PDB-6ohp: Structure of compound 1 (halopemide) bound human Phospholipase D2...

ID or keywords:

Entry

Database: PDB / ID: 6ohp

Title

Structure of compound 1 (halopemide) bound human Phospholipase D2 catalytic domain

Components

Phospholipase D2

Keywords

hydrolase/hydrolase inhibitor / phosphodiesterase / HYDROLASE / HKD motif / hydrolase-hydrolase inhibitor complex

Function / homology

Function and homology information

Synthesis of PG / phosphatidic acid biosynthetic process / Synthesis of PA / synaptic vesicle recycling / regulation of vesicle-mediated transport / phospholipase D / phospholipid catabolic process / G protein-coupled receptor internalization / phospholipase D activity / small GTPase-mediated signal transduction ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Metrick, C.M. / Chodaparambil, J.V.

Citation

Journal: Nat.Chem.Biol. / Year: 2020
Title: Human PLD structures enable drug design and characterization of isoenzyme selectivity.
Authors: Metrick, C.M. / Peterson, E.A. / Santoro, J.C. / Enyedy, I.J. / Murugan, P. / Chen, T. / Michelsen, K. / Cullivan, M. / Spilker, K.A. / Kumar, P.R. / May-Dracka, T.L. / Chodaparambil, J.V.

History

Deposition	Apr 6, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Nov 15, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ohp.cif.gz	946.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6ohp.ent.gz	788.9 KB	Display	PDB format
PDBx/mmJSON format	6ohp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ohp_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6ohp_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6ohp_validation.xml.gz	87.8 KB	Display
Data in CIF	6ohp_validation.cif.gz	115.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oh/6ohp ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6ohp	HTTPS FTP

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Related structure data

Related structure data	6ohmSC 6ohoC 6ohqC 6ohrC 6ohsC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ohs-1 6ohs-2 6ohs-4 6oho-2 6oho-1 6ohq-2 6ohm-1 5fiw-2 6wy0-1 4dl1-12 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

6ohmSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#239 - Nov 2019 Phospholipase A2 similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (2) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #245 - May 2020 Spliceosomes similarity (1) #136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #148 - Apr 2012 Ras Protein similarity (1)

Deposited unit

A: Phospholipase D2

B: Phospholipase D2

C: Phospholipase D2

D: Phospholipase D2

hetero molecules

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

1

A: Phospholipase D2

hetero molecules

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

2

B: Phospholipase D2

hetero molecules

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

3

C: Phospholipase D2

hetero molecules

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

4

D: Phospholipase D2

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.186, 132.509, 114.638
Angle α, β, γ (deg.)	90.00, 100.34, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Phospholipase D2 / hPLD2 / Choline phosphatase 2 / PLD1C / Phosphatidylcholine-hydrolyzing phospholipase D2 Mass: 72926.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14939, phospholipase D
#2: Chemical	ChemComp-MJV / N-{2-[4-(5-chloro-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]ethyl}-4-fluorobenzamide / Halopemide Mass: 416.876 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₂ClFN₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.28 Å³/Da / Density % sol: 46.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium tartrate di-basic, 22% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 80186 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC_1/2: 0.99 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2.6→2.7 Å / Num. unique obs: 7999

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6OHM

6ohm

Resolution: 2.6→48.293 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.38

	R_factor	Num. reflection	% reflection
R_free	0.2758	4008	5 %
R_work	0.2397	-	-
obs	0.2415	80186	99.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.6→48.293 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18797	0	159	245	19201

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	19449
X-RAY DIFFRACTION	f_angle_d	0.68	26440
X-RAY DIFFRACTION	f_dihedral_angle_d	15.295	11415
X-RAY DIFFRACTION	f_chiral_restr	0.046	2893
X-RAY DIFFRACTION	f_plane_restr	0.005	3353

