1KBO - Header Asymmetric Unit

HEADER OXIDOREDUCTASE 06-NOV-01 1KBO

TITLE COMPLEX OF HUMAN RECOMBINANT NAD(P)H:QUINONE OXIDE TITLE 2 REDUCTASE TYPE 1 WITH 5-METHOXY-1,2-DIMETHYL-3- TITLE 3 (PHENOXYMETHYL)INDOLE-4,7-DIONE (ES1340)

COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD(P)H DEHYDROGENASE [QUINONE] 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: QUINONE REDUCTASE 1, DT-DIAPHORASE, QR1, DTD, COMPND 5 AZOREDUCTASE, PHYLLOQUINONE REDUCTASE, MENADIONE REDUCTASE; COMPND 6 EC: 1.6.99.2; COMPND 7 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562

KEYWDS FLAVOENZYME, PRODRUG-ENZYME COMPLEX, OXIDOREDUCTASE

EXPDTA X-RAY DIFFRACTION

AUTHOR M.FAIG,M.A.BIANCHET,L.M.AMZEL

REVDAT 3 24-FEB-09 1KBO 1 VERSN REVDAT 2 01-APR-03 1KBO 1 JRNL REVDAT 1 16-JAN-02 1KBO 0

JRNL AUTH S.L.WINSKI,M.FAIG,M.A.BIANCHET,D.SIEGEL,E.SWANN, JRNL AUTH 2 K.FUNG,M.W.DUNCAN,C.J.MOODY,L.M.AMZEL,D.ROSS JRNL TITL CHARACTERIZATION OF A MECHANISM-BASED INHIBITOR OF JRNL TITL 2 NAD(P)H:QUINONE OXIDOREDUCTASE 1 BY BIOCHEMICAL, JRNL TITL 3 X-RAY CRYSTALLOGRAPHIC, AND MASS SPECTROMETRIC JRNL TITL 4 APPROACHES. JRNL REF BIOCHEMISTRY V. 40 15135 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11735396 JRNL DOI 10.1021/BI011324I

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.FAIG,M.A.BIANCHET,S.WINSKI,R.HARGREAVES, REMARK 1 AUTH 2 C.J.MOODY,A.R.HUDNOTT,D.ROSS,L.M.AMZEL REMARK 1 TITL STRUCTURE-BASED DEVELOPMENT OF ANTICANCER DRUGS: REMARK 1 TITL 2 COMPLEXES OF NAD(P)H:QUINONE REDUCTASE 1 WITH REMARK 1 TITL 3 CHEMOTHERAPEUTIC QUINONES REMARK 1 REF STRUCTURE V. 9 659 2001 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(01)00636-0 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.FAIG,M.A.BIANCHET,S.CHEN,S.L.WINSKI,D.ROSS, REMARK 1 AUTH 2 P.TALALAY,L.M.AMZEL REMARK 1 TITL STRUCTURES OF RECOMBINANT MOUSE AND HUMAN REMARK 1 TITL 2 NAD(P)H:QUINONE OXIDOREDUCTASES: SPECIES REMARK 1 TITL 3 COMPARISON AND STRUCTURAL CHANGES WITH SUBSTRATE REMARK 1 TITL 4 BINDING AND RELEASE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 97 3177 2000 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.050585797

REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 461040.100 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 74.4 REMARK 3 NUMBER OF REFLECTIONS : 37344 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 3825 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 40.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3052 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 334 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8700 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 304 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.29000 REMARK 3 B22 (A**2) : -1.41000 REMARK 3 B33 (A**2) : -3.88000 REMARK 3 B12 (A**2) : -1.53000 REMARK 3 B13 (A**2) : 1.40000 REMARK 3 B23 (A**2) : 3.61000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.35 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.83 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.200 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.370 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.150 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.260 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 33.79 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NEWFAD_XPLOR.PAR REMARK 3 PARAMETER FILE 3 : 340.PAR REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1KBO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-01. REMARK 100 THE RCSB ID CODE IS RCSB014784.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47881 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 35.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.22100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4K, NA ACETATE, PH 8.5, REMARK 280 TEMPERATURE 293K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.

REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 106 23.04 44.92 REMARK 500 GLU A 123 -51.13 73.88 REMARK 500 TYR A 132 -122.88 41.32 REMARK 500 ASP A 133 -7.46 -54.24 REMARK 500 ILE A 175 -64.30 -105.18 REMARK 500 PHE A 181 155.47 -47.76 REMARK 500 SER A 191 51.87 29.84 REMARK 500 PRO A 196 152.80 -43.10 REMARK 500 LEU A 230 68.16 -65.40 REMARK 500 GLU A 245 -18.74 -44.68 REMARK 500 HIS A 257 57.28 -107.19 REMARK 500 ARG A 272 52.65 156.82 REMARK 500 ALA B 10 73.52 -118.78 REMARK 500 GLU B 123 -54.15 93.40 REMARK 500 TYR B 132 -134.46 61.97 REMARK 500 ASP B 133 -15.52 -47.01 REMARK 500 PHE B 137 39.03 -92.54 REMARK 500 ILE B 175 -65.05 -96.44 REMARK 500 SER B 191 61.47 22.33 REMARK 500 HIS B 257 61.74 -106.85 REMARK 500 THR B 265 132.36 -34.85 REMARK 500 ASP B 266 47.94 39.94 REMARK 500 ARG B 272 77.89 86.15 REMARK 500 ARG C 3 -22.45 -140.98 REMARK 500 LYS C 32 29.41 -71.15 REMARK 500 LYS C 53 0.75 -63.92 REMARK 500 ASP C 61 81.34 -155.83 REMARK 500 PHE C 106 19.67 49.15 REMARK 500 GLU C 123 -55.60 73.73 REMARK 500 ALA C 129 -84.65 -74.84 REMARK 500 ALA C 130 72.58 -69.69 REMARK 500 TYR C 132 -109.48 30.38 REMARK 500 SER C 191 71.87 37.52 REMARK 500 SER C 254 -175.82 -172.13 REMARK 500 HIS C 257 52.00 -104.76 REMARK 500 ARG C 272 94.72 148.11 REMARK 500 ARG D 3 -26.80 -154.98 REMARK 500 LYS D 31 2.26 -58.21 REMARK 500 LEU D 41 -48.23 -24.02 REMARK 500 ASP D 61 76.78 -173.12 REMARK 500 GLU D 123 -26.55 69.41 REMARK 500 PHE D 124 -69.85 -94.84 REMARK 500 TYR D 132 -114.24 32.24 REMARK 500 SER D 191 51.81 24.64 REMARK 500 LEU D 230 30.51 -65.98 REMARK 500 LYS D 261 -168.27 -104.82 REMARK 500 ASP D 266 48.27 34.15 REMARK 500 ARG D 272 76.80 79.40 REMARK 500 REMARK 500 REMARK: NULL

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 340 C 701 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 340 D 702 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 340 A 703 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 340 B 704 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 601 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD B 602 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD C 603 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD D 604

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D4A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE REMARK 900 AT 1.7 A RESOLUTION REMARK 900 RELATED ID: 1QRD RELATED DB: PDB REMARK 900 QUINONE REDUCTASE/FAD/CIBACRON BLUE/DUROQUINONE COMPLEX REMARK 900 RELATED ID: 1H66 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A COMPLEX OF HUMAN NAD[P]H-QUINONE REMARK 900 OXIDOREDUCTASE WITH 2,5-DIAZIRIDINYL-3-HYDROXYL-6-METHYL-1, REMARK 900 4-BENZOQUINONE REMARK 900 RELATED ID: 1GG5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A COMPLEX OF HUMAN NAD[P]H-QUINONE REMARK 900 OXIDOREDUCTASE AND A CHEMOTHERAPEUTIC DRUG (E09) AT 2.5 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 1H69 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A COMPLEX OF HUMAN NAD[P]H-QUINONE REMARK 900 OXIDOREDUCTASE WITH AND ARH019 REMARK 900 RELATED ID: 1KBQ RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN NAD(P)H QUINONE OXIDOREDUCTASE WITH 5- REMARK 900 METHOXY-1,2-DIMETHYL-3-(4-NITROPHENOXYMETHYL)INDOLE-4,7- REMARK 900 DIONE

