5UVF: Human vaccinia-related kinase

Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870. Determined by X-ray diffraction at 2.0 Å resolution. Released 22 Mar 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,449
Mol. weight: 167.21 kDa
Ligands: PO4, 7DZ
Released: 22 Mar 2017

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

Secondary structure: helices and β-sheets

5UVF contains 69 α-helices and 49 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: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	36-42	7	1
β-strand	51-56	6	1
α-helix	61-62	2
β-strand	68-74	7	1
α-helix	78-90	13
α-helix	93-103	11
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	174	1	3
α-helix	180-182	3
β-strand	183-186	4	2
β-strand	193-195	3	2
β-strand	202	1	3
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 B: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	4
β-strand	36-42	7	4
β-strand	50-56	7	4
β-strand	68-74	7	4
α-helix	78-90	13
α-helix	93-102	10
α-helix	111-112	2
β-strand	113-121	9	4
β-strand	124-132	9	4
β-strand	134-137	4	5
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	6
α-helix	180-182	3
β-strand	183-186	4	5
β-strand	193-195	3	5
β-strand	202-203	2	6
α-helix	206-208	3
α-helix	210-212	3
α-helix	230-233	4
α-helix	236-238	3
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 C: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	7
β-strand	36-44	9	7
β-strand	51-56	6	7
β-strand	68-74	7	7
α-helix	79-90	12
α-helix	93-102	10
α-helix	111-112	2
β-strand	113-118	6	7
β-strand	126-132	7	7
β-strand	137	1	8
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	9
α-helix	180-182	3
β-strand	183-185	3	8
β-strand	193-195	3	8
β-strand	202-203	2	9
α-helix	206-208	3
α-helix	210-213	4
β-strand	215	1	10
α-helix	217-219	3
α-helix	230-233	4
β-strand	236	1	10
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

Chain D: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	11
β-strand	36-38	3	11
β-strand	39-42	4	12
β-strand	51-54	4	12
β-strand	68-72	5	12
α-helix	79-90	12
α-helix	93-102	10
α-helix	111-112	2
β-strand	113-117	5	12
β-strand	128-132	5	12
β-strand	134-137	4	13
α-helix	138-144	7
α-helix	151-170	20
β-strand	173-174	2	14
α-helix	180-182	3
β-strand	183-186	4	13
β-strand	189-195	7	13
β-strand	202-203	2	14
α-helix	206-208	3
α-helix	210-213	4
β-strand	215	1	15
α-helix	217-219	3
α-helix	230-233	4
β-strand	236	1	15
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase VRK1	A, B, C, D	protein	364	Homo sapiens	Q99986 (AlphaFold model)

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

>5UVF_1 Serine/threonine-protein kinase VRK1 (chains A, B, C, D)
SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSE
SVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHD
KNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKA
SNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSR
RGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIA
KYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAA
EIEE

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	10
7DZ	(7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8…	C19 H23 F2 N5 O2	4

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…
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…
6CQH 2.15 Å, Crystal Structure of the Human vaccinia-related kinase bound to a…

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