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 (%)
2.6-2.6306	0.411	146	0.3746	2593	X-RAY DIFFRACTION	99
2.6306-2.6627	0.4015	149	0.3496	2622	X-RAY DIFFRACTION	100
2.6627-2.6964	0.3995	140	0.3503	2633	X-RAY DIFFRACTION	100
2.6964-2.7319	0.3731	125	0.3529	2613	X-RAY DIFFRACTION	100
2.7319-2.7693	0.3968	130	0.3488	2634	X-RAY DIFFRACTION	100
2.7693-2.8088	0.3531	139	0.335	2621	X-RAY DIFFRACTION	100
2.8088-2.8508	0.3624	135	0.3145	2622	X-RAY DIFFRACTION	100
2.8508-2.8953	0.3914	135	0.3202	2625	X-RAY DIFFRACTION	100
2.8953-2.9428	0.3431	125	0.2965	2636	X-RAY DIFFRACTION	100
2.9428-2.9935	0.3091	144	0.2881	2594	X-RAY DIFFRACTION	100
2.9935-3.0479	0.3168	135	0.285	2628	X-RAY DIFFRACTION	100
3.0479-3.1065	0.3374	119	0.2725	2652	X-RAY DIFFRACTION	100
3.1065-3.1699	0.2891	117	0.2623	2686	X-RAY DIFFRACTION	100
3.1699-3.2389	0.3328	138	0.2684	2590	X-RAY DIFFRACTION	100
3.2389-3.3142	0.2819	132	0.2611	2681	X-RAY DIFFRACTION	100
3.3142-3.397	0.289	155	0.2435	2611	X-RAY DIFFRACTION	100
3.397-3.4889	0.2777	150	0.2313	2592	X-RAY DIFFRACTION	100
3.4889-3.5915	0.2375	136	0.2184	2634	X-RAY DIFFRACTION	100
3.5915-3.7074	0.2447	135	0.2159	2615	X-RAY DIFFRACTION	99
3.7074-3.8398	0.2852	143	0.2078	2618	X-RAY DIFFRACTION	100
3.8398-3.9935	0.2389	147	0.2146	2628	X-RAY DIFFRACTION	100
3.9935-4.1752	0.2464	142	0.208	2625	X-RAY DIFFRACTION	100
4.1752-4.3951	0.2277	131	0.1968	2632	X-RAY DIFFRACTION	100
4.3951-4.6703	0.2349	149	0.1927	2622	X-RAY DIFFRACTION	99
4.6703-5.0305	0.2199	146	0.1929	2622	X-RAY DIFFRACTION	99
5.0305-5.5361	0.3028	134	0.2091	2667	X-RAY DIFFRACTION	100
5.5361-6.3357	0.2536	138	0.2322	2643	X-RAY DIFFRACTION	100
6.3357-7.9765	0.2474	146	0.2225	2641	X-RAY DIFFRACTION	99
7.9765-48.3013	0.2204	147	0.2062	2598	X-RAY DIFFRACTION	96

