PDB-5lbw: Structure of the human quinone reductase 2 (NQO2) in complex with...

ID or keywords:

Entry

Database: PDB / ID: 5lbw

Title

Structure of the human quinone reductase 2 (NQO2) in complex with volitinib

Components

Ribosyldihydronicotinamide dehydrogenase [quinone]

Keywords

OXIDOREDUCTASE / quinone reductase 2 / kinase inhibitor / volitinib / Ribosyldihydronicotinamide dehydrogenase

Function / homology

Function and homology information

ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.9 Å

Authors

Schneider, S. / Medard, G. / Kuester, B.

Funding support

Germany, 1items

Citation

Journal: Science / Year: 2017
Title: The target landscape of clinical kinase drugs.
Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / ...

History

Deposition	Jun 17, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 29, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Dec 13, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Jan 10, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lbw.cif.gz	200.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5lbw.ent.gz	160.3 KB	Display	PDB format
PDBx/mmJSON format	5lbw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5lbw_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5lbw_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5lbw_validation.xml.gz	19.6 KB	Display
Data in CIF	5lbw_validation.cif.gz	25.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lb/5lbw ftp://data.pdbj.org/pub/pdb/validation_reports/lb/5lbw	HTTPS FTP

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Related structure data

Related structure data	5lbyC 5lbzC 5m5aC 5mafC 5magC 5mahC 5maiC 5lbuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3owh-d 3ox1-d 3ovm-d 4fgk-d 3owx-d 4qoe-d 3ox3-d 4qog-d 3ox2-d 5lbz-d 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

Deposited unit

A: Ribosyldihydronicotinamide dehydrogenase [quinone]

B: Ribosyldihydronicotinamide dehydrogenase [quinone]

hetero molecules

55.9 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)	57.398, 81.372, 106.403
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 3 - 228 / Label seq-ID: 4 - 229

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	Ribosyldihydronicotinamide dehydrogenase [quinone] / NRH dehydrogenase [quinone] 2 / NRH:quinone oxidoreductase 2 / Quinone reductase 2 / QR2 Mass: 26775.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) References: UniProt: P16083, ribosyldihydronicotinamide dehydrogenase (quinone)
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#4: Chemical	ChemComp-V0L / volitinib Mass: 345.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₁₅N₉ / Comment: inhibitor*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 39 / 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: 46.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 200 mM sodium sulphate, 2.2 M ammonium sulphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.9→44.5 Å / Num. obs: 36213 / % possible obs: 90 % / Redundancy: 4.7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.11 / Net I/σ(I): 7.49
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 4 % / R_merge(I) obs: 0.97 / Mean I/σ(I) obs: 1.3 / % possible all: 93

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0151	refinement
XDS		data reduction
XDS		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5LBU

5lbu

Resolution: 1.9→44.5 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.93 / SU B: 18.294 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2705	1803	5 %	RANDOM
R_work	0.25317	-	-	-
obs	0.25404	34410	90.5 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å

Displacement parameters

B_iso mean: 42.198 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.01 Å²	0 Å²	0 Å²
2-	-	-2.77 Å²	0 Å²
3-	-	-	-5.24 Å²

Refinement step

Cycle: 1 / Resolution: 1.9→44.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3608	0	160	39	3807

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	3924
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3599
X-RAY DIFFRACTION	r_angle_refined_deg	1.317	1.994	5362
X-RAY DIFFRACTION	r_angle_other_deg	0.896	3	8299
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.189	5	467
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.722	24.118	170
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.839	15	624
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.944	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	569
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	4357
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	922
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.274	2.437	1832
X-RAY DIFFRACTION	r_mcbond_other	0.273	2.437	1831
X-RAY DIFFRACTION	r_mcangle_it	0.478	3.654	2290
X-RAY DIFFRACTION	r_mcangle_other	0.478	3.655	2291
X-RAY DIFFRACTION	r_scbond_it	0.278	2.639	2092
X-RAY DIFFRACTION	r_scbond_other	0.278	2.64	2093
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.481	3.958	3066
X-RAY DIFFRACTION	r_long_range_B_refined	2.888	29.189	4649
X-RAY DIFFRACTION	r_long_range_B_other	2.887	29.192	4650
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 14996 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.438	133	-
R_work	0.457	2562	-
obs	-	-	92.83 %

