PDB-7qjk: Crystal structure of PDE6D in complex with Compound-2

ID or keywords:

Entry

Database: PDB / ID: 7qjk

Title

Crystal structure of PDE6D in complex with Compound-2

Components

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Keywords

TRANSPORT PROTEIN / Inhibitor complex

Function / homology

Function and homology information

ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / small GTPase binding / cilium / RAS processing / cytoplasmic vesicle / cytoskeleton ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Yelland, T. / Ismail, S.

Funding support

United Kingdom, 1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.
Authors: Yelland, T. / Garcia, E. / Parry, C. / Kowalczyk, D. / Wojnowska, M. / Gohlke, A. / Zalar, M. / Cameron, K. / Goodwin, G. / Yu, Q. / Zhu, P.C. / ElMaghloob, Y. / Pugliese, A. / Archibald, L. ...

History

Deposition	Dec 16, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 26, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7qjk.cif.gz	235.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qjk_validation.pdf.gz	484 KB	Display	wwPDB validaton report
Full document	7qjk_full_validation.pdf.gz	496 KB	Display
Data in XML	7qjk_validation.xml.gz	24.3 KB	Display
Data in CIF	7qjk_validation.cif.gz	31.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/7qjk ftp://data.pdbj.org/pub/pdb/validation_reports/qj/7qjk	HTTPS FTP

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Related structure data

Related structure data	7q9qC 7q9rC 7q9sC 7q9uC 7qf9C 5tb5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3t5i-3 7qjk-4 2wp7-d 3t5i-1 7qjk-2 7q9s-2 7qjk-3 2je1-3 7q9u-4 6v4b-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

BBB: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

AAA: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

CCC: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

DDD: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

hetero molecules

71.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

BBB: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

hetero molecules

defined by author
Evidence: surface plasmon resonance, and ligand observed NMR
17.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

AAA: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

hetero molecules

defined by author
17.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

CCC: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

hetero molecules

defined by author
17.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

DDD: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

hetero molecules

defined by author
17.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.548, 76.548, 238.018
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains BBB AAA
2	1	Chains BBB CCC
3	1	Chains BBB DDD
4	1	Chains AAA CCC
5	1	Chains AAA DDD
6	1	Chains CCC DDD

#1: Protein	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GMP-PDE delta / Protein p17 Mass: 17512.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli (E. coli) / References: UniProt: O43924
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-9VO / N-(phenylmethyl)pyridin-2-amine Mass: 184.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₂H₁₂N₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 51.93 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.2 M AmSO4 and 0.1 M ammonium acetate pH 4.9 at 291K

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97951 Å / Relative weight: 1
Reflection	Resolution: 3.1→76.55 Å / Num. obs: 12108 / % possible obs: 90.6 % / Redundancy: 8 % / CC_1/2: 0.975 / Net I/σ(I): 5.6
Reflection shell	Resolution: 3.1→3.31 Å / Num. unique obs: 2194 / CC_1/2: 0.343

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5TB5

5tb5

Resolution: 3.1→64.463 Å / Cor.coef. F_o:F_c: 0.908 / Cor.coef. F_o:F_c free: 0.895 / WR_factor R_free: 0.242 / WR_factor R_work: 0.206 / SU B: 75.858 / SU ML: 0.56 / Average fsc free: 0.8077 / Average fsc work: 0.8319 / Cross valid method: FREE R-VALUE / ESU R Free: 0.601
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2831	625	5.167 %
R_work	0.2464	11470	-
all	0.248	-	-
obs	-	12095	88.829 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 76.627 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.979 Å²	0 Å²	0 Å²
2-	-	-0.979 Å²	0 Å²
3-	-	-	1.958 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→64.463 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4674	0	79	26	4779

