6FAD: SR protein kinase 1

SR protein kinase 1 (SRPK1) in complex with the RGG-box of HSV1 ICP27. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Sept 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Herpes simplex virus (type 1 / strain 17)
Chains: 8
Atoms: 12,099
Mol. weight: 287.93 kDa
Ligands: PO4
Released: 25 Sept 2019

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

Secondary structure: helices and β-sheets

6FAD contains 94 α-helices and 60 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: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
β-strand	75-76	2	1
β-strand	80-88	9	1
β-strand	92-99	8	1
β-strand	104-111	8	1
α-helix	115-133	19
α-helix	139-143	5
β-strand	144	1	2
β-strand	147-154	8	1
β-strand	159-165	7	1
β-strand	171	1	2
α-helix	172-178	7
α-helix	186-201	16
α-helix	202-207	6
β-strand	209-210	2	3
α-helix	216-218	3
β-strand	219-221	3	2
α-helix	225-229	5
α-helix	485-490	6
β-strand	493-495	3	2
α-helix	498-500	3
β-strand	502-503	2	3
β-strand	506	1	3
α-helix	515-517	3
α-helix	520-524	5
α-helix	531-546	16
α-helix	561-573	13
α-helix	575-577	3
α-helix	578-583	6
α-helix	587-589	3
β-strand	591	1	4
β-strand	597	1	4
α-helix	608-610	3
α-helix	611-615	5
α-helix	620-630	11
α-helix	631-634	4
α-helix	638-640	3
α-helix	642-643	2
α-helix	644-648	5

Chain B: 25 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
β-strand	75-76	2	5
β-strand	80-88	9	5
β-strand	92-99	8	5
β-strand	104-111	8	5
α-helix	115-133	19
α-helix	139-143	5
β-strand	144	1	6
β-strand	147-155	9	5
β-strand	158-165	8	5
β-strand	171	1	6
α-helix	172-178	7
α-helix	186-201	16
α-helix	202-207	6
β-strand	209-210	2	7
α-helix	216-218	3
β-strand	219-221	3	6
α-helix	225-230	6
α-helix	485-490	6
β-strand	493-495	3	6
β-strand	502-503	2	7
β-strand	506	1	7
α-helix	515-517	3
α-helix	520-524	5
α-helix	531-546	16
α-helix	561-573	13
α-helix	575-577	3
α-helix	578-583	6
α-helix	587-589	3
β-strand	591	1	8
β-strand	597	1	8
α-helix	608-610	3
α-helix	611-615	5
α-helix	616	1
α-helix	620-630	11
α-helix	631-634	4
α-helix	638-640	3
α-helix	642-643	2
α-helix	644-648	5
α-helix	651-654	4

Chain C: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
α-helix	67-69	3
β-strand	75-76	2	9
β-strand	80-88	9	9
β-strand	92-99	8	9
β-strand	104-111	8	9
α-helix	115-133	19
α-helix	139-143	5
β-strand	144	1	10
β-strand	147-155	9	9
β-strand	158-165	8	9
β-strand	171	1	10
α-helix	172-178	7
α-helix	186-201	16
α-helix	202-207	6
β-strand	209-210	2	11
α-helix	216-218	3
β-strand	219-221	3	10
α-helix	225-230	6
α-helix	485-490	6
β-strand	493-495	3	10
β-strand	502-503	2	11
β-strand	506	1	11
α-helix	515-517	3
α-helix	520-524	5
α-helix	531-546	16
α-helix	561-573	13
α-helix	575-577	3
α-helix	578-583	6
α-helix	587-589	3
β-strand	591	1	12
β-strand	597	1	12
α-helix	608-610	3
α-helix	611-615	5
α-helix	620-633	14
α-helix	638-640	3
α-helix	642-643	2
α-helix	644-648	5
α-helix	651-654	4