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	2.478	-0.5475	-0.1928	1.0247	-0.7981	4.7442	0.0501	0.0617	-0.0683	-0.0923	0.0556	-0.0405	-0.052	0.1475	-0.1056	0.0131	-0.0053	0.0108	0.0685	0.0298	0.1996	-6.497	-1.708	-2.856
2	0.4139	-1.111	-0.2947	3.1482	1.8174	6.8286	0.0063	0.0098	0.0318	0.0288	0.0057	-0.116	0.1948	0.3123	-0.012	0.047	-0.0201	-0.0135	0.2107	0.0279	0.2181	-10.816	-2.905	-9.918
3	5.1588	3.6064	-1.3823	2.5635	-1.2735	2.7524	0.1743	-0.1048	0.4657	0.189	-0.025	0.3418	-0.5703	-0.449	-0.1494	0.1216	0.1081	0.0229	0.1734	0.0114	0.3653	-21.925	4.556	12.013
4	7.8723	-4.4805	-2.7431	2.7247	2.7161	8.6798	-0.0922	-0.3134	0.3136	0.0154	-0.1125	-0.1001	-0.3323	-1.7799	0.2047	0.3615	0.0753	0.2223	0.5531	-0.0562	0.7117	-33.491	-2.47	18.604
5	5.6254	-2.4152	-3.1443	4.0271	2.5882	6.7809	0.2912	0.3618	-0.0509	-0.1686	-0.279	0.3666	-0.5574	-0.7597	-0.0122	0.0619	0.0401	-0.0458	0.2328	0.0167	0.2836	-28.734	-1.513	2.599
6	0.3251	0.1598	0.0034	1.8131	-0.0401	0.8569	-0.1181	0.0365	0.0575	0.0366	0.1006	0.1132	0.0278	-0.1369	0.0176	0.05	-0.0025	-0.0126	0.0831	0.0143	0.2171	-14.028	-6.704	7.173
7	4.6883	1.7895	-0.123	1.6663	0.3279	2.7848	-0.0849	0.1016	-0.1983	-0.0154	0.0343	0.0104	0.2225	-0.1273	0.0506	0.0222	-0.0108	0.0303	0.02	-0.0105	0.2248	-13.656	-16.197	4.812
8	2.6135	0.0457	0.6238	1.5203	-0.5179	2.9968	0.0428	0.0041	-0.1161	0.0738	0.0119	-0.0012	0.4265	0.0447	-0.0547	0.0791	0.0053	0.0137	0.0484	-0.025	0.253	-9.494	-18.012	6.529
9	7.401	2.7123	3.5023	3.8792	2.2065	5.2138	0.0297	0.245	0.2269	-0.0502	-0.0167	-0.2767	-0.12	0.5392	-0.013	0.0444	0.0445	0.0162	0.1612	0.0443	0.2454	4.485	-9.556	-3.885
10	2.1576	2.2804	-2.0684	2.6873	-1.8632	8.0632	0.0162	0.2713	-0.0456	-0.1422	0.2039	0.1109	0.4796	0.1079	-0.2201	0.2451	0.0895	-0.0747	0.1533	-0.049	0.2557	-10.929	-22.793	-0.892
11	1.9563	0.6132	0.0765	1.7969	-0.4291	4.3043	0.0468	-0.217	0.0387	0.4257	-0.0225	0.1125	0.2619	-0.1455	-0.0243	0.1407	-0.0005	0.0202	0.0877	-0.0413	0.207	-18.192	-4.618	34.709
12	10.4395	4.0747	-3.8375	4.3596	-1.1551	3.8832	0.066	-0.0079	0.3064	-0.1083	-0.0066	-0.0995	-0.3434	0.2889	-0.0594	0.0839	0.0129	-0.0336	0.1054	0.0094	0.2291	-3.203	9.214	14.604