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	2.4587	-0.0122	0.1237	4.6435	-0.3242	2.2896	0.0879	0.5913	0.2895	-0.5848	-0.2457	-0.3694	-0.2519	0.2284	0.2149	0.3759	0.0365	-0.0416	0.6159	0.1092	0.588	-10.2597	-41.0596	45.8896
2	3.9885	0.0521	0.0866	1.3311	-0.8367	2.1679	0.0266	-0.487	-0.2236	0.1784	-0.0826	-0.274	0.1596	0.1109	0.0467	0.4079	-0.0294	-0.0187	0.4461	-0.013	0.3781	-10.359	-53.5955	69.5901
3	2.457	-1.7467	0.8231	1.4144	-0.5214	4.5499	-0.1375	0.071	0.337	0.3469	0.251	0.2952	-0.6502	0.2926	0.0162	0.396	-0.0305	0.0598	0.1972	0.0516	0.4945	36.4209	-7.1101	6.5717
4	0.6326	0.4464	0.3082	3.3123	0.0576	1.1783	-0.0285	0.089	0.0587	-0.3267	-0.0669	-0.0719	-0.0266	0.1026	0.0568	0.2641	0.0058	0.0145	0.2865	0.0451	0.3788	43.0417	-13.6799	-8.5083
5	0.7363	0.2593	-0.3668	2.8348	-0.3349	1.269	0.0514	-0.0264	-0.1946	0.1332	0.0491	-0.1463	-0.0552	0.0538	-0.0146	0.2711	0.0119	-0.0131	0.2981	-0.0157	0.4537	48.1015	-20.7931	16.3188
6	0.5029	-0.0542	0.4306	2.1431	-0.065	1.1886	0.0291	-0.0124	-0.1674	0.1543	-0.0172	-0.0569	0.1848	-0.0544	-0.0022	0.3226	-0.0149	-0.0386	0.3146	0.0337	0.4723	40.9424	-32.0928	12.979
7	1.6478	-0.2187	0.1037	0.7294	0.0274	1.9583	0.0095	-0.3916	0.117	0.2312	-0.0031	-0.0958	-0.0139	0.0072	0.0088	0.4348	-0.0034	0.0357	0.2639	-0.0408	0.252	39.6707	-39.8616	61.7853
8	1.4018	0.3319	0.1407	1.7383	0.1034	0.7036	0.0596	-0.2751	-0.0244	0.3231	-0.029	0.025	0.0159	-0.1437	-0.018	0.435	-0.0193	0.0572	0.3164	0.0269	0.1862	35.6359	-46.8681	63.6995
9	1.342	-0.4791	-0.3149	2.3812	0.3102	1.3544	0.0133	0.1575	-0.0358	-0.3375	-0.0799	0.4422	0.0577	-0.2114	-0.0091	0.4243	0.0012	-0.0808	0.2889	0.0275	0.3268	30.8202	-46.3214	43.8502
10	1.6238	0.2419	-0.1321	1.8618	-0.4106	0.7424	0.0427	0.1327	-0.3556	-0.2668	-0.0212	0.165	0.0859	-0.0402	-0.0339	0.4948	0.0156	-0.0397	0.2745	-0.0388	0.2385	37.9578	-61.559	43.3118
11	1.6723	-0.3201	0.7175	0.549	-0.4858	3.7688	-0.1148	-0.5109	0.2561	0.1416	-0.0061	0.0897	-0.0463	-0.2758	0.2419	0.3407	-0.0235	0.0514	0.5942	-0.0421	0.7081	4.7144	-12.9894	11.0027
12	2.5636	-0.212	0.669	0.8705	0.3643	1.7723	0.0678	-0.7588	-0.1606	0.3136	-0.1006	0.3316	0.1566	-0.3429	0.0309	0.3779	-0.0706	0.0263	0.6665	0.0586	0.5248	0.558	-23.7193	12.2322
13	2.6689	0.0886	-0.2408	2.0537	0.1713	2.5733	-0.0262	0.0023	0.3674	-0.0877	-0.054	0.1957	-0.1154	-0.2262	0.0916	0.301	0.0572	-0.0469	0.6091	0.0403	0.7417	-3.5732	-13.1932	-5.7957
14	1.6809	-0.3141	-0.4716	1.2688	0.2239	1.6018	-0.0758	0.2102	-0.203	-0.032	-0.1105	0.1687	0.2928	-0.181	0.1722	0.4164	-0.0031	-0.0481	0.5368	0.0098	0.6374	3.0056	-28.1306	-12.9852
15	2.368	0.0108	-0.1433	1.2246	-0.2009	4.0123	-0.1387	0.5524	0.5643	-0.1102	0.0322	-0.1478	0.0204	0.3542	0.0062	0.3726	0.0289	0.0593	0.5397	0.106	0.5565	-15.1556	-41.9864	45.6567
16	2.4908	-0.8251	0.8424	1.5412	-0.6028	1.8256	0.0395	0.5642	0.2447	-0.3231	-0.0521	-0.3335	0.1772	0.2926	-0.0025	0.4017	0.0346	0.1266	0.558	-0.0368	0.4544	-10.9692	-51.4841	44.3793

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 526 through 599 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 600 through 933 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 317 through 353 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 354 through 594 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 595 through 716 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 717 through 933 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 318 through 412 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 413 through 568 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 569 through 716 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 717 through 933 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 319 through 412 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 413 through 535 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 536 through 716 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 717 through 933 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 317 through 412 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 413 through 525 )

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