5EUQ: Ras-related protein Rab-11A

Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with a potent and selective inhibitor in complex with GDP loaded Rab11. Determined by X-ray diffraction at 3.2 Å resolution. Released 24 Feb 2016.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,040
Mol. weight: 86.5 kDa
Ligands: GDP, 5S8
Released: 24 Feb 2016

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

Secondary structure: helices and β-sheets

5EUQ contains 35 α-helices and 21 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 B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	13-17	5	1
α-helix	24-32	9
β-strand	47-55	9	1
β-strand	58-66	9	1
α-helix	78-81	4
β-strand	86-92	7	1
α-helix	96-100	5
α-helix	102-112	11
α-helix	117	1
β-strand	118-124	7	1
α-helix	129-131	3
α-helix	136-145	10
β-strand	149-152	4	1
β-strand	154	1	2
β-strand	159	1	2
α-helix	161-171	11

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	176-184	9
α-helix	188-204	17
α-helix	206-218	13
α-helix	234-240	7
α-helix	308-322	15
α-helix	323-325	3
α-helix	330-342	13
α-helix	344-347	4
β-strand	350	1	3
β-strand	361-365	5	3
α-helix	368-370	3
β-strand	372-373	2	3
α-helix	380-381	2
β-strand	382-390	9	3
α-helix	398-401	4
α-helix	522-531	10
β-strand	541-549	9	3
α-helix	555-573	19
β-strand	585-587	3	3
β-strand	593-595	3	3
β-strand	601-603	3	4
α-helix	604-611	8
α-helix	615-622	8
α-helix	629-651	23
β-strand	654	1	5
β-strand	662-665	4	4
β-strand	670-672	3	4
β-strand	678	1	5
α-helix	697-702	6
α-helix	709-726	18
α-helix	729-740	12
α-helix	746-748	3
α-helix	753-759	7
α-helix	767-781	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-11A	B	protein	219	Homo sapiens	P62491 (AlphaFold model)
Phosphatidylinositol 4-kinase beta	E	protein	529	Homo sapiens	O02810 (AlphaFold model), Q9UBF8 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5EUQ_1 Ras-related protein Rab-11A (chains B)
GSHMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDG
KTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI
VIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS
QKQMSDRRENDMSPSNNVVPIHVPPTTENKPKVQCCQNI

Sequence of entity 2 (E), FASTA

>5EUQ_2 Phosphatidylinositol 4-kinase beta (chains E)
GSHMQNNSAKQSWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYL
PQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSDMHISTQRHSRGTKL
RKLILSDELKPANLKRTAANPKVENEDEPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQ
RLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFD
TTSVPARIPENRRDPEDPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLR
QELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSL
LDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDF
GFILSSSPRNLGFETSAFKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQI
VEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSMRS

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
5S8	~{N}-[5-[3-[[(4-hydroxyphenyl)amino]-bis(oxidanyl)-$l^{4}-sulfanyl]-4-methoxy-p…	C23 H27 N3 O5 S2	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Design and Structural Characterization of Potent and Selective Inhibitors of Phosphatidylinositol 4 Kinase III beta. Rutaganira, F.U., Fowler, M.L., McPhail, J.A. et al. J Med Chem (2016) 59:1830-1839. DOI 10.1021/acs.jmedchem.5b01311 · PubMed

Other PDB entries of the same protein (UniProt P62491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OIX 1.7 Å, X-ray structure of the small G protein Rab11a in complex with GDP and Pi
2D7C 1.75 Å, Crystal structure of human Rab11 in complex with FIP3 Rab-binding domain
2HV8 1.86 Å, Crystal structure of GTP-bound Rab11 in complex with FIP3
1OIV 1.98 Å, X-ray structure of the small G protein Rab11a in complex with GDP
1YZK 2.0 Å, GppNHp bound Rab11 GTPase
4C4P 2.0 Å, Crystal Structure of Wild-Type Rab11 Complexed to FIP2
1OIW 2.05 Å, X-ray structure of the small G protein Rab11a in complex with GTPgammaS
5JCZ 2.06 Å, Rab11 bound to MyoVa-GTD
6IY1 2.11 Å, Structure of human Ras-related protein Rab11
4LX0 2.19 Å, Crystal structure of Myo5b globular tail domain in complex with active Rab11a
5EZ5 2.4 Å, Crystal structure of active Rab11A (S20V) in complex with GTP
2GZD 2.44 Å, Crystal Structure of Rab11 in Complex with Rab11-FIP2

Browse structure collections

About this viewer

MolViewer shows 5EUQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.