PDB-5fuq: CRYSTAL STRUCTURE OF THE H80R VARIANT OF NQO1 BOUND TO DICOUMAROL

ID or keywords:

Entry

Database: PDB / ID: 5fuq

Title

CRYSTAL STRUCTURE OF THE H80R VARIANT OF NQO1 BOUND TO DICOUMAROL

Components

NAD(P)H DEHYDROGENASE [QUINONE] 1

Keywords

OXIDOREDUCTASE / NADPH-QUINONE OXIDOREDUCTASE 1 / NQO1 / FAD / DICOUMAROL

Function / homology

Function and homology information

ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / vitamin K metabolic process / cytochrome-b5 reductase activity, acting on NAD(P)H / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Gavira, J.A. / Medina-Carmona, E. / Pey, A.L.

Citation

Journal: Hum.Mol.Genet. / Year: 2017
Title: Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution.
Authors: Medina-Carmona, E. / Fuchs, J.E. / Gavira, J.A. / Mesa-Torres, N. / Neira, J.L. / Salido, E. / Palomino-Morales, R. / Burgos, M. / Timson, D.J. / Pey, A.L.

History

Deposition	Jan 29, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_database_status / struct_site Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Jan 10, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5fuq.cif.gz	254.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5fuq.ent.gz	208.8 KB	Display	PDB format
PDBx/mmJSON format	5fuq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fuq_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	5fuq_full_validation.pdf.gz	2 MB	Display
Data in XML	5fuq_validation.xml.gz	28.3 KB	Display
Data in CIF	5fuq_validation.cif.gz	40 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fu/5fuq ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fuq	HTTPS FTP

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Related structure data

Related structure data	1d4aS S: Starting model for refinement
Similar structure data	3jsx-1 5eai-3 6fy4-2 1dxo-1 5eai-6 1kbq-1 6fy4-1 6llc-4 1kbo-2 6llc-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#172 - Apr 2014 RecA and Rad51 similarity (1)

Deposited unit

A: NAD(P)H DEHYDROGENASE [QUINONE] 1

B: NAD(P)H DEHYDROGENASE [QUINONE] 1

hetero molecules

64.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	104.828, 104.828, 201.908
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	NAD(P)H DEHYDROGENASE [QUINONE] 1 / AZOREDUCTASE / DT-DIAPHORASE / DTD / MENADIONE REDUCTASE / NADPH / QUINONE OXIDOREDUCTASE 1 / ...AZOREDUCTASE / DT-DIAPHORASE / DTD / MENADIONE REDUCTASE / NADPH / QUINONE OXIDOREDUCTASE 1 / PHYLLOQUINONE REDUCTASE / QUINONE REDUCTASE 1 / QR1 / NADPH DEHYDROGENASE QUINONE 1 Mass: 30926.658 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET46 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P15559, NAD(P)H dehydrogenase (quinone)
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-DTC / BISHYDROXY[2H-1-BENZOPYRAN-2-ONE,1,2-BENZOPYRONE] / DICOUMAROL Mass: 336.295 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₉H₁₂O₆ / Comment: anticoagulant, inhibitor*YM
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 47 % / Description: NONE
Crystal grow	pH: 9 Details: CAPILLARY COUNTERDIFFUSION METHOD: 30% OF PEG 3350, 200 MM SODIUM-ACETATE, 100 MM SODIUM-TRICINE AT PH 9.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2015 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977 Å / Relative weight: 1
Reflection	Resolution: 2.04→49.83 Å / Num. obs: 72281 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / B_iso Wilson estimate: 43.63 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 16.38
Reflection shell	Resolution: 2.04→2.11 Å / Redundancy: 8.8 % / R_merge(I) obs: 1.49 / Mean I/σ(I) obs: 1.45 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D4A

1d4a

Resolution: 2.04→49.828 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML / Details: H80R MUTANT

	R_factor	Num. reflection	% reflection
R_free	0.1768	3646	5 %
R_work	0.1589	-	-
obs	0.1598	72272	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 49.87 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→49.828 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4348	0	197	396	4941

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4961
X-RAY DIFFRACTION	f_angle_d	0.926	6753
X-RAY DIFFRACTION	f_dihedral_angle_d	14.66	2914
X-RAY DIFFRACTION	f_chiral_restr	0.066	691
X-RAY DIFFRACTION	f_plane_restr	0.005	863

