6TKZ: DHR2 domain of DOCK10

Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42. Determined by X-ray diffraction at 2.64 Å resolution. Released 22 Jan 2020.

Method: X-ray diffraction
Resolution: 2.64 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,582
Mol. weight: 149.06 kDa
Ligands: GDP
Released: 22 Jan 2020

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

Secondary structure: helices and β-sheets

6TKZ contains 66 α-helices and 30 β-strands across 4 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1696-1712	17
α-helix	1716-1737	22
α-helix	1773-1775	3
α-helix	1777-1780	4
α-helix	1785-1791	7
α-helix	1806-1822	17
α-helix	1826-1828	3
α-helix	1829-1843	15
α-helix	1846-1866	21
β-strand	1876-1883	8	5
β-strand	1895-1900	6	5
α-helix	1906-1920	15
β-strand	1926-1929	4	5
α-helix	1934-1936	3
α-helix	1937-1939	3
β-strand	1945-1952	8	5
β-strand	1953-1954	2	2
α-helix	1958-1961	4
α-helix	1969-1971	3
β-strand	1974-1984	11	2
β-strand	1996-2009	14	2
β-strand	2015-2017	3	5
β-strand	2018-2026	9	2
α-helix	2028-2047	20
α-helix	2054-2065	12
α-helix	2073-2080	8
α-helix	2083-2086	4
α-helix	2091-2116	26
α-helix	2121-2123	3
α-helix	2124-2145	22

Chain B: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1696-1713	18
α-helix	1716-1736	21
α-helix	1777-1780	4
α-helix	1785-1791	7
α-helix	1806-1823	18
α-helix	1826-1828	3
α-helix	1829-1842	14
α-helix	1846-1866	21
β-strand	1876-1883	8	1
β-strand	1895-1900	6	1
α-helix	1906-1921	16
β-strand	1926-1929	4	1
α-helix	1934-1936	3
α-helix	1937-1939	3
β-strand	1945-1952	8	1
β-strand	1953-1954	2	2
α-helix	1969-1971	3
β-strand	1974-1983	10	2
β-strand	1997-2009	13	2
β-strand	2015-2017	3	1
β-strand	2018-2026	9	2
α-helix	2028-2047	20
α-helix	2054-2065	12
α-helix	2074-2080	7
α-helix	2083-2086	4
α-helix	2091-2116	26
α-helix	2121-2123	3
α-helix	2124-2145	22

Chain C: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	3
α-helix	16-25	10
α-helix	29-31	3
α-helix	32-34	3
β-strand	40-46	7	3
β-strand	49-56	8	3
α-helix	62-65	4
α-helix	68-71	4
β-strand	77-83	7	3
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	3
α-helix	117-119	3
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	3
α-helix	165-176	12

Chain D: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	4
α-helix	16-25	10
α-helix	29-31	3
α-helix	33-34	2
β-strand	40-46	7	4
β-strand	49-57	9	4
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	4
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	4
α-helix	117-121	5
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	4
α-helix	165-176	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dedicator of cytokinesis protein 10	A, B	protein	458	Homo sapiens	Q96BY6 (AlphaFold model)
Cell division control protein 42 homolog	C, D	protein	188	Homo sapiens	P60953 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6TKZ_1 Dedicator of cytokinesis protein 10 (chains A, B)
STPELRRTWLESMAKIHARNGDLSEAAMCYIHIAALIAEYLKRKGYWKVEKICTASLLSE
DTHPCDSNSLLTTPSGGSMFSMGWPAFLSITPNIKEEGAMKEDSGMQDTPYNENILVEQL
YMCVEFLWKSERYELIADVNKPIIAVFEKQRDFKKLSDLYYDIHRSYLKVAEVVNSEKRL
FGRYYRVAFYGQGFFEEEEGKEYIYKEPKLTGLSEISQRLLKLYADKFGADNVKIIQDSN
KVNPKDLDPKYAYIQVTYVTPFFEEKEIEDRKTDFEMHHNINRFVFETPFTLSGKKHGGV
AEQCKRRTILTTSHLFPYVKKRIQVISQSSTELNPIEVAIDEMSKKVSELNQLCTMEEVD
MIRLQLKLQGSVSVKVNAGPMAYARAFLEETNAKKYPDNQVKLLKEIFRQFADACGQALD
VNERLIKEDQLEYQEELRSHYKDMLSELSTVMNEQITG

Sequence of entity 2 (C, D), FASTA

>6TKZ_2 Cell division control protein 42 homolog (chains C, D)
MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAG
QEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLR
DDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEPP
EPKKSRRC

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

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

Primary citation

Structural basis for CDC42 and RAC activation by the dual specificity GEF DOCK10. Fan, D., Yang, J., Cronin, N. et al. bioRxiv (2022). DOI 10.1101/2022.06.15.496229

Other PDB entries of the same protein (UniProt Q96BY6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Q43 2.4 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
6TKY 2.55 Å, Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42
6TM1 3.71 Å, Crystal structure of the DHR2 domain of DOCK10 in complex with RAC3

Browse structure collections

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