HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 16-JUL-12 4G47 TITLE STRUCTURE OF CYTOCHROME P450 CYP121 IN COMPLEX WITH 4-(1H-1,2,4- TITLE 2 TRIAZOL-1-YL)PHENOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 121; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME P450 MT2; COMPND 5 EC: 1.14.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV2276; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS P450, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.A.HUDSON,K.J.MCLEAN,S.SURADE,Y.-Q.YANG,D.LEYS,A.CIULLI,A.W.MUNRO, AUTHOR 2 C.ABELL REVDAT 3 20-MAR-24 4G47 1 REMARK REVDAT 2 19-SEP-12 4G47 1 JRNL REVDAT 1 05-SEP-12 4G47 0 JRNL AUTH S.A.HUDSON,K.J.MCLEAN,S.SURADE,Y.-Q.YANG,D.LEYS,A.CIULLI, JRNL AUTH 2 A.W.MUNRO,C.ABELL JRNL TITL APPLICATION OF FRAGMENT SCREENING AND MERGING TO THE JRNL TITL 2 DISCOVERY OF INHIBITORS OF THE MYCOBACTERIUM TUBERCULOSIS JRNL TITL 3 CYTOCHROME P450 CYP121 JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 51 9311 2012 JRNL REFN ISSN 1433-7851 JRNL PMID 22890978 JRNL DOI 10.1002/ANIE.201202544 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 97114 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 + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5059 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4193 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2980 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.047 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.699 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3232 ; 0.030 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4424 ; 3.136 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 393 ; 5.630 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;29.243 ;23.154 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 535 ;12.343 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;16.424 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 517 ; 0.168 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2423 ; 0.017 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4G47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97114 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 33.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULPHATE, PH 6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 175.73333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.86667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 131.80000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.93333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 219.66667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 175.73333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 87.86667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 43.93333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 131.80000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 219.66667 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 43.93333 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1012 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1027 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1099 