DBREF 1KBO A 1 273 UNP P15559 NQO1_HUMAN 2 274 DBREF 1KBO B 1 273 UNP P15559 NQO1_HUMAN 2 274 DBREF 1KBO C 1 273 UNP P15559 NQO1_HUMAN 2 274 DBREF 1KBO D 1 273 UNP P15559 NQO1_HUMAN 2 274

SEQRES 1 A 273 VAL GLY ARG ARG ALA LEU ILE VAL LEU ALA HIS SER GLU SEQRES 2 A 273 ARG THR SER PHE ASN TYR ALA MET LYS GLU ALA ALA ALA SEQRES 3 A 273 ALA ALA LEU LYS LYS LYS GLY TRP GLU VAL VAL GLU SER SEQRES 4 A 273 ASP LEU TYR ALA MET ASN PHE ASN PRO ILE ILE SER ARG SEQRES 5 A 273 LYS ASP ILE THR GLY LYS LEU LYS ASP PRO ALA ASN PHE SEQRES 6 A 273 GLN TYR PRO ALA GLU SER VAL LEU ALA TYR LYS GLU GLY SEQRES 7 A 273 HIS LEU SER PRO ASP ILE VAL ALA GLU GLN LYS LYS LEU SEQRES 8 A 273 GLU ALA ALA ASP LEU VAL ILE PHE GLN PHE PRO LEU GLN SEQRES 9 A 273 TRP PHE GLY VAL PRO ALA ILE LEU LYS GLY TRP PHE GLU SEQRES 10 A 273 ARG VAL PHE ILE GLY GLU PHE ALA TYR THR TYR ALA ALA SEQRES 11 A 273 MET TYR ASP LYS GLY PRO PHE ARG SER LYS LYS ALA VAL SEQRES 12 A 273 LEU SER ILE THR THR GLY GLY SER GLY SER MET TYR SER SEQRES 13 A 273 LEU GLN GLY ILE HIS GLY ASP MET ASN VAL ILE LEU TRP SEQRES 14 A 273 PRO ILE GLN SER GLY ILE LEU HIS PHE CYS GLY PHE GLN SEQRES 15 A 273 VAL LEU GLU PRO GLN LEU THR TYR SER ILE GLY HIS THR SEQRES 16 A 273 PRO ALA ASP ALA ARG ILE GLN ILE LEU GLU GLY TRP LYS SEQRES 17 A 273 LYS ARG LEU GLU ASN ILE TRP ASP GLU THR PRO LEU TYR SEQRES 18 A 273 PHE ALA PRO SER SER LEU PHE ASP LEU ASN PHE GLN ALA SEQRES 19 A 273 GLY PHE LEU MET LYS LYS GLU VAL GLN ASP GLU GLU LYS SEQRES 20 A 273 ASN LYS LYS PHE GLY LEU SER VAL GLY HIS HIS LEU GLY SEQRES 21 A 273 LYS SER ILE PRO THR ASP ASN GLN ILE LYS ALA ARG LYS SEQRES 1 B 273 VAL GLY ARG ARG ALA LEU ILE VAL LEU ALA HIS SER GLU SEQRES 2 B 273 ARG THR SER PHE ASN TYR ALA MET LYS GLU ALA ALA ALA SEQRES 3 B 273 ALA ALA LEU LYS LYS LYS GLY TRP GLU VAL VAL GLU SER SEQRES 4 B 273 ASP LEU TYR ALA MET ASN PHE ASN PRO ILE ILE SER ARG SEQRES 5 B 273 LYS ASP ILE THR GLY LYS LEU LYS ASP PRO ALA ASN PHE SEQRES 6 B 