5FBW: PI4KB

PI4KB in complex with Rab11 and the MI369 Inhibitor. Determined by X-ray diffraction at 3.49 Å resolution. Released 28 Dec 2016.

Method: X-ray diffraction
Resolution: 3.49 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,023
Mol. weight: 91.14 kDa
Ligands: 5W8, GSP
Released: 28 Dec 2016

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

Secondary structure: helices and β-sheets

5FBW contains 35 α-helices and 20 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: 28 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	129-134	6
α-helix	141-150	10
α-helix	154-163	10
α-helix	164-166	3
α-helix	169-173	5
α-helix	176-185	10
α-helix	188-204	17
α-helix	206-218	13
α-helix	233-241	9
α-helix	308-323	16
α-helix	324-326	3
α-helix	330-342	13
α-helix	343-347	5
β-strand	361-365	5	1
α-helix	368-370	3
β-strand	372-373	2	1
β-strand	382-390	9	1
α-helix	394-396	3
α-helix	398-402	5
α-helix	537-547	11
β-strand	556-564	9	1
α-helix	570-588	19
β-strand	600-602	3	1
β-strand	608-610	3	1
α-helix	611-613	3
β-strand	616-618	3	2
α-helix	619-626	8
α-helix	630-638	9
α-helix	644-666	23
β-strand	677-680	4	2
β-strand	685-687	3	2
α-helix	712-717	6
α-helix	724-741	18
α-helix	744-754	11
α-helix	761-763	3
α-helix	768-774	7
α-helix	782-797	16

Chain B: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	3
α-helix	24-33	10
α-helix	41-43	3
β-strand	47-51	5	3
β-strand	54-55	2	4
β-strand	58-59	2	4
β-strand	60-66	7	3
β-strand	86-92	7	3
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	3
α-helix	129-131	3
α-helix	136-145	10
β-strand	149	1	3
β-strand	152	1	3
β-strand	154	1	5
β-strand	159	1	5
α-helix	161-173	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta	A	protein	572	Homo sapiens	Q9UBF8 (AlphaFold model)
Ras-related protein Rab-11A	B	protein	221	Homo sapiens	P62491 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5FBW_1 Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta (chains A)
SWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYLPQLLNMYIHMD
EDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSDMHISTQRHSRGTKLRKLILSDELKP
AHRKRELPSLSPAPDTGLSPSKRTHQRSKSDATASISLSSNLKRTASNPKVENEDEELSS
STESIDNSFSSPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARV
WLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPENRRDPED
PSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWE
QERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFL
SAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPRNLGFETSA
FKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSS
TIRNLKERFHMSMTEEQLQLLVEQMVDGSMRS

Sequence of entity 2 (B), FASTA

>5FBW_2 Ras-related protein Rab-11A (chains B)
GAMGSMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV
DGKTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADS
NIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRI
VSQKQMSDRRENDMSPSNNVVPIHVPPTTENKPKVQCCQNI

Ligands and cofactors

ID	Name	Formula	Copies
5W8	~{N}-[2-[[6-chloranyl-3-[4-methoxy-3-[[(2~{R})-1-oxidanylbutan-2-yl]sulfamoyl]p…	C22 H29 Cl N6 O5 S	1
GSP	5'-guanosine-diphosphate-monothiophosphate	C10 H16 N5 O13 P3 S	1

Primary citation

PI4KB in complex with Rab11 and the MI369 Inhibitor. Chalupska, D., Mejdrova, I., Nencka, R. et al. To be published.

Other PDB entries of the same protein (UniProt Q9UBF8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Q6F 1.51 Å, Human PI4KIIIB in complex with covalently bound inhibitor (compound 4)
8Q6G 1.54 Å, Human PI4KIIIB in complex with covalently bound inhibitor (compound 8)
8Q6H 1.94 Å, Human PI4KIIIB in complex with covalently bound inhibitor (compound 11)
5NAS 2.08 Å, Crystal structure of human 14-3-3 zeta in complex with PI4KIIIB peptide
5LX2 2.58 Å, Lt 14-3-3 in complex with PI4KIIIB peptide
5C46 2.65 Å, Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta…
6GL3 2.77 Å, Crystal structure of human Phosphatidylinositol 4-kinase III beta (PI4KIIIbeta) in…
4D0L 2.94 Å, Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS
8VOF 3.0 Å, GI targeted CpPI4K inhibitor
5C4G 3.2 Å, Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta…
5EUQ 3.2 Å, Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta…
5FBR 3.28 Å, PI4KB in complex with Rab11 and the MI359 Inhibitor

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