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 (%)
2.04-2.0669	0.3209	125	0.3066	2603	X-RAY DIFFRACTION	100
2.0669-2.0952	0.3074	142	0.2869	2593	X-RAY DIFFRACTION	100
2.0952-2.1251	0.3026	138	0.2656	2603	X-RAY DIFFRACTION	100
2.1251-2.1568	0.2566	136	0.2367	2581	X-RAY DIFFRACTION	100
2.1568-2.1905	0.2457	145	0.222	2612	X-RAY DIFFRACTION	100
2.1905-2.2264	0.2436	140	0.2178	2597	X-RAY DIFFRACTION	100
2.2264-2.2648	0.2436	138	0.206	2574	X-RAY DIFFRACTION	100
2.2648-2.306	0.2162	149	0.1969	2609	X-RAY DIFFRACTION	100
2.306-2.3504	0.2279	125	0.1957	2638	X-RAY DIFFRACTION	100
2.3504-2.3984	0.1963	116	0.1819	2637	X-RAY DIFFRACTION	100
2.3984-2.4505	0.2108	141	0.1716	2590	X-RAY DIFFRACTION	100
2.4505-2.5075	0.2046	153	0.1712	2613	X-RAY DIFFRACTION	100
2.5075-2.5702	0.1934	145	0.1592	2593	X-RAY DIFFRACTION	100
2.5702-2.6397	0.1807	136	0.1777	2637	X-RAY DIFFRACTION	100
2.6397-2.7174	0.2106	123	0.1714	2626	X-RAY DIFFRACTION	100
2.7174-2.8051	0.2108	147	0.168	2622	X-RAY DIFFRACTION	100
2.8051-2.9053	0.2009	148	0.1713	2624	X-RAY DIFFRACTION	100
2.9053-3.0216	0.1945	148	0.1703	2633	X-RAY DIFFRACTION	100
3.0216-3.1591	0.1883	131	0.1771	2662	X-RAY DIFFRACTION	100
3.1591-3.3256	0.1893	154	0.1668	2617	X-RAY DIFFRACTION	100
3.3256-3.534	0.1958	149	0.1543	2656	X-RAY DIFFRACTION	100
3.534-3.8067	0.166	153	0.1431	2649	X-RAY DIFFRACTION	100
3.8067-4.1896	0.1281	147	0.1328	2696	X-RAY DIFFRACTION	100
4.1896-4.7955	0.1263	138	0.1114	2708	X-RAY DIFFRACTION	100
4.7955-6.0401	0.1519	133	0.1359	2746	X-RAY DIFFRACTION	100
6.0401-49.8427	0.1459	146	0.1561	2907	X-RAY DIFFRACTION	100