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	4873
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.018	4516
X-RAY DIFFRACTION	r_angle_refined_deg	1.091	1.659	6562
X-RAY DIFFRACTION	r_angle_other_deg	1.105	1.597	10439
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.988	5	576
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.758	22.654	260
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.209	15	865
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.759	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.034	0.2	614
X-RAY DIFFRACTION	r_chiral_restr_other	2.517	0.2	5
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	5378
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1111
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	770
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.221	0.2	4285
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	2175
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	2254
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	133
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.054	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.306	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.307	0.2	36
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.208	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	4.159	5.904	2322
X-RAY DIFFRACTION	r_mcbond_other	4.153	5.904	2321
X-RAY DIFFRACTION	r_mcangle_it	6.668	8.852	2892
X-RAY DIFFRACTION	r_mcangle_other	6.667	8.852	2893
X-RAY DIFFRACTION	r_scbond_it	4.284	6.165	2551
X-RAY DIFFRACTION	r_scbond_other	4.282	6.161	2548
X-RAY DIFFRACTION	r_scangle_it	7.244	9.096	3670
X-RAY DIFFRACTION	r_scangle_other	7.242	9.09	3665
X-RAY DIFFRACTION	r_lrange_it	10.666	65.166	5058
X-RAY DIFFRACTION	r_lrange_other	10.665	65.161	5059
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.178	0.05	3971
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.181	0.05	3838
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.209	0.05	3558
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.182	0.05	3890
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.212	0.05	3546
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.213	0.05	3537

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.1-3.181	0.438	54	0.371	856	X-RAY DIFFRACTION	91.4573
3.181-3.268	0.371	44	0.359	799	X-RAY DIFFRACTION	90.9385
3.268-3.362	0.395	35	0.324	815	X-RAY DIFFRACTION	90.715
3.362-3.465	0.281	46	0.31	761	X-RAY DIFFRACTION	89.9666
3.465-3.579	0.303	37	0.285	751	X-RAY DIFFRACTION	89.5455
3.579-3.704	0.297	41	0.275	705	X-RAY DIFFRACTION	89.5558
3.704-3.844	0.316	45	0.244	707	X-RAY DIFFRACTION	88.7839
3.844-4	0.288	39	0.253	673	X-RAY DIFFRACTION	90.4701
4-4.177	0.254	33	0.225	643	X-RAY DIFFRACTION	88.7139
4.177-4.38	0.204	28	0.194	622	X-RAY DIFFRACTION	88.6767
4.38-4.616	0.31	32	0.175	583	X-RAY DIFFRACTION	89.2598
4.616-4.895	0.291	37	0.174	564	X-RAY DIFFRACTION	88.6431
4.895-5.232	0.207	27	0.196	524	X-RAY DIFFRACTION	87.3217
5.232-5.648	0.247	23	0.225	499	X-RAY DIFFRACTION	88.4746
5.648-6.184	0.348	21	0.269	458	X-RAY DIFFRACTION	86.9328
6.184-6.907	0.317	24	0.274	412	X-RAY DIFFRACTION	85.6581
6.907-7.964	0.271	24	0.254	355	X-RAY DIFFRACTION	85.3604
7.964-9.725	0.251	14	0.219	327	X-RAY DIFFRACTION	85.25
9.725-13.632	0.172	11	0.211	259	X-RAY DIFFRACTION	84.6395
13.632-64.46	0.228	10	0.316	157	X-RAY DIFFRACTION	81.068

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.8833	-0.2182	0.02	0.1686	0.3968	1.5265	0.0995	-0.0531	0.013	-0.0477	-0.0298	-0.0111	0.0056	-0.0081	-0.0697	0.1583	-0.0164	-0.0179	0.1666	0.012	0.3855	25.4388	-30.3751	3.3325
2	0.6472	-0.0532	0.6442	0.632	0.4537	1.2563	0.2298	0.0896	0.1242	-0.0025	-0.1854	0.0844	0.1438	0.0596	-0.0444	0.1673	-0.0457	0.1083	0.1283	-0.0729	0.5001	21.6677	-2.7442	-2.5165
3	0.9912	0.9591	0.4384	1.3492	1.0705	1.2025	0.0225	-0.0321	0.2946	0.1344	-0.0459	0.2014	0.2034	-0.0101	0.0234	0.1116	-0.0618	0.0594	0.189	-0.0546	0.4229	1.8318	-16.2178	10.5483
4	1.1222	-0.2298	0.3343	0.2421	-0.3796	0.6351	-0.0781	-0.0572	0.0212	0.0135	-0.0676	-0.0204	-0.0408	0.1282	0.1457	0.0643	-0.1095	-0.0087	0.3044	-0.0689	0.3872	-9.3316	-34.9871	23.4969

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	BBB	0 - 150
2	X-RAY DIFFRACTION	2	ALL	AAA	0 - 150
3	X-RAY DIFFRACTION	3	ALL	CCC	1 - 150
4	X-RAY DIFFRACTION	4	ALL	DDD	4 - 150

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