273 GLN TYR PRO ALA GLU SER VAL LEU ALA TYR LYS GLU GLY SEQRES 7 B 273 HIS LEU SER PRO ASP ILE VAL ALA GLU GLN LYS LYS LEU SEQRES 8 B 273 GLU ALA ALA ASP LEU VAL ILE PHE GLN PHE PRO LEU GLN SEQRES 9 B 273 TRP PHE GLY VAL PRO ALA ILE LEU LYS GLY TRP PHE GLU SEQRES 10 B 273 ARG VAL PHE ILE GLY GLU PHE ALA TYR THR TYR ALA ALA SEQRES 11 B 273 MET TYR ASP LYS GLY PRO PHE ARG SER LYS LYS ALA VAL SEQRES 12 B 273 LEU SER ILE THR THR GLY GLY SER GLY SER MET TYR SER SEQRES 13 B 273 LEU GLN GLY ILE HIS GLY ASP MET ASN VAL ILE LEU TRP SEQRES 14 B 273 PRO ILE GLN SER GLY ILE LEU HIS PHE CYS GLY PHE GLN SEQRES 15 B 273 VAL LEU GLU PRO GLN LEU THR TYR SER ILE GLY HIS THR SEQRES 16 B 273 PRO ALA ASP ALA ARG ILE GLN ILE LEU GLU GLY TRP LYS SEQRES 17 B 273 LYS ARG LEU GLU ASN ILE TRP ASP GLU THR PRO LEU TYR SEQRES 18 B 273 PHE ALA PRO SER SER LEU PHE ASP LEU ASN PHE GLN ALA SEQRES 19 B 273 GLY PHE LEU MET LYS LYS GLU VAL GLN ASP GLU GLU LYS SEQRES 20 B 273 ASN LYS LYS PHE GLY LEU SER VAL GLY HIS HIS LEU GLY SEQRES 21 B 273 LYS SER ILE PRO THR ASP ASN GLN ILE LYS ALA ARG LYS SEQRES 1 C 273 VAL GLY ARG ARG ALA LEU ILE VAL LEU ALA HIS SER GLU SEQRES 2 C 273 ARG THR SER PHE ASN TYR ALA MET LYS GLU ALA ALA ALA SEQRES 3 C 273 ALA ALA LEU LYS LYS LYS GLY TRP GLU VAL VAL GLU SER SEQRES 4 C 273 ASP LEU TYR ALA MET ASN PHE ASN PRO ILE ILE SER ARG SEQRES 5 C 273 LYS ASP ILE THR GLY LYS LEU LYS ASP PRO ALA ASN PHE SEQRES 6 C 273 GLN TYR PRO ALA GLU SER VAL LEU ALA TYR LYS GLU GLY SEQRES 7 C 273 HIS LEU SER PRO ASP ILE VAL ALA GLU GLN LYS LYS LEU SEQRES 8 C 273 GLU ALA ALA ASP LEU VAL ILE PHE GLN PHE PRO LEU GLN SEQRES 9 C 273 TRP PHE GLY VAL PRO ALA ILE LEU LYS GLY TRP PHE GLU SEQRES 10 C 273 ARG VAL PHE ILE GLY GLU PHE ALA TYR THR TYR ALA ALA SEQRES 11 C 273 MET TYR ASP LYS GLY PRO PHE ARG SER LYS LYS ALA VAL SEQRES 12 C 273 LEU SER ILE THR THR GLY GLY SER GLY SER MET TYR SER SEQRES 13 C 273 LEU GLN GLY ILE HIS GLY ASP MET ASN VAL ILE LEU TRP SEQRES 14 