5MY6: HER2-Nb complex

Crystal structure of a HER2-Nb complex. Determined by X-ray diffraction at 2.25 Å resolution. Released 9 Aug 2017.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Homo sapiens, Camelus dromedarius
Chains: 2
Atoms: 5,581
Mol. weight: 82.04 kDa
Ligands: NAG
Released: 9 Aug 2017

Explore 5MY6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MY6 contains 28 α-helices and 68 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: 27 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	1
β-strand	29	1	2
α-helix	34-36	3
α-helix	39-50	12
β-strand	55-57	3	1
β-strand	59	1	2
β-strand	60-63	4	3
α-helix	72-74	3
β-strand	79-80	2	1
β-strand	84-87	4	3
β-strand	101-102	2	1
β-strand	108	1	3
β-strand	112-117	6	3
β-strand	147-148	2	1
β-strand	152-156	5	3
α-helix	169-172	4
β-strand	173	1	1
β-strand	183-184	2	3
α-helix	193-196	4
α-helix	200-202	3
β-strand	204	1	4
α-helix	209-211	3
β-strand	212	1	4
α-helix	213-215	3
α-helix	221-223	3
β-strand	227	1	5
α-helix	232-234	3
β-strand	235	1	5
α-helix	236-237	2
β-strand	240-244	5	6
β-strand	252-255	4	6
β-strand	258-260	3	7
β-strand	263-265	3	7
α-helix	268-270	3
β-strand	272-274	3	8
β-strand	281-283	3	8
β-strand	289-291	3	7
β-strand	294-296	3	7
α-helix	299-300	2
α-helix	303	1
β-strand	304-305	2	9
α-helix	306	1
β-strand	310	1	7
β-strand	311-312	2	9
β-strand	319-323	5	9
β-strand	329-333	5	9
α-helix	338-340	3
β-strand	342-343	2	10
β-strand	345	1	11
α-helix	348-350	3
α-helix	361-364	4
β-strand	369-371	3	10
β-strand	373	1	11
β-strand	374-376	3	12
α-helix	378-382	5
β-strand	384	1	13
α-helix	385-387	3
β-strand	389	1	13
α-helix	390-393	4
α-helix	394-400	7
β-strand	405-406	2	10
β-strand	410-412	3	12
α-helix	423-425	3
β-strand	430-431	2	10
β-strand	437	1	12
β-strand	441-446	6	12
β-strand	460-461	2	10
β-strand	465-469	5	12
α-helix	482-485	4
β-strand	493-496	4	12
α-helix	501-506	6
β-strand	515	1	14
α-helix	516-518	3
β-strand	520	1	15
β-strand	528	1	15
β-strand	531	1	14
β-strand	534-536	3	16
β-strand	539-541	3	16
β-strand	553-555	3	17
β-strand	559	1	16
β-strand	560-562	3	17
α-helix	568-570	3
β-strand	576	1	18
β-strand	584	1	18

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	10-13	4	20
β-strand	18-25	8	19
β-strand	34-39	6	20
β-strand	45-51	7	20
β-strand	57-59	3	20
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	87-89	3
β-strand	91-99	9	20
β-strand	102-105	4	20
β-strand	109-114	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor tyrosine-protein kinase erbB-2	A	protein	622	Homo sapiens	P04626 (AlphaFold model)
Nanobody 2Rs15d	B	protein	115	Camelus dromedarius

Sequence of entity 1 (A), FASTA

>5MY6_1 Receptor tyrosine-protein kinase erbB-2 (chains A)
QVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGY
VLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLR
SLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSR
CWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGI
CELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVT
AEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDG
DPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSL
TLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDE
CVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPC
HPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGAC
QPCPINCTHSCVDLDDKGCPAE

Sequence of entity 2 (B), FASTA

>5MY6_2 Nanobody 2Rs15d (chains B)
QVQLQESGGGSVQAGGSLKLTCAASGYIFNSCGMGWYRQSPGRERELVSRISGDGDTWHK
ESVKGRFTISQDNVKKTLYLQMNSLKPEDTAVYFCAVCYNLETYWGQGTQVTVSS

Ligands and cofactors

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

Water and common crystallization additives (GOL) are not listed.

Primary citation

(131)I-labeled Anti-HER2 Camelid sdAb as a Theranostic Tool in Cancer Treatment. D'Huyvetter, M., De Vos, J., Xavier, C. et al. Clin Cancer Res (2017) 23:6616-6628. DOI 10.1158/1078-0432.CCR-17-0310 · PubMed

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…
3PP0 2.25 Å, Crystal Structure of the Kinase domain of Human HER2 (erbB2).

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