13	2.0317	-2.3015	3.4627	3.7358	-2.1781	12.6874	-0.056	0.233	-0.0351	-0.129	-0.1052	-0.3319	-0.2309	0.7264	0.1611	0.0872	-0.042	0.0552	0.1029	-0.0439	0.3167	4.207	4.782	14.705
14	5.146	1.2791	-0.2956	5.0537	-2.5406	5.6349	-0.1556	-0.1515	0.2535	0.4892	0.1339	-0.2158	-0.1465	0.1411	0.0217	0.0777	0.0277	-0.0351	0.0812	-0.0664	0.2343	-0.982	6.246	27.077
15	2.5912	-0.4775	1.4722	1.0577	-0.339	6.3241	0.1423	-0.4426	0.2245	0.0059	-0.1865	-0.0608	0.2406	-0.3476	0.0442	0.0479	-0.0303	0.0132	0.1531	-0.033	0.1974	-12.372	-7.819	27.661
16	1.6412	0.2385	1.3255	0.0582	0.3044	2.8245	-0.1394	-0.0401	0.0735	-0.0149	0.0113	-0.0503	0.0039	0.0015	0.1282	0.0258	0.0189	0.0173	0.05	-0.0051	0.297	-7.163	-3.859	20.833
17	3.2283	-0.396	0.9999	1.2838	1.0444	2.1302	0.1481	-0.0824	-0.1355	0.1435	-0.0278	-0.1303	0.3306	0.0622	-0.1203	0.0524	0.0139	-0.0091	0.0673	0.0599	0.1989	-8.582	-16.521	23.513
18	4.1287	0.8392	-0.8863	1.1313	0.3525	1.9391	0.1427	0.0533	-0.0763	0.1749	-0.0178	0.0688	0.4605	-0.0336	-0.1249	0.1531	0.0147	-0.0087	0.0521	0.0291	0.2155	-9.997	-16.879	24.453
19	5.9836	1.6731	2.9341	4.5691	0.4897	5.6143	-0.345	-0.4348	-0.5909	0.2904	0.3413	0.6879	0.0245	-1.0311	0.0037	0.2781	-0.0477	0.1363	0.305	0.0364	0.3486	-25.767	-17.465	35.097
20	2.6264	-1.9864	-2.3792	3.3031	4.4248	10.3827	0.0079	-0.1617	-0.0471	0.3112	0.0683	-0.0656	0.4581	0.3217	-0.0763	0.1719	0.022	-0.0067	0.0665	0.0342	0.2097	-5.78	-21.893	30.706

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 26
2	X-RAY DIFFRACTION	2	A	27 - 41
3	X-RAY DIFFRACTION	3	A	42 - 58
4	X-RAY DIFFRACTION	4	A	59 - 72
5	X-RAY DIFFRACTION	5	A	73 - 94
6	X-RAY DIFFRACTION	6	A	95 - 125
7	X-RAY DIFFRACTION	7	A	126 - 157
8	X-RAY DIFFRACTION	8	A	158 - 189
9	X-RAY DIFFRACTION	9	A	190 - 213
10	X-RAY DIFFRACTION	10	A	214 - 229
11	X-RAY DIFFRACTION	11	B	2 - 44
12	X-RAY DIFFRACTION	12	B	45 - 63
13	X-RAY DIFFRACTION	13	B	64 - 75
14	X-RAY DIFFRACTION	14	B	76 - 91
15	X-RAY DIFFRACTION	15	B	92 - 105
16	X-RAY DIFFRACTION	16	B	106 - 126
17	X-RAY DIFFRACTION	17	B	127 - 163
18	X-RAY DIFFRACTION	18	B	164 - 193
19	X-RAY DIFFRACTION	19	B	194 - 213
20	X-RAY DIFFRACTION	20	B	214 - 229

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Yorodumi