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1154 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1161 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 2 N CA CB OG1 CG2 REMARK 470 ARG A 17 CZ NH1 NH2 REMARK 470 GLU A 24 CD OE1 OE2 REMARK 470 ARG A 28 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 96 CE NZ REMARK 470 LYS A 100 NZ REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 GLU A 127 CD OE1 OE2 REMARK 470 LYS A 148 CE NZ REMARK 470 LYS A 159 CD CE NZ REMARK 470 ARG A 162 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 184 CD NE CZ NH1 NH2 REMARK 470 GLU A 261 CD OE1 OE2 REMARK 470 LYS A 262 CE NZ REMARK 470 GLU A 317 CD OE1 OE2 REMARK 470 ARG A 353 CD NE CZ NH1 NH2 REMARK 470 LYS A 364 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 730 O HOH A 845 1.29 REMARK 500 O HOH A 643 O HOH A 796 1.41 REMARK 500 O HOH A 741 O HOH A 977 1.70 REMARK 500 O HOH A 1023 O HOH A 1167 1.75 REMARK 500 O HOH A 741 O HOH A 1100 1.78 REMARK 500 O HOH A 784 O HOH A 1062 1.80 REMARK 500 OE2 GLU A 326 O HOH A 830 1.83 REMARK 500 O HOH A 994 O HOH A 1063 1.86 REMARK 500 O HOH A 784 O HOH A 1101 1.91 REMARK 500 O HOH A 1062 O HOH A 1065 1.92 REMARK 500 O HOH A 978 O HOH A 982 1.92 REMARK 500 O HOH A 672 O HOH A 741 1.92 REMARK 500 O HOH A 916 O HOH A 999 1.93 REMARK 500 O HOH A 1064 O HOH A 1071 1.94 REMARK 500 NE ARG A 383 O HOH A 1163 1.96 REMARK 500 O HOH A 653 O HOH A 1091 1.97 REMARK 500 OE2 GLU A 194 O HOH A 1179 2.00 REMARK 500 O HOH A 792 O HOH A 826 2.00 REMARK 500 O HOH A 814 O HOH A 1170 2.02 REMARK 500 O HOH A 606 O HOH A 1001 2.02 REMARK 500 O4 SO4 A 405 O HOH A 1093 2.02 REMARK 500 O HOH A 642 O HOH A 1021 2.04 REMARK 500 O HOH A 1067 O HOH A 1086 2.05 REMARK 500 OE2 GLU A 41 O HOH A 789 2.08 REMARK 500 O HOH A 614 O HOH A 1056 2.09 REMARK 500 O HOH A 810 O HOH A 1236 2.09 REMARK 500 OE1 GLU A 29 O HOH A 1167 2.10 REMARK 500 OG SER A 12 O HOH A 831 2.11 REMARK 500 O HOH A 1007 O HOH A 1011 2.12 REMARK 500 O HOH A 616 O HOH A 1109 2.13 REMARK 500 O HOH A 648 O HOH A 899 2.14 REMARK 500 CD GLU A 8 O HOH A 1060 2.15 REMARK 500 OE1 GLU A 29 O HOH A 1023 2.15 REMARK 500 O HOH A 711 O HOH A 1056 2.16 REMARK 500 O HOH A 639 O HOH A 1045 2.16 REMARK 500 CD1 ILE A 37 O HOH A 1163 2.16 REMARK 500 O HOH A 1105 O HOH A 1116 2.17 REMARK 500 O HOH A 916 O HOH A 953 2.19 REMARK 500 O HOH A 976 O HOH A 1061 2.19 REMARK 500 O HOH A 972 O HOH A 975 2.19 REMARK 500 O HOH A 580 O HOH A 889 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 56 CG GLU A 56 CD -0.100 REMARK 500 GLU A 56 CD GLU A 56 OE2 0.107 REMARK 500 GLU A 81 CD GLU A 81 OE1 0.082 REMARK 500 GLU A 221 CG GLU A 221 CD 0.091 REMARK 500 GLU A 221 CD GLU A 221 OE2 0.067 REMARK 500 GLU A 272 CD GLU A 272 OE2 0.092 REMARK 500 GLU A 310 CD GLU A 310 OE1 0.075 REMARK 500 GLU A 326 CD GLU A 326 OE1 0.077 REMARK 500 HIS A 335 CG HIS A 335 CD2 0.059 REMARK 500 HIS A 343 CG HIS A 343 CD2 0.055 REMARK 500 TRP A 396 CG TRP A 396 CD1 0.090 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 GLU A 56 OE1 - CD - OE2 ANGL. DEV. = 15.5 DEGREES REMARK 500 GLU