LTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQC
AAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACP
YNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSAN
IQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLP
DLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTV
PWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQEC
VEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARC
PSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTHHHHHH

Sequence of entity 2 (A), FASTA

>6BGT_2 Herceptin light chain mutant (chains A)
DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSADFLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B), FASTA

>6BGT_3 Herceptin heavy chain Fab fragment mutant (chains B)
EVQLVESGGGLVQPGGSLRLSCAASGFNIDDTYIHWVRQAPGKGLEWVARIYPTNGYTRY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Ligands and cofactors

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

Primary citation

Stable human IgG antibody therapeutics with native framework structure. Christie, M., Rouet, R., Nevoltris, D. et al. To be published.

Other PDB entries of the same protein (UniProt P04626 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MFG 1.25 Å, The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor
8VB5 1.48 Å, Crystal structure of kinase domain of HER2 Exon 20 insertion mutant in complex with…
8JYR 1.69 Å, Crystal structure of anti-HER2 antibody H2Mab-119 in complex with HER2 domain I
8U8X 1.69 Å, crystal structure of the receptor tyrosine kinase Human HER2 (ERBB2) YVMA mutant kinase…
8JYQ 1.75 Å, Crystal structure of cancer-specific anti-HER2 antibody H2Mab-214 in complex with…
7PCD 1.77 Å, HER2 in complex with a covalent inhibitor
5TQS 1.88 Å, Phospholipase C gamma-1 C-terminal SH2 domain bound to a phosphopeptide derived from the…
1MFL 1.88 Å, The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor
4GFU 2.0 Å, PTPN18 in complex with HER2-pY1248 phosphor-peptides
6LBX 2.03 Å, Crystal structure of HER2 Domain IV and Rb-H2
9IUT 2.09 Å, Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with…
5MY6 2.25 Å, Crystal structure of a HER2-Nb complex

Browse structure collections

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