C 273 PRO ILE GLN SER GLY ILE LEU HIS PHE CYS GLY PHE GLN SEQRES 15 C 273 VAL LEU GLU PRO GLN LEU THR TYR SER ILE GLY HIS THR SEQRES 16 C 273 PRO ALA ASP ALA ARG ILE GLN ILE LEU GLU GLY TRP LYS SEQRES 17 C 273 LYS ARG LEU GLU ASN ILE TRP ASP GLU THR PRO LEU TYR SEQRES 18 C 273 PHE ALA PRO SER SER LEU PHE ASP LEU ASN PHE GLN ALA SEQRES 19 C 273 GLY PHE LEU MET LYS LYS GLU VAL GLN ASP GLU GLU LYS SEQRES 20 C 273 ASN LYS LYS PHE GLY LEU SER VAL GLY HIS HIS LEU GLY SEQRES 21 C 273 LYS SER ILE PRO THR ASP ASN GLN ILE LYS ALA ARG LYS SEQRES 1 D 273 VAL GLY ARG ARG ALA LEU ILE VAL LEU ALA HIS SER GLU SEQRES 2 D 273 ARG THR SER PHE ASN TYR ALA MET LYS GLU ALA ALA ALA SEQRES 3 D 273 ALA ALA LEU LYS LYS LYS GLY TRP GLU VAL VAL GLU SER SEQRES 4 D 273 ASP LEU TYR ALA MET ASN PHE ASN PRO ILE ILE SER ARG SEQRES 5 D 273 LYS ASP ILE THR GLY LYS LEU LYS ASP PRO ALA ASN PHE SEQRES 6 D 273 GLN TYR PRO ALA GLU SER VAL LEU ALA TYR LYS GLU GLY SEQRES 7 D 273 HIS LEU SER PRO ASP ILE VAL ALA GLU GLN LYS LYS LEU SEQRES 8 D 273 GLU ALA ALA ASP LEU VAL ILE PHE GLN PHE PRO LEU GLN SEQRES 9 D 273 TRP PHE GLY VAL PRO ALA ILE LEU LYS GLY TRP PHE GLU SEQRES 10 D 273 ARG VAL PHE ILE GLY GLU PHE ALA TYR THR TYR ALA ALA SEQRES 11 D 273 MET TYR ASP LYS GLY PRO PHE ARG SER LYS LYS ALA VAL SEQRES 12 D 273 LEU SER ILE THR THR GLY GLY SER GLY SER MET TYR SER SEQRES 13 D 273 LEU GLN GLY ILE HIS GLY ASP MET ASN VAL ILE LEU TRP SEQRES 14 D 273 PRO ILE GLN SER GLY ILE LEU HIS PHE CYS GLY PHE GLN SEQRES 15 D 273 VAL LEU GLU PRO GLN LEU THR TYR SER ILE GLY HIS THR SEQRES 16 D 273 PRO ALA ASP ALA ARG ILE GLN ILE LEU GLU GLY TRP LYS SEQRES 17 D 273 LYS ARG LEU GLU ASN ILE TRP ASP GLU THR PRO LEU TYR SEQRES 18 D 273 PHE ALA PRO SER SER LEU PHE ASP LEU ASN PHE GLN ALA SEQRES 19 D 273 GLY PHE LEU MET LYS LYS GLU VAL GLN ASP GLU GLU LYS SEQRES 20 D 273 ASN LYS LYS PHE GLY LEU SER VAL GLY HIS HIS LEU GLY SEQRES 21 D 273 LYS SER ILE PRO THR ASP ASN GLN ILE LYS ALA ARG LYS