A 56 CG - CD - OE2 ANGL. DEV. = -15.5 DEGREES REMARK 500 ASP A 57 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 59 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 MET A 99 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 MET A 99 CB - CA - C ANGL. DEV. = 15.6 DEGREES REMARK 500 LEU A 113 CA - CB - CG ANGL. DEV. = 19.8 DEGREES REMARK 500 PHE A 137 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ASP A 139 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 183 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 208 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG A 208 CD - NE - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG A 286 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP A 291 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 329 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 340 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 352 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 LEU A 362 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 ASP A 370 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 LEU A 371 CB - CG - CD2 ANGL. DEV. = -11.8 DEGREES REMARK 500 ASP A 376 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 TRP A 396 CD1 - NE1 - CE2 ANGL. DEV. = 5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 84 34.07 -88.62 REMARK 500 PHE A 137 -73.82 -141.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 72 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 345 SG REMARK 620 2 HEM A 401 NA 100.8 REMARK 620 3 HEM A 401 NB 92.0 90.0 REMARK 620 4 HEM A 401 NC 88.5 170.7 88.8 REMARK 620 5 HEM A 401 ND 101.5 88.5 166.4 90.5 REMARK 620 6 HOH A1093 O 173.6 84.3 84.1 86.5 82.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TZF A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G44 RELATED DB: PDB REMARK 900 CYP121 IN COMPLEX WITH OTHER LEAD COMPOUNDS REMARK 900 RELATED ID: 4G45 RELATED DB: PDB REMARK 900 RELATED ID: 4G46 RELATED DB: PDB REMARK 900 RELATED ID: 4G48 RELATED DB: PDB DBREF 4G47 A 1 396 UNP P0A514 CP121_MYCTU 1 396 SEQRES 1 A 396 MET THR ALA THR VAL LEU LEU GLU VAL PRO PHE SER ALA SEQRES 2 A 396 ARG GLY ASP ARG ILE PRO ASP ALA VAL ALA GLU LEU ARG SEQRES 3 A 396 THR ARG GLU PRO ILE ARG LYS VAL ARG THR ILE THR GLY SEQRES 4 A 396 ALA GLU ALA TRP LEU VAL SER SER TYR ALA LEU CYS THR SEQRES 5 A 396 GLN VAL LEU GLU ASP ARG ARG PHE SER MET LYS GLU THR SEQRES 6 A 396 ALA ALA ALA GLY ALA PRO ARG LEU ASN ALA LEU THR VAL SEQRES 7 A 396 PRO PRO GLU VAL VAL ASN ASN MET GLY ASN ILE ALA ASP SEQRES 8 A 396 ALA GLY LEU ARG LYS ALA VAL MET LYS ALA ILE THR PRO SEQRES 9 A 396 LYS ALA PRO GLY LEU GLU GLN PHE LEU ARG ASP THR ALA SEQRES 10 A 396 ASN SER LEU LEU ASP ASN LEU ILE THR GLU GLY ALA PRO SEQRES 11 A 396 ALA ASP LEU ARG ASN ASP PHE ALA ASP PRO LEU ALA THR SEQRES 12 A 396 ALA LEU HIS CYS LYS VAL LEU GLY ILE PRO GLN GLU ASP SEQRES 13 A 396 GLY PRO LYS LEU PHE ARG SER LEU SER ILE ALA PHE MET SEQRES 14 A 396 SER SER ALA ASP PRO ILE PRO ALA ALA LYS ILE ASN TRP SEQRES 15 A 396 ASP ARG ASP ILE GLU TYR MET ALA GLY ILE LEU GLU ASN SEQRES 16 A 396 PRO