1OPJ: The auto-inhibition of c-Abl tyrosine kinase

Structural basis for the auto-inhibition of c-Abl tyrosine kinase. Determined by X-ray diffraction at 1.75 Å resolution. Released 8 Apr 2003.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Mus musculus
Chains: 2
Atoms: 5,001
Mol. weight: 69 kDa
Ligands: MYR, STI
Released: 8 Apr 2003

Explore 1OPJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1OPJ contains 43 α-helices and 24 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: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	255	1	1
α-helix	258-260	3
β-strand	261-266	6	1
β-strand	275-280	6	1
α-helix	281-283	3
β-strand	285-291	7	1
α-helix	292-293	2
α-helix	299-311	13
β-strand	317	1	2
α-helix	318-319	2
β-strand	320-324	5	1
α-helix	330	1
β-strand	331-335	5	1
β-strand	341	1	2
α-helix	342-348	7
α-helix	356-375	20
α-helix	385-387	3
β-strand	388-390	3	2
α-helix	392-394	3
β-strand	396-398	3	2
β-strand	413-415	3	3
β-strand	418-420	3	3
α-helix	422-424	3
α-helix	427-432	6
α-helix	437-452	16
α-helix	456-457	2
α-helix	464-472	9
α-helix	477-480	4
α-helix	485-494	10
α-helix	499-501	3
α-helix	503-504	2
α-helix	505-514	10
α-helix	521-528	8

Chain B: 22 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	255	1	4
α-helix	258-260	3
β-strand	262-266	5	4
α-helix	267-270	4
β-strand	275-280	6	4
α-helix	281-283	3
β-strand	285-290	6	4
α-helix	299-311	13
β-strand	317	1	5
α-helix	318-319	2
β-strand	320-324	5	4
α-helix	330	1
β-strand	331-335	5	4
α-helix	336-337	2
β-strand	341	1	5
α-helix	342-348	7
α-helix	356-375	20
α-helix	385-387	3
β-strand	388-390	3	5
α-helix	392-394	3
β-strand	396-398	3	5
β-strand	413-415	3	6
β-strand	418-420	3	6
α-helix	422-424	3
α-helix	427-432	6
α-helix	437-452	16
α-helix	456-457	2
α-helix	464-472	9
α-helix	477-480	4
α-helix	485-494	10
α-helix	499-501	3
α-helix	503-504	2
α-helix	505-512	8
α-helix	521-529	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase ABL1	A, B	protein	293	Mus musculus	P00520 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1OPJ_1 Proto-oncogene tyrosine-protein kinase ABL1 (chains A, B)
GAMDPSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEE
FLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVSAVVLLY
MATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFP
IKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPE
GCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKRGT

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	2
STI	4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-yla…	C29 H31 N7 O	2

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

Primary citation

Structural basis for the autoinhibition of c-Abl tyrosine kinase. Nagar, B., Hantschel, O., Young, M.A. et al. Cell (2003) 112:859-871. DOI 10.1016/S0092-8674(03)00194-6 · PubMed

Other PDB entries of the same protein (UniProt P00520 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KFA 1.22 Å, Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl…
3K5V 1.74 Å, Structure of Abl kinase in complex with imatinib and GNF-2
1OPK 1.8 Å, Structural basis for the auto-inhibition of c-Abl tyrosine kinase
3MS9 1.8 Å, ABL kinase in complex with imatinib and a fragment (FRAG1) in the myristate pocket
5IH2 1.8 Å, Structure, thermodynamics, and the role of conformational dynamics in the interactions…
3IK3 1.9 Å, AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the…
3KF4 1.9 Å, Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl…
2QOH 1.95 Å, Crystal Structure of Abl kinase bound with PPY-A
2Z60 1.95 Å, Crystal Structure of the T315I Mutant of Abl kinase bound with PPY-A
3MSS 1.95 Å, Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site
3OY3 1.95 Å, Crystal structure of ABL T315I mutant kinase domain bound with a DFG-out inhibitor AP24589
1ABO 2.0 Å, Crystal structure of the complex of the abl tyrosine kinase SH3 domain with 3BP-1…

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