4D0L: Phosphatidylinositol 4-kinase beta

Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS. Determined by X-ray diffraction at 2.94 Å resolution. Released 28 May 2014.

Method: X-ray diffraction
Resolution: 2.94 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 15,864
Mol. weight: 270.72 kDa
Ligands: 093, GSP, MG
Released: 28 May 2014

Explore 4D0L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4D0L contains 110 α-helices and 51 β-strands across 6 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: 27 helices, 10 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	400-402	3
α-helix	522-532	11
β-strand	541-549	9	1
α-helix	555-573	19
β-strand	585-587	3	1
β-strand	593-595	3	1
α-helix	597-598	2
β-strand	601-603	3	2
α-helix	604-611	8
α-helix	615-623	9
β-strand	628	1	3
α-helix	629-652	24
β-strand	662-665	4	2
β-strand	670-672	3	2
α-helix	697-702	6
α-helix	709-726	18
α-helix	729-739	11
α-helix	746-748	3
α-helix	753-759	7
α-helix	767-783	17

Chain B: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	4
β-strand	10-18	9	5
α-helix	24-33	10
β-strand	47-55	9	5
β-strand	58-66	9	5
α-helix	71-73	3
α-helix	74-77	4
α-helix	78-81	4
β-strand	86-92	7	5
α-helix	96-100	5
α-helix	102-107	6
α-helix	109-112	4
β-strand	118-124	7	5
α-helix	129-131	3
α-helix	136-145	10
β-strand	149-153	5	5
α-helix	161-173	13

Chain C: 27 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	232-242	11
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	6
α-helix	368-370	3
β-strand	372-373	2	6
β-strand	382-390	9	6
α-helix	398-402	5
α-helix	522-532	11
β-strand	541-549	9	6
α-helix	555-573	19
β-strand	585-589	5	6
β-strand	592-595	4	6
α-helix	596-598	3
β-strand	601-603	3	7
α-helix	604-609	6
α-helix	615-623	9
α-helix	629-652	24
β-strand	662-665	4	7
β-strand	670-672	3	7
α-helix	697-702	6
α-helix	709-726	18
α-helix	729-739	11
α-helix	746-748	3
α-helix	753-759	7
α-helix	767-783	17

Chain D: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	3
β-strand	10-18	9	8
α-helix	24-33	10
β-strand	46-55	10	8
β-strand	58-67	10	8
α-helix	71-73	3
α-helix	74-77	4
α-helix	78-81	4
β-strand	86-92	7	8
α-helix	96-100	5
α-helix	104-107	4
β-strand	118-124	7	8
α-helix	129-131	3
α-helix	136-145	10
β-strand	149-153	5	8
α-helix	161-181	21

Chain E: 27 helices, 12 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	206-219	14
α-helix	233-242	10
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	9
α-helix	368-370	3
β-strand	372-373	2	9
β-strand	382-390	9	9
α-helix	398-402	5
α-helix	522-532	11
β-strand	541-549	9	9
α-helix	555-573	19
β-strand	585-589	5	9
β-strand	592-595	4	9
α-helix	597-598	2
β-strand	601-603	3	10
α-helix	604-611	8
α-helix	615-623	9
β-strand	628	1	4
α-helix	629-652	24
β-strand	655	1	11
β-strand	662-665	4	10
β-strand	670-672	3	10
β-strand	692	1	11
α-helix	697-702	6
α-helix	709-726	18
α-helix	729-739	11
α-helix	746-748	3
α-helix	753-759	7
α-helix	767-783	17

Chain F: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	12
α-helix	24-33	10
β-strand	46-55	10	12
β-strand	58-67	10	12
α-helix	71-73	3
α-helix	74-77	4
α-helix	78-81	4
β-strand	86-92	7	12
α-helix	96-100	5
α-helix	104-107	4
β-strand	118-124	7	12
α-helix	129-131	3
α-helix	136-145	10
β-strand	149-153	5	12
α-helix	161-176	16
α-helix	178-181	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4-kinase beta	A, C, E	protein	566	HOMO SAPIENS	Q9UBF8 (AlphaFold model)
Ras-related protein rab-11A	B, D, F	protein	219	HOMO SAPIENS	P62491 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>4D0L_1 PHOSPHATIDYLINOSITOL 4-KINASE BETA (chains A, C, E)
GSQNNSAKQSWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYLPQ
LLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSDMHISTQRHSRGTKLRK
LILSDELKPAHRKRELPSLSPAPDTGLSPSKRTHQRSKSDATASISLSSNLKRTAANPKV
ENEDEPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAG
FDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPENRRDPEDPSAVAL
KEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVPL
WIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRNF
VQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPRNLGFETSAFKLTTE
FVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNLK
ERFHMSMTEEQLQLLVEQMVDGSMRS

Sequence of entity 2 (B, D, F), FASTA

>4D0L_2 RAS-RELATED PROTEIN RAB-11A (chains B, D, F)
GSHMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDG
KTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI
VIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS
QKQMSDRRENDMSPSNNVVPIHVPPTTENKPKVQCCQNI

Ligands and cofactors

ID	Name	Formula	Copies
093	N-(5-(4-chloro-3-(2-hydroxy-ethylsulfamoyl)- phenylthiazole-2-yl)-acetamide	C14 H16 Cl N3 O4 S2	3
GSP	5'-guanosine-diphosphate-monothiophosphate	C10 H16 N5 O13 P3 S	3
MG	Magnesium ion	Mg	3

Primary citation

Structures of Pi4Kiiibeta Complexes Show Simultaneous Recruitment of Rab11 and its Effectors. Burke, J.E., Inglis, A.J., Perisic, O. et al. Science (2014) 344:1035. DOI 10.1126/SCIENCE.1253397 · PubMed

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…
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
5FBV 3.29 Å, PI4KB in complex with Rab11 and the MI364 Inhibitor

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