HET 340 C 701 23 HET 340 D 702 23 HET 340 A 703 23 HET 340 B 704 23 HET FAD A 601 53 HET FAD B 602 53 HET FAD C 603 53 HET FAD D 604 53

HETNAM 340 5-METHOXY-1,2-DIMETHYL-3-(PHENOXYMETHYL)INDOLE-4,7- HETNAM 2 340 DIONE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE

FORMUL 5 340 4(C18 H17 N O4) FORMUL 9 FAD 4(C27 H33 N9 O15 P2) FORMUL 13 HOH *165(H2 O)

HELIX 1 1 SER A 16 LYS A 32 1 17 HELIX 2 2 LEU A 41 ASN A 45 1 5 HELIX 3 3 SER A 51 ILE A 55 5 5 HELIX 4 4 GLN A 66 GLY A 78 1 13 HELIX 5 5 SER A 81 ALA A 94 1 14 HELIX 6 6 PRO A 109 PHE A 120 1 12 HELIX 7 7 MET A 131 GLY A 135 5 5 HELIX 8 8 ASP A 163 SER A 173 1 11 HELIX 9 9 LEU A 176 GLY A 180 5 5 HELIX 10 10 SER A 191 THR A 195 5 5 HELIX 11 11 PRO A 196 GLU A 212 1 17 HELIX 12 12 PRO A 224 PHE A 228 5 5 HELIX 13 13 ASN A 231 GLY A 235 5 5 HELIX 14 14 LYS A 239 LYS A 247 1 9 HELIX 15 15 SER B 16 LYS B 32 1 17 HELIX 16 16 LEU B 41 ASN B 45 1 5 HELIX 17 17 SER B 51 ILE B 55 5 5 HELIX 18 18 GLN B 66 GLY B 78 1 13 HELIX 19 19 SER B 81 ALA B 93 1 13 HELIX 20 20 PRO B 109 PHE B 120 1 12 HELIX 21 21 MET B 131 GLY B 135 5 5 HELIX 22 22 SER B 151 SER B 156 5 6 HELIX 23 23 ASP B 163 SER B 173 1 11 HELIX 24 24 SER B 191 THR B 195 5 5 HELIX 25 25 PRO B 196 GLU B 212 1 17 HELIX 26 26 ASN B 213 GLU B 217 5 5 HELIX 27 27 PRO B 224 PHE B 228 5 5 HELIX 28 28 ASN B 231 GLY B 235 5 5 HELIX 29 29 LYS B 239 LYS B 247 1 9 HELIX 30 30 SER C 16 LYS C 32 1 17 HELIX 31 31 SER C 51 ILE C 55 5 5 HELIX 32 32 GLN C 66 GLY C 78 1 13 HELIX 33 33 SER C 81 ALA C 94 1 14 HELIX 34 34 PRO C 109 PHE C 120 1 12 HELIX 35 35 MET C 131 SER C 139 5 9 HELIX 36 36 SER C 151 SER C 156 5 6 HELIX 37 37 ASP C 163 SER C 173 1 11 HELIX 38 38 LEU C 176 GLY C 180 5 5 HELIX 39 39 SER C 191 THR C 195 5 5 HELIX 40 40 PRO C 196 GLU C 212 1 17 HELIX 41 41 PRO C 224 PHE C 228 5 5 HELIX 42 42 LYS C 239 GLU C 246 1 8 HELIX 43 43 SER D 16 LYS D 31 1 16 HELIX 44 44 SER D 51 ILE D 55 5 5 HELIX 45 45 GLN D 66 GLY D 78 1 13 HELIX 46 46 SER D 81 ALA D 94 1 14 HELIX 47 47 PRO D 109 PHE D 120 1 12 HELIX 48 48 MET D 131 GLY D 135 5 5 HELIX 49 49 SER D 151 SER D 156 5 6 HELIX 50 50 ASP D 163 SER D 173 1 11 HELIX 51 51 LEU D 176 GLY D 180 5 5 HELIX 52 52 PRO D 196 LEU D 211 1 16 HELIX 53 53 ASN D 213 GLU D 217 5 5 HELIX 54 54 PRO D 224 PHE D 228 5 5 HELIX 55 55 LYS D 239 LYS D 247 1 9

