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- PDB-1zx1: Human quinone oxidoreductase 2 (NQO2) in complex with the cytosta... -

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Basic information

Entry
Database: PDB / ID: 1zx1
TitleHuman quinone oxidoreductase 2 (NQO2) in complex with the cytostatic prodrug CB1954
ComponentsNRH dehydrogenase [quinone] 2
KeywordsOXIDOREDUCTASE / Quinone oxidoreductase 2 / reductions of quinones / dihydronicotinamide ribose / electrondonor / 5-(aziridin-1-yl)-2 / 4-dinitrobenamide (CB1954) / flavin-containing / Structural Genomics / Structural Genomics Consortium / SGC
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 ...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 / electron transfer activity / oxidoreductase activity / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsJansson, A. / Wu, X. / Kavanagh, K. / Kerr, D. / Knox, R. / Walton, R. / Gunther, U. / Ludwig, C. / Edwards, A. / Arrowsmith, C. ...Jansson, A. / Wu, X. / Kavanagh, K. / Kerr, D. / Knox, R. / Walton, R. / Gunther, U. / Ludwig, C. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human quinone oxidoreductase 2 (NQO2) in complex with the cytostatic prodrug CB1954
Authors: Jansson, A. / Wu, X. / Kavanagh, K. / Kerr, D. / Knox, R. / Walton, R. / Gunther, U. / Ludwig, C. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Oppermann, U.
History
DepositionJun 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 12, 2018Group: Data collection / Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NRH dehydrogenase [quinone] 2
B: NRH dehydrogenase [quinone] 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1678
Polymers51,9612
Non-polymers2,2066
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-26 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.328, 84.341, 106.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAILEILE2AA1 - 552 - 56
211GLYGLYILEILE2BB2 - 553 - 56
122THRTHRPHEPHE4AA56 - 6557 - 66
222THRTHRPHEPHE4BB56 - 6557 - 66
133ASNASNPROPRO2AA66 - 12967 - 130
233ASNASNPROPRO2BB66 - 12967 - 130
144PHEPHEGLYGLY4AA131 - 135132 - 136
244GLYGLYGLYGLY4BB130 - 135131 - 136
155LEULEUPHEPHE2AA136 - 228137 - 229
255LEULEUGLNGLN2BB136 - 230137 - 231

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein NRH dehydrogenase [quinone] 2 / Quinone reductase 2 / QR2 / NRH:quinone oxidoreductase 2


Mass: 25980.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: NQO2A-c001 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P16083, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-CB1 / 5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE / CB1954 / Tretazicar


Mass: 252.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N4O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Hepes, ammonium sulphate, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9001 Å
DetectorDetector: CCD / Date: Feb 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9001 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 29187 / Num. obs: 29187 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.128 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.411 / % possible all: 82.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QR2

1qr2


Resolution: 2.16→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.671 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual isotropic B-factor refinement for each atom
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: There is some unidentified density at the N-terminal that was not modeled. Some aminoacids have been truncated due to lack of density. Gly130 is cut out due to disordered density. HYDROGENS ...Details: There is some unidentified density at the N-terminal that was not modeled. Some aminoacids have been truncated due to lack of density. Gly130 is cut out due to disordered density. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20656 1365 5.1 %RANDOM
Rwork0.17418 ---
all0.17591 25637 --
obs0.17591 25637 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.16→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 144 154 3863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223829
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9825236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62823.827162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07115571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1921516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022924
X-RAY DIFFRACTIONr_nbd_refined0.1970.21762
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2220
X-RAY DIFFRACTIONr_metal_ion_refined0.0050.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.29
X-RAY DIFFRACTIONr_mcbond_it0.8081.52338
X-RAY DIFFRACTIONr_mcangle_it1.27923673
X-RAY DIFFRACTIONr_scbond_it2.09331878
X-RAY DIFFRACTIONr_scangle_it3.3574.51556
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
846tight positional0.060.05
985medium positional0.350.5
846tight thermal0.190.5
985medium thermal0.812
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 79 -
Rwork0.209 1476 -
obs--78.18 %
Refinement TLS params.

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

IDL11 (°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)
12.53360.02920.32392.07340.1885.11730.1032-0.1063-0.24840.16860.0613-0.09660.63690.0122-0.1645-0.109-0.0113-0.0494-0.2226-0.0145-0.1849-15.5832-8.5716-4.1201
21.9514-0.0890.02772.32580.27773.25450.0430.1057-0.1158-0.09330.04130.00480.2482-0.0019-0.0843-0.2117-0.0188-0.0043-0.21870.0049-0.2058-18.7948-7.6016-26.8495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2282 - 229
2X-RAY DIFFRACTION2BB2 - 2283 - 229

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