4ZVZ: Co-crystal structures of PP5

Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid. Determined by X-ray diffraction at 2.0 Å resolution. Released 27 Apr 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,431
Mol. weight: 153.26 kDa
Ligands: 4TF, MN
Released: 27 Apr 2016

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

Secondary structure: helices and β-sheets

4ZVZ contains 54 α-helices and 74 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: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	182	1	1
β-strand	185	1	1
α-helix	188-199	12
α-helix	202-205	4
α-helix	206-221	16
β-strand	226-229	4	2
β-strand	237-240	4	3
α-helix	247-257	11
β-strand	261	1	4
β-strand	264	1	4
β-strand	266-269	4	3
α-helix	279-292	14
β-strand	297-300	4	3
α-helix	307-313	7
α-helix	315-322	8
α-helix	325-335	11
β-strand	341-344	4	2
β-strand	348-351	4	2
α-helix	363-367	5
α-helix	374-376	3
α-helix	380-386	7
β-strand	388-389	2	5
β-strand	395-397	3	5
β-strand	404-406	3	5
α-helix	408-417	10
β-strand	422-425	4	2
β-strand	434-437	4	2
α-helix	438-440	3
β-strand	442-445	4	2
α-helix	451-453	3
β-strand	459-464	6	3
β-strand	472-476	5	3

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	182	1	6
β-strand	185	1	6
α-helix	188-199	12
α-helix	206-221	16
β-strand	226-229	4	7
β-strand	236-240	5	8
α-helix	247-257	11
β-strand	261	1	9
β-strand	264	1	9
β-strand	266-269	4	8
α-helix	279-292	14
β-strand	297-300	4	8
α-helix	307-313	7
α-helix	315-322	8
α-helix	325-335	11
β-strand	341-344	4	7
β-strand	348-350	3	7
α-helix	363-367	5
α-helix	374-376	3
α-helix	380-386	7
β-strand	388-389	2	10
β-strand	395-397	3	10
β-strand	404-406	3	10
α-helix	408-417	10
β-strand	422-425	4	7
β-strand	434-437	4	7
α-helix	438-440	3
β-strand	442-445	4	7
α-helix	451-453	3
β-strand	459-465	7	8
β-strand	468-476	9	8

Chain C: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	182	1	11
β-strand	185	1	11
α-helix	188-199	12
α-helix	206-221	16
β-strand	226-229	4	12
β-strand	238-240	3	13
β-strand	242	1	14
α-helix	247-257	11
β-strand	261	1	15
β-strand	264	1	15
β-strand	266-269	4	13
α-helix	279-292	14
β-strand	297-300	4	13
α-helix	307-313	7
α-helix	315-322	8
α-helix	325-335	11
β-strand	341-344	4	12
β-strand	348-350	3	12
α-helix	363-367	5
α-helix	374-376	3
α-helix	380-386	7
β-strand	388-389	2	16
β-strand	395-397	3	16
β-strand	404-406	3	16
α-helix	408-417	10
β-strand	422-425	4	12
β-strand	434-437	4	12
α-helix	438-440	3
β-strand	442-445	4	12
β-strand	446	1	14
α-helix	451-453	3
β-strand	459-463	5	13
β-strand	472-476	5	13

Chain D: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	182	1	17
β-strand	185	1	17
α-helix	188-199	12
α-helix	202-205	4
α-helix	206-221	16
β-strand	226-229	4	18
α-helix	230-232	3
β-strand	236-240	5	19
β-strand	242	1	20
α-helix	247-257	11
β-strand	266-269	4	19
α-helix	279-292	14
β-strand	297-300	4	19
α-helix	307-313	7
α-helix	315-322	8
α-helix	325-335	11
β-strand	341-344	4	18
β-strand	348-351	4	18
α-helix	363-368	6
α-helix	374-376	3
α-helix	380-386	7
β-strand	388-389	2	21
β-strand	395-397	3	21
β-strand	404-406	3	21
α-helix	408-417	10
β-strand	422-425	4	18
β-strand	434-437	4	18
β-strand	442-445	4	18
β-strand	446	1	20
α-helix	451-453	3
β-strand	459-465	7	19
β-strand	468-476	9	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein phosphatase 5	A, B, C, D	protein	333	Homo sapiens	P53041 (AlphaFold model)

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

>4ZVZ_1 Serine/threonine-protein phosphatase 5 (chains A, B, C, D)
GASMTIEDEYSGPKLEDGKVTISFMKELMQWYKDQKKLHRKCAYQILVQVKEVLSKLSTL
VETTLKETEKITVCGDTHGQFYDLLNIFELNGLPSETNPYIFNGDFVDRGSFSVEVILTL
FGFKLLYPDHFHLLRGNHETDNMNQIYGFEGEVKAKYTAQMYELFSEVFEWLPLAQCING
KVLIMHGGLFSEDGVTLDDIRKIERNRQPPDSGPMCDLLWSDPQPQNGRSISKRGVSCQF
GPDVTKAFLEENNLDYIIRSHEVKAEGYEVAHGGRCVTVFSAPNYCDQMGNKASYIHLQG
SDLRPQFHQFTAVPHPNVKPMAYANTLLQLGMM

Ligands and cofactors

ID	Name	Formula	Copies
4TF	(1R,2S,3R,4S,5S)-5-(propoxymethyl)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic…	C12 H18 O6	4
MN	Manganese (II) ion	Mn	8

Water and common crystallization additives (PEG, NA) are not listed.

Primary citation

Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C. Chattopadhyay, D., Swingle, M.R., Salter, E.A. et al. Biochem Pharmacol (2016) 109:14-26. DOI 10.1016/j.bcp.2016.03.011 · PubMed

Other PDB entries of the same protein (UniProt P53041 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ZX2 1.23 Å, Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dica…
3H63 1.3 Å, Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms…
3H62 1.4 Å, Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms…
3H61 1.45 Å, Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms…
3H68 1.5 Å, Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Zn2+ atoms…
1S95 1.6 Å, Structure of serine/threonine protein phosphatase 5
3H67 1.65 Å, Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Zn2+ atoms…
5WG8 1.65 Å, Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled…
3H64 1.9 Å, Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms…
5UI1 1.96 Å, Crystal Structure of Human Protein Phosphatase 5C (PP5C) in complex with a triazole…
3H60 2.0 Å, Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Mn2+ atoms
3H69 2.1 Å, Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Zn2+ atoms…

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