SHEET 1 A 5 GLU A 35 ASP A 40 0 SHEET 2 A 5 ARG A 4 LEU A 9 1 N ALA A 5 O VAL A 37 SHEET 3 A 5 LEU A 96 PRO A 102 1 O ILE A 98 N VAL A 8 SHEET 4 A 5 LYS A 141 THR A 147 1 O SER A 145 N PHE A 99 SHEET 5 A 5 GLN A 182 VAL A 183 1 O GLN A 182 N ALA A 142 SHEET 1 B 5 GLU A 35 ASP A 40 0 SHEET 2 B 5 ARG A 4 LEU A 9 1 N ALA A 5 O VAL A 37 SHEET 3 B 5 LEU A 96 PRO A 102 1 O ILE A 98 N VAL A 8 SHEET 4 B 5 LYS A 141 THR A 147 1 O SER A 145 N PHE A 99 SHEET 5 B 5 GLN A 187 THR A 189 1 O THR A 189 N ILE A 146 SHEET 1 C 5 GLU B 35 ASP B 40 0 SHEET 2 C 5 ARG B 4 LEU B 9 1 N ALA B 5 O GLU B 35 SHEET 3 C 5 LEU B 96 PRO B 102 1 O ILE B 98 N VAL B 8 SHEET 4 C 5 LYS B 141 THR B 147 1 O SER B 145 N PHE B 99 SHEET 5 C 5 GLN B 182 VAL B 183 1 O GLN B 182 N ALA B 142 SHEET 1 D 5 GLU B 35 ASP B 40 0 SHEET 2 D 5 ARG B 4 LEU B 9 1 N ALA B 5 O GLU B 35 SHEET 3 D 5 LEU B 96 PRO B 102 1 O ILE B 98 N VAL B 8 SHEET 4 D 5 LYS B 141 THR B 147 1 O SER B 145 N PHE B 99 SHEET 5 D 5 GLN B 187 THR B 189 1 O THR B 189 N ILE B 146 SHEET 1 E 5 GLU C 35 ASP C 40 0 SHEET 2 E 5 ARG C 4 LEU C 9 1 N ALA C 5 O GLU C 35 SHEET 3 E 5 LEU C 96 PRO C 102 1 O LEU C 96 N LEU C 6 SHEET 4 E 5 LYS C 141 THR C 147 1 O VAL C 143 N PHE C 99 SHEET 5 E 5 GLN C 182 VAL C 183 1 O GLN C 182 N ALA C 142 SHEET 1 F 5 GLU C 35 ASP C 40 0 SHEET 2 F 5 ARG C 4 LEU C 9 1 N ALA C 5 O GLU C 35 SHEET 3 F 5 LEU C 96 PRO C 102 1 O LEU C 96 N LEU C 6 SHEET 4 F 5 LYS C 141 THR C 147 1 O VAL C 143 N PHE C 99 SHEET 5 F 5 GLN C 187 THR C 189 1 O GLN C 187 N ILE C 146 SHEET 1 G 5 GLU D 35 ASP D 40 0 SHEET 2 G 5 ARG D 4 LEU D 9 1 N ALA D 5 O GLU D 35 SHEET 3 G 5 LEU D 96 PRO D 102 1 O ILE D 98 N VAL D 8 SHEET 4 G 5 LYS D 141 THR D 147 1 O SER D 145 N PHE D 99 SHEET 5 G 5 GLN D 182 VAL D 183 1 O GLN D 182 N ALA D 142 SHEET 1 H 5 GLU D 35 ASP D 40 0 SHEET 2 H 5 ARG D 4 LEU D 9 1 N ALA D 5 O GLU D 35 SHEET 3 H 5 LEU D 96 PRO D 102 1 O ILE D 98 N VAL D 8 SHEET 4 H 5 LYS D 141 THR D 147 1 O SER D 145 N PHE D 99 SHEET 5 H 5 GLN D 187 THR D 189 1 O THR D 189 N ILE D 146

