6VQM: Crystal Structure Analysis of human ACK1

Crystal Structure Analysis of human ACK1. Determined by X-ray diffraction at 2.87 Å resolution. Released 10 Feb 2021.

Method: X-ray diffraction
Resolution: 2.87 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,189
Mol. weight: 66.58 kDa
Ligands: R7P
Released: 10 Feb 2021

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

Secondary structure: helices and β-sheets

6VQM contains 36 α-helices and 28 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: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	119-120	2	1
α-helix	123-125	3
β-strand	126-135	10	1
β-strand	138-146	9	1
β-strand	152-159	8	1
α-helix	169-182	14
β-strand	189	1	2
β-strand	192-196	5	1
α-helix	201	1
β-strand	202-206	5	1
β-strand	212	1	2
α-helix	213-219	7
α-helix	226-245	20
β-strand	248-249	2	3
α-helix	255-257	3
β-strand	258-260	3	2
β-strand	266-268	3	2
β-strand	275-276	2	3
α-helix	277-278	2
β-strand	284-285	2	4
α-helix	286-287	2
α-helix	299-304	6
β-strand	306-307	2	4
α-helix	309-324	16
α-helix	328-329	2
α-helix	336-340	5
α-helix	341-345	5
α-helix	350-353	4
α-helix	358-367	10
α-helix	372-374	3
α-helix	376-377	2
α-helix	378-387	10

Chain B: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	119-120	2	5
α-helix	123-125	3
β-strand	126-134	9	5
β-strand	139-146	8	5
β-strand	152-159	8	5
α-helix	171-182	12
β-strand	189	1	6
β-strand	192-196	5	5
α-helix	201	1
β-strand	202-206	5	5
β-strand	212	1	6
α-helix	213-219	7
α-helix	221-223	3
α-helix	226-245	20
β-strand	248-249	2	7
α-helix	255-257	3
β-strand	258-260	3	6
β-strand	266-268	3	6
β-strand	275-276	2	7
α-helix	277-278	2
β-strand	284-285	2	8
α-helix	299-304	6
β-strand	306-307	2	8
α-helix	309-324	16
α-helix	328-329	2
α-helix	336-340	5
α-helix	341-345	5
α-helix	350-353	4
α-helix	358-367	10
α-helix	376-377	2
α-helix	378-387	10
α-helix	389-391	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activated CDC42 kinase 1	A, B	protein	289	Homo sapiens	Q07912 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6VQM_1 Activated CDC42 kinase 1 (chains A, B)
GSAGEGPLQSLTCLIGEKDLRLLEKLGDGSFGVVRRGEWDAPSGKTVSVAVKCLKPDVLS
QPEAMDDFIREVNAMHSLDHRNLIRLYGVVLTPPMKMVTELAPLGSLLDRLRKHQGHFLL
GTLSRYAVQVAEGMGYLESKRFIHRDLAARNLLLATRDLVKIGDFGLMRALPQNDDHYVM
QEHRKVPFAWCAPESLKTRTFSHASDTWMFGVTLWEMFTYGQEPWIGLNGSQILHKIDKE
GERLPRPEDCPQDIYNVMVQCWAHKPEDRPTFVALRDFLLEAQPTDMRA

Ligands and cofactors

ID	Name	Formula	Copies
R7P	2-({4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]-2-methoxyphenyl}amino)-9-methyl-5,7-…	C25 H29 N7 O2	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal Structure Analysis of human ACK1. Seo, H.-S., Dhe-Paganon, S. To be published.

Other PDB entries of the same protein (UniProt Q07912 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HZR 1.31 Å, Crystal structure of Ack1 kinase domain
8THA 1.68 Å, 1TEL, non-compressed, double-helical crystal form
7KP6 1.79 Å, Structure of Ack1 kinase in complex with a selective inhibitor
8Q5P 1.81 Å, Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from…
1U46 2.0 Å, Crystal Structure of the Unphosphorylated Kinase Domain of the Tyrosine Kinase ACK1
3EQR 2.0 Å, Crystal Structure of Ack1 with compound T74
1U4D 2.1 Å, Structure of the ACK1 Kinase Domain bound to Debromohymenialdisine
5ZXB 2.2 Å, Crystal structure of ACK1 with compound 10d
3EQP 2.3 Å, Crystal Structure of Ack1 with compound T95
4EWH 2.5 Å, Co-crystal structure of ACK1 with inhibitor
8FZ3 2.78 Å, Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form
1U54 2.8 Å, Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the…

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