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	3.6544	5.4712	-0.1803	8.5538	-0.5265	6.5532	-0.3046	0.3648	0.6862	-0.4297	0.3856	0.5652	-0.6306	-0.1178	-0.1644	0.3079	-0.0103	-0.0507	0.4069	-0.0235	0.5038	-16.9028	34.1022	-43.6863
2	3.0514	2.512	-0.4011	2.8101	-1.7408	2.8137	-0.0735	0.1594	0.1642	-0.3236	-0.1143	0.4531	-0.1753	-0.2452	0.0777	0.3453	0.0137	-0.0547	0.4705	-0.0515	0.4514	-22.5704	37.1416	-42.5739
3	2.7416	-2.6595	-0.7984	3.0753	0.4399	1.2179	-0.0276	0.0477	0.2617	-0.4951	0.0628	-0.0221	-0.1161	-0.046	-0.0365	0.3726	-0.0844	-0.0378	0.4094	-0.0659	0.4246	-9.7063	29.3073	-45.7382
4	8.4004	-4.9307	0.0116	8.7751	-4.803	3.9241	-0.0332	0.3599	-0.321	-0.2758	-0.3743	-0.7798	0.3497	0.6579	0.3335	0.4345	-0.0078	0.0659	0.6168	-0.1175	0.5251	13.9709	21.0461	-44.7275
5	1.8425	0.101	-0.087	0.7938	-0.0767	1.068	-0.0626	-0.2096	0.3423	-0.0289	0.0831	0.0062	-0.1671	0.0987	-0.0217	0.3223	-0.0434	-0.0222	0.4141	-0.1092	0.4084	-5.0517	31.6762	-33.7852
6	4.6277	2.5094	-1.1038	4.8841	-1.1639	2.4721	-0.0929	-0.1815	0.4727	-0.2998	0.0804	0.3416	-0.2071	-0.3059	0.0426	0.2904	0.0656	-0.0138	0.4804	-0.1168	0.4558	-26.482	36.1728	-33.1751
7	3.1193	-1.2963	1.0628	1.5817	-0.0803	1.9405	-0.1379	-0.3943	0.513	-0.0029	0.131	-0.3749	-0.1188	0.1572	0.0528	0.3974	-0.0306	-0.0213	0.5423	-0.2112	0.579	3.1565	39.7659	-19.7999
8	5.3265	1.9333	4.5849	4.9397	3.3856	4.684	-0.3388	-1.3463	0.5766	0.7267	0.3007	-0.2594	-0.377	0.0178	0.0961	0.6649	0.0122	-0.0871	0.9153	-0.2501	0.5421	-0.2737	40.3728	-7.4428
9	5.8719	-1.3479	1.4408	2.3555	-0.4236	4.9852	-0.242	-0.9206	0.5614	0.2395	0.1699	0.0419	-0.3534	-0.2028	0.0954	0.3707	0.0262	-0.0114	0.6521	-0.2369	0.475	-9.7437	36.8382	-14.714
10	3.6569	4.1918	-3.6926	5.7564	-2.3879	8.2779	-0.035	-0.2014	-1.024	0.0592	-0.2721	-0.716	0.8933	0.4009	0.2881	0.3488	0.052	-0.0408	0.4492	0.0179	0.5882	3.3804	3.3338	-29.1549
11	3.5931	1.0983	-0.4817	5.7405	-2.4121	3.4919	0.099	-0.2307	-0.4707	-0.0892	-0.3154	-0.7665	0.2903	0.4725	0.0736	0.3702	0.0467	-0.0375	0.5352	-0.0883	0.6196	9.887	3.3938	-26.7656
12	2.8705	-0.1535	0.5027	2.2631	-1.7004	2.5523	0.0922	0.2654	-0.2422	-0.1932	0.0312	-0.1878	0.5336	0.0775	-0.2297	0.4343	-0.0302	-0.0127	0.3961	-0.1027	0.3912	-3.9292	6.6165	-37.1508
13	2.7056	-1.0751	2.1536	3.7797	-1.0158	3.5208	0.2546	-0.2812	-0.1925	0.033	-0.1902	0.3621	0.1642	-0.2733	-0.122	0.4108	-0.1512	-0.0244	0.5206	-0.0135	0.4136	-24.4357	8.162	-40.8583
14	1.8701	0.1773	-0.1226	1.793	0.2733	1.3139	-0.027	-0.3433	-0.1158	0.0853	0.0438	0.0024	0.0743	-0.085	-0.0191	0.2767	-0.0163	-0.0205	0.4564	-0.0262	0.3198	-6.5995	13.4837	-24.7706
15	5.8408	2.4597	-1.1421	4.2778	-0.9961	2.049	0.0424	-0.513	-0.46	0.2445	-0.026	-0.545	0.1733	0.3558	0.0045	0.3259	0.0165	-0.081	0.5225	-0.0382	0.4002	11.7373	10.3755	-19.6254
16	6.0628	-1.8961	-0.1882	1.2976	-0.4631	1.6601	-0.0421	-0.7845	-0.1301	0.1027	0.2325	0.1539	0.0665	-0.252	-0.1575	0.3607	-0.0254	0.0105	0.6969	0.0224	0.3707	-20.7434	16.1347	-11.9929
17	3.7936	-0.494	-4.157	4.1002	1.1271	9.1452	-0.1428	-1.2866	0.4453	0.7859	0.0956	0.3846	0.0992	-0.1626	-0.0059	0.581	0.0191	0.0236	0.933	-0.1225	0.4623	-18.2101	23.2928	-2.1783
18	8.4384	-2.5664	1.1914	3.6005	0.7388	2.6104	-0.0541	-0.795	0.188	0.5037	-0.0203	-0.0853	0.2041	-0.3192	-0.0047	0.4255	-0.0324	-0.0039	0.7785	-0.0914	0.342	-6.8427	21.5557	-8.8173

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 17 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 18 THROUGH 33 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 34 THROUGH 52 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 53 THROUGH 67 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 68 THROUGH 187 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 188 THROUGH 217 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 218 THROUGH 240 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 241 THROUGH 257 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 258 THROUGH 273 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 1 THROUGH 17 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 18 THROUGH 32 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 33 THROUGH 55 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 56 THROUGH 82 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 83 THROUGH 187 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 188 THROUGH 217 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 218 THROUGH 240 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 241 THROUGH 257 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 258 THROUGH 273 )

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