SITE 1 AC1 13 TRP A 105 PHE A 106 GLY A 149 GLY A 150 SITE 2 AC1 13 MET A 154 HIS A 161 FAD A 601 PRO C 68 SITE 3 AC1 13 TYR C 126 TYR C 128 MET C 131 PHE C 178 SITE 4 AC1 13 PHE C 232 SITE 1 AC2 11 TRP B 105 PHE B 106 MET B 154 HIS B 161 SITE 2 AC2 11 FAD B 602 PRO D 68 TYR D 126 TYR D 128 SITE 3 AC2 11 MET D 131 PHE D 178 PHE D 236 SITE 1 AC3 9 PRO A 68 TYR A 126 TYR A 128 PHE A 178 SITE 2 AC3 9 TRP C 105 GLY C 149 GLY C 150 HIS C 161 SITE 3 AC3 9 FAD C 603 SITE 1 AC4 10 PRO B 68 TYR B 126 TYR B 128 MET B 131 SITE 2 AC4 10 PHE B 178 TRP D 105 GLY D 149 MET D 154 SITE 3 AC4 10 HIS D 161 FAD D 604 SITE 1 AC5 25 HIS A 11 THR A 15 SER A 16 PHE A 17 SITE 2 AC5 25 ASN A 18 ALA A 20 PRO A 102 LEU A 103 SITE 3 AC5 25 GLN A 104 TRP A 105 PHE A 106 THR A 147 SITE 4 AC5 25 THR A 148 GLY A 149 GLY A 150 TYR A 155 SITE 5 AC5 25 ILE A 192 ARG A 200 ILE A 201 LEU A 204 SITE 6 AC5 25 GLN C 66 TYR C 67 PRO C 68 GLU C 117 SITE 7 AC5 25 340 C 701 SITE 1 AC6 23 HIS B 11 THR B 15 SER B 16 PHE B 17 SITE 2 AC6 23 ASN B 18 ALA B 20 PRO B 102 LEU B 103 SITE 3 AC6 23 GLN B 104 TRP B 105 PHE B 106 THR B 147 SITE 4 AC6 23 THR B 148 GLY B 149 GLY B 150 TYR B 155 SITE 5 AC6 23 ILE B 192 ARG B 200 LEU B 204 GLN D 66 SITE 6 AC6 23 TYR D 67 PRO D 68 340 D 702 SITE 1 AC7 24 ILE A 50 GLN A 66 TYR A 67 GLU A 117 SITE 2 AC7 24 340 A 703 HIS C 11 THR C 15 SER C 16 SITE 3 AC7 24 PHE C 17 ASN C 18 ALA C 20 PRO C 102 SITE 4 AC7 24 LEU C 103 GLN C 104 TRP C 105 PHE C 106 SITE 5 AC7 24 THR C 147 THR C 148 GLY C 149 GLY C 150 SITE 6 AC7 24 TYR C 155 ILE C 192 ARG C 200 LEU C 204 SITE 1 AC8 25 ILE B 50 GLN B 66 TYR B 67 PRO B 68 SITE 2 AC8 25 340 B 704 HIS D 11 THR D 15 SER D 16 SITE 3 AC8 25 PHE D 17 ASN D 18 ALA D 20 PRO D 102 SITE 4 AC8 25 LEU D 103 GLN D 104 TRP D 105 PHE D 106 SITE 5 AC8 25 THR D 147 THR D 148 GLY D 149 GLY D 150 SITE 6 AC8 25 TYR D 155 ILE D 192 ARG D 200 LEU D 204 SITE 7 AC8 25 HOH D 727

CRYST1 55.636 57.026 96.878 76.80 76.93 86.28 P 1 4

ORIGX1 1.000000 0.000000 0.000000 0.00000

ORIGX2 0.000000 1.000000 0.000000 0.00000

ORIGX3 0.000000 0.000000 1.000000 0.00000

SCALE1 0.017974 -0.001168 -0.004014 0.00000

SCALE2 0.000000 0.017573 -0.003961 0.00000

SCALE3 0.000000 0.000000 0.010863 0.00000