5UKF: Human Vaccinia-related Kinase 1

Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor. Determined by X-ray diffraction at 2.4 Å resolution. Released 29 Mar 2017.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,854
Mol. weight: 166.71 kDa
Ligands: 8E1, PO4
Released: 29 Mar 2017

Explore 5UKF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UKF contains 66 α-helices and 44 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: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	36-42	7	1
β-strand	50-56	7	1
β-strand	68-74	7	1
α-helix	78-90	13
α-helix	93-102	10
α-helix	111-112	2
β-strand	113-121	9	1
β-strand	124-132	9	1
β-strand	134-137	4	2
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	3
α-helix	180-182	3
β-strand	183-186	4	2
β-strand	193-195	3	2
β-strand	202-203	2	3
α-helix	206-208	3
α-helix	210-212	3
α-helix	230-233	4
α-helix	240-256	17
α-helix	268-280	13
α-helix	282-289	8
α-helix	291-293	3
α-helix	297-307	11
α-helix	313-315	3
α-helix	317-330	14

Chain B: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	52	1	4
β-strand	70-72	3	4
α-helix	79-90	12
α-helix	93-103	11
α-helix	111-112	2
β-strand	113-117	5	4
β-strand	128-131	4	4
β-strand	134-137	4	5
α-helix	138-144	7
α-helix	151-170	20
β-strand	174	1	6
α-helix	180-182	3
β-strand	183-186	4	5
β-strand	193-195	3	5
β-strand	202	1	6
α-helix	206-208	3
α-helix	210-213	4
β-strand	215	1	7
α-helix	217-219	3
α-helix	230-234	5
β-strand	236	1	7
α-helix	237-238	2
α-helix	240-256	17
α-helix	268-280	13
α-helix	282-289	8
α-helix	297-307	11
α-helix	313-315	3
α-helix	317-330	14

Chain C: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	8
β-strand	36-42	7	8
β-strand	51-56	6	8
β-strand	68-74	7	8
α-helix	78-90	13
α-helix	93-103	11
α-helix	111-112	2
β-strand	113-121	9	8
β-strand	124-132	9	8
β-strand	134-137	4	9
α-helix	138-144	7
α-helix	151-170	20
β-strand	174	1	10
α-helix	180-182	3
β-strand	183-186	4	9
β-strand	193-195	3	9
β-strand	202	1	10
α-helix	206-208	3
α-helix	210-212	3
α-helix	230-233	4
α-helix	240-256	17
α-helix	262-264	3
α-helix	268-280	13
α-helix	282-289	8
α-helix	297-307	11
α-helix	313-315	3
α-helix	317-330	14

Chain D: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	51-52	2	11
β-strand	70-71	2	11
α-helix	79-90	12
α-helix	93-102	10
β-strand	113-116	4	11
β-strand	129-131	3	11
β-strand	134-137	4	12
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	13
α-helix	180-182	3
β-strand	183-186	4	12
β-strand	193-195	3	12
β-strand	202-203	2	13
α-helix	206-208	3
α-helix	210-213	4
β-strand	215	1	14
α-helix	217-219	3
α-helix	230-234	5
β-strand	236	1	14
α-helix	237-238	2
α-helix	240-256	17
α-helix	262-264	3
α-helix	268-280	13
α-helix	282-289	8
α-helix	297-307	11
α-helix	313-315	3
α-helix	317-330	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase VRK1	A, B, C, D	protein	363	Homo sapiens	Q99986 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5UKF_1 Serine/threonine-protein kinase VRK1 (chains A, B, C, D)
MRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSES
VGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDK
NGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKAS
NLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRR
GDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAK
YMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAE
IEE

Ligands and cofactors

ID	Name	Formula	Copies
8E1	4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}…	C16 H12 N4 O3 S2	4
PO4	Phosphate ion	O4 P	7

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

Primary citation

Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations. Counago, R.M., Allerston, C.K., Savitsky, P. et al. Sci Rep (2017) 7:7501-7501. DOI 10.1038/s41598-017-07755-y · PubMed

Other PDB entries of the same protein (UniProt Q99986 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M10 1.15 Å, PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1
6BRU 1.8 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…
6BU6 1.8 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…
6BP0 1.9 Å, Crystal Structure of the Human vaccinia-related kinase 1 bound to…
6BTW 1.9 Å, Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone…
5UVF 2.0 Å, Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870
6CNX 2.0 Å, Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an…
6VXU 2.0 Å, Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471
9ZKG 2.06 Å, VRK1 in complex with the inhibitor MP-60
6AC9 2.07 Å, Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP
6CMM 2.1 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…
6DD4 2.1 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…

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