Chain D: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	67-69	3
β-strand	75-76	2	13
β-strand	80-88	9	13
β-strand	92-99	8	13
β-strand	104-111	8	13
α-helix	115-133	19
α-helix	139-143	5
β-strand	144	1	14
β-strand	147-155	9	13
β-strand	158-165	8	13
β-strand	171	1	14
α-helix	172-177	6
α-helix	186-201	16
α-helix	202-207	6
β-strand	209-210	2	15
α-helix	216-218	3
β-strand	219-221	3	14
α-helix	225-230	6
α-helix	485-490	6
β-strand	493-495	3	14
β-strand	502-503	2	15
β-strand	506	1	15
α-helix	515-517	3
α-helix	520-524	5
α-helix	531-546	16
α-helix	561-573	13
α-helix	575-577	3
α-helix	578-583	6
α-helix	587-589	3
β-strand	591	1	16
β-strand	597	1	16
α-helix	608-614	7
α-helix	620-633	14
α-helix	638-640	3
α-helix	644-648	5
α-helix	651-654	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SRSF protein kinase 1	A, B, C, D	protein	618	Homo sapiens	Q96SB4 (AlphaFold model)
mRNA export factor	E, F, G, H	protein	16	Herpes simplex virus (type 1 / strain 17)	P10238

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

>6FAD_1 SRSF protein kinase 1 (chains A, B, C, D)
GSHMPEQEEEILGSDDDEQEDPNDYCKGGYHLVKIGDLFNGRYHVIRKLGWGHFSTVWLS
WDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSDPNDPNREMVVQLLDDFKISGVN
GTHICMVFEVLGHHLLKWIIKSNYQGLPLPCVKKIIQQVLQGLDYLHTKCRIIHTDIKPE
NILLSVNEQYIRRLAAEATEWQRSGAPPPSGSAVSTAPQPKPADKMSKNKKKKLKKKQKR
QAELLEKRMQEIEEMEKESGPGQKRPNKQEESESPVERPLKENPPNKMTQEKLEESSTIG
QDQTLMERDTEGGAAEINCNGVIEVINYTQNSNNETLRHKEDLHNANDCDVQNLNQESSF
LSSQNGDSSTSQETDSCTPITSEVSDTMVCQSSSTVGQSFSEQHISQLQESIRAEIPCED
EQEQEHNGPLDNKGKSTAGNFLVNPLEPKNAEKLKVKIADLGNACWVHKHFTEDIQTRQY
RSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEEYTRDEDHIALIIELLGKVP
RKLIVAGKYSKEFFTKKGDLKHITKLKPWGLFEVLVEKYEWSQEEAAGFTDFLLPMLELI
PEKRATAAECLRHPWLNS

Sequence of entity 2 (E, F, G, H), FASTA

>6FAD_2 mRNA export factor (chains E, F, G, H)
ARGGRRGRRRGRGRGG

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	5

Primary citation

Molecular Mechanism of SR Protein Kinase 1 Inhibition by the Herpes Virus Protein ICP27. Tunnicliffe, R.B., Hu, W.K., Wu, M.Y. et al. mBio (2019) 10. DOI 10.1128/mBio.02551-19 · PubMed

Other PDB entries of the same protein (UniProt Q96SB4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NNG 1.2 Å, Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated…
5MY8 1.7 Å, Crystal structure of SRPK1 in complex with SPHINX31
1WAK 1.73 Å, X-ray structure of SRPK1
5MXX 1.75 Å, Crystal structure of human SR protein kinase 1 (SRPK1) in complex with compound 1
4WUA 2.0 Å, Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340
7DD1 2.05 Å, Crystal structure of SRPK1 in complex with a peptide inhibitor
7PQS 2.2 Å, SRPK1 in complex with MSC2711186
7ZKS 2.28 Å, SRPK1 in complex with inhibitor
5XV7 2.32 Å, SRPK1 in complex with Alectinib
1WBP 2.4 Å, SRPK1 bound to 9mer docking motif peptide
3BEG 2.9 Å, Crystal structure of SR protein kinase 1 complexed to its substrate ASF/SF2

Browse structure collections

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