6LBX: HER2 Domain IV and Rb-H2

Crystal structure of HER2 Domain IV and Rb-H2. Determined by X-ray diffraction at 2.03 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 2.03 Å
Organisms: Cyclostomata, Homo sapiens
Chains: 2
Atoms: 2,788
Mol. weight: 41.78 kDa
Ligands: NAG
Released: 18 Nov 2020

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

Secondary structure: helices and β-sheets

6LBX contains 10 α-helices and 27 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: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	1
α-helix	10-13	4
α-helix	17-26	10
β-strand	35-36	2	1
α-helix	38-42	5
β-strand	46-48	3	2
α-helix	60-62	3
β-strand	68-70	3	2
α-helix	80-82	3
β-strand	90-92	3	2
β-strand	114-116	3	2
β-strand	138-140	3	2
β-strand	162-164	3	2
β-strand	186-188	3	2
β-strand	210-212	3	2
β-strand	218	1	3
α-helix	226-234	9
β-strand	239	1	2
β-strand	240	1	4
β-strand	246	1	4
α-helix	248-250	3
β-strand	252	1	5
β-strand	253	1	3
β-strand	259	1	5
α-helix	260-262	3

Chain B: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	534-536	3	6
β-strand	539-541	3	6
β-strand	553-556	4	6
β-strand	559-562	4	6
α-helix	563-564	2
β-strand	567	1	7
α-helix	568-570	3
β-strand	576	1	8
β-strand	584	1	8
β-strand	587	1	7
β-strand	590-592	3	9
β-strand	595-597	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Repebody (Rb-H2)	A	protein	275	Cyclostomata
Receptor tyrosine-protein kinase erbB-2	B	protein	97	Homo sapiens	P04626 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6LBX_1 Repebody (Rb-H2) (chains A)
METITVSTPIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDLISAPHSDIKSVQGI
QYLPNVRLLYLGGNKLHDISALKELTNLTTLILSGNQLQSLPNGVFDKLTNLKVLWLSVN
QLQSLPDGVFDKLTNLTSLRLHRNQLQSLPKGVFDKLTNLTVLRLSENQLQSLPEGVFDK
LTQLKVLWLGRNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVR
NSAGSVAPDSAKCSGSGKPVRSIICPTLEHHHHHH

Sequence of entity 2 (B), FASTA

>6LBX_2 Receptor tyrosine-protein kinase erbB-2 (chains B)
QCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAH
YKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPC

Ligands and cofactors

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

Primary citation

Computationally-guided design and affinity improvement of a protein binder targeting a specific site on HER2. Kim, T.Y., Cha, J.S., Kim, H. et al. Comput Struct Biotechnol J (2021) 19:1325-1334. DOI 10.1016/j.csbj.2021.02.013

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

Browse structure collections

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