3PP0: Kinase domain of Human HER2 (erbB2)

Crystal Structure of the Kinase domain of Human HER2 (erbB2). Determined by X-ray diffraction at 2.25 Å resolution. Released 30 Mar 2011.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,924
Mol. weight: 77.45 kDa
Ligands: 03Q
Released: 30 Mar 2011

Explore 3PP0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PP0 contains 41 α-helices and 32 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: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	714	1	1
α-helix	717-719	3
β-strand	720-728	9	1
β-strand	732-739	8	1
β-strand	748-755	8	1
α-helix	756	1
α-helix	761-774	14
β-strand	782	1	2
β-strand	785-790	6	1
β-strand	794-799	6	1
β-strand	805	1	2
α-helix	806-812	7
α-helix	819-838	20
β-strand	841-842	2	3
α-helix	848-850	3
β-strand	851-855	5	2
β-strand	858-861	4	2
β-strand	868-869	2	3
α-helix	870-871	2
β-strand	877-878	2	4
α-helix	886-888	3
α-helix	891-896	6
β-strand	898-899	2	4
α-helix	901-916	16
α-helix	920-921	2
α-helix	928-930	3
α-helix	931-936	6
α-helix	941-944	4
β-strand	947	1	5
α-helix	949-958	10
α-helix	963-965	3
α-helix	967-968	2
α-helix	969-980	12
α-helix	983-986	4
β-strand	987	1	5
α-helix	989-992	4

Chain B: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	713-714	2	6
α-helix	717-719	3
β-strand	720-729	10	6
β-strand	732-739	8	6
β-strand	748-755	8	6
α-helix	761-775	15
β-strand	782	1	7
α-helix	783-784	2
β-strand	785-789	5	6
β-strand	795-799	5	6
β-strand	805	1	7
α-helix	806-812	7
α-helix	819-838	20
β-strand	841-842	2	8
α-helix	848-850	3
β-strand	851-855	5	7
β-strand	858-861	4	7
β-strand	868-869	2	8
α-helix	870-871	2
β-strand	877-878	2	9
α-helix	886-888	3
α-helix	891-896	6
β-strand	898-899	2	9
α-helix	901-916	16
α-helix	920-921	2
α-helix	928-930	3
α-helix	931-936	6
α-helix	941-944	4
β-strand	947	1	10
α-helix	949-958	10
α-helix	963-965	3
α-helix	967-968	2
α-helix	969-981	13
α-helix	983-986	4
β-strand	987	1	10
α-helix	989-991	3
α-helix	1003-1007	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor tyrosine-protein kinase erbB-2	A, B	protein	338	Homo sapiens	P04626 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3PP0_1 Receptor tyrosine-protein kinase erbB-2 (chains A, B)
MSGAAPNQALLRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSP
KANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQD
LLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADG
GKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERL
PQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLD
STFYRSLLEDDDMGDLVDAEEYLVPQQGAAASHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
03Q	2-{2-[4-({5-chloro-6-[3-(trifluoromethyl)phenoxy]pyridin-3-yl}amino)-5H-pyrrolo…	C22 H19 Cl F3 N5 O3	2

Primary citation

Structural Analysis of the Mechanism of Inhibition and Allosteric Activation of the Kinase Domain of HER2 Protein. Aertgeerts, K., Skene, R., Yano, J. et al. J Biol Chem (2011) 286:18756-18765. DOI 10.1074/jbc.M110.206193 · 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…
5MY6 2.25 Å, Crystal structure of a HER2-Nb complex

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