5D3Y: PDB entry 5D3Y

Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound. Determined by X-ray diffraction at 1.95 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,548
Mol. weight: 39.57 kDa
Ligands: 4IP
Released: 20 Apr 2016

Explore 5D3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D3Y contains 14 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	250-255	6
β-strand	257-258	2	1
β-strand	262	1	2
α-helix	265-268	4
β-strand	272-282	11	1
β-strand	285-294	10	1
β-strand	297-303	7	1
α-helix	304-305	2
β-strand	325-332	8	1
α-helix	333-335	3
β-strand	337-340	4	1
β-strand	358-363	6	1
α-helix	364-366	3
β-strand	368-373	6	1
α-helix	377-395	19
α-helix	397-398	2

Chain B: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	250-255	6
β-strand	257-258	2	3
α-helix	265-268	4
β-strand	272-282	11	3
β-strand	285-294	10	3
β-strand	297-303	7	3
α-helix	304-305	2
β-strand	325-332	8	3
α-helix	333-335	3
β-strand	337-340	4	3
β-strand	343	1	2
β-strand	345	1	4
β-strand	355	1	4
β-strand	358-363	6	3
α-helix	364-366	3
β-strand	368-373	6	3
α-helix	377-395	19
α-helix	397-398	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein	A, B	protein	167	Homo sapiens	Q8TCU6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5D3Y_1 Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein (chains A, B)
GEFEKLEALEQLQSHIEGWEGSNLTDICTQLLLQGTLLKISAGNIQERAFFLFDNLLVYC
KRKSRVTGSKKSTKRTKSINGSLYIFRGRINTEVMEVENVEDGTADYHSNGYTVTNGWKI
HNTAKNKWFVCMAKTAEEKQKWLDAIIREREQRESLKLGMERDAYVM

Ligands and cofactors

ID	Name	Formula	Copies
4IP	Inositol-(1,3,4,5)-tetrakisphosphate	C6 H16 O18 P4	2

Primary citation

Structural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3. Cash, J.N., Davis, E.M., Tesmer, J.J. Structure (2016) 24:730-740. DOI 10.1016/j.str.2016.02.022 · PubMed

Other PDB entries of the same protein (UniProt Q8TCU6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5D3X 1.69 Å, Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound
5D3V 1.85 Å, Crystal Structure of the P-Rex1 PH domain with Citrate Bound
5D3W 1.85 Å, Crystal Structure of the P-Rex1 PH domain with Sulfate Bound
5D27 1.92 Å, Crystal Structure of the P-Rex1 PH domain
4YON 1.95 Å, P-Rex1:Rac1 complex
3QIK 2.29 Å, Crystal structure of the first PDZ domain of PREX1
6VSK 3.12 Å, Crystal structure of the P-Rex1 DEP1 domain
6PCV 3.2 Å, Single Particle Reconstruction of Phosphatidylinositol (3,4,5) trisphosphate-dependent…
5FI1 3.2 Å, Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42
7RX9 3.22 Å, Structure of autoinhibited P-Rex1
5FI0 3.28 Å, Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1
8TUA 4.1 Å, Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4)

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