ASN ILE THR THR GLY LEU MET GLY GLU LEU SER ARG SEQRES 17 A 396 LEU ARG LYS ASP PRO ALA TYR SER HIS VAL SER ASP GLU SEQRES 18 A 396 LEU PHE ALA THR ILE GLY VAL THR PHE PHE GLY ALA GLY SEQRES 19 A 396 VAL ILE SER THR GLY SER PHE LEU THR THR ALA LEU ILE SEQRES 20 A 396 SER LEU ILE GLN ARG PRO GLN LEU ARG ASN LEU LEU HIS SEQRES 21 A 396 GLU LYS PRO GLU LEU ILE PRO ALA GLY VAL GLU GLU LEU SEQRES 22 A 396 LEU ARG ILE ASN LEU SER PHE ALA ASP GLY LEU PRO ARG SEQRES 23 A 396 LEU ALA THR ALA ASP ILE GLN VAL GLY ASP VAL LEU VAL SEQRES 24 A 396 ARG LYS GLY GLU LEU VAL LEU VAL LEU LEU GLU GLY ALA SEQRES 25 A 396 ASN PHE ASP PRO GLU HIS PHE PRO ASN PRO GLY SER ILE SEQRES 26 A 396 GLU LEU ASP ARG PRO ASN PRO THR SER HIS LEU ALA PHE SEQRES 27 A 396 GLY ARG GLY GLN HIS PHE CYS PRO GLY SER ALA LEU GLY SEQRES 28 A 396 ARG ARG HIS ALA GLN ILE GLY ILE GLU ALA LEU LEU LYS SEQRES 29 A 396 LYS MET PRO GLY VAL ASP LEU ALA VAL PRO ILE ASP GLN SEQRES 30 A 396 LEU VAL TRP ARG THR ARG PHE GLN ARG ARG ILE PRO GLU SEQRES 31 A 396 ARG LEU PRO VAL LEU TRP HET HEM A 401 43 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET TZF A 406 24 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM SO4 SULFATE ION HETNAM TZF 4-(1H-1,2,4-TRIAZOL-1-YL)PHENOL HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 TZF C8 H7 N3 O FORMUL 8 HOH *736(H2 O) HELIX 1 1 ASP A 20 GLU A 29 1 10 HELIX 2 2 SER A 47 GLU A 56 1 10 HELIX 3 3 MET A 62 ALA A 67 5 6 HELIX 4 4 PRO A 79 VAL A 83 5 5 HELIX 5 5 ASN A 84 ALA A 92 1 9 HELIX 6 6 LEU A 94 ILE A 102 1 9 HELIX 7 7 GLY A 108 GLY A 128 1 21 HELIX 8 8 PHE A 137 GLY A 151 1 15 HELIX 9 9 PRO A 153 GLU A 155 5 3 HELIX 10 10 ASP A 156 SER A 163 1 8 HELIX 11 11 SER A 163 PHE A 168 1 6 HELIX 12 12 ILE A 175 ASN A 195 1 21 HELIX 13 13 THR A 200 LYS A 211 1 12 HELIX 14 14 ASP A 212 SER A 216 5 5 HELIX 15 15 SER A 219 GLN A 251 1 33 HELIX 16 16 ARG A 252 LYS A 262 1 11 HELIX 17 17 LEU A 265 ILE A 276 1 12 HELIX 18 18 LEU A 308 PHE A 314 1 7 HELIX 19 19 ARG A 340 PHE A 344 5 5 HELIX 20 20 GLY A 347 MET A 366 1 20 HELIX 21 21 PRO A 374 LEU A 378 5 5 SHEET 1 A 5 ILE A 31 ARG A 35 0 SHEET 2 A 5 GLU A 41 VAL A 45 -1 O LEU A 44 N ARG A 32 SHEET 3 A 5 LEU A 304 VAL A 307 1 O LEU A 306 N TRP A 43 SHEET 4 A 5 LEU A 284 ALA A 288 -1 N ARG A 286 O VAL A 305 SHEET 5 A 5 PHE A 60 SER A 61 -1 N SER A 61 O LEU A 287 SHEET 1 B 3 ALA A 131 ASP A 132 0 SHEET 2 B 3 PRO A 393 LEU A 395 -1 O VAL A 394 N ALA A 131 SHEET 3 B 3 ASP A 370 LEU A 371 -1 N ASP A 370 O LEU A 395 SHEET 1 C 2 ILE A 292 VAL A 294 0 SHEET 2 C 2 VAL A 297 VAL A 299 -1 O VAL A 297 N VAL A 294 LINK SG CYS A 345 FE HEM A 401 1555 1555 2.35 LINK FE HEM A 401 O HOH A1093 1555 1555 2.41 CISPEP 1 VAL A 9 PRO A 10 0 -1.85 CISPEP 2 ALA A 129 PRO A 130 0 0.23 SITE 1 AC1 21 MET A 62 MET A 86 HIS A 146 PHE A 230 SITE 2 AC1 21 GLY A 234 SER A 237 PHE A 280 LEU A 284 SITE 3 AC1 21 ARG A 286 ALA A 337 PHE A 338 GLY A 339 SITE 4 AC1 21 HIS A 343 CYS A 345 PRO A 346 HOH A 549 SITE 5 AC1 21 HOH A 558 HOH A 602 HOH A 637 HOH A 777 SITE 6 AC1 21 HOH A1093 SITE 1 AC2 8 LYS A 211 PRO A 330 ASN A 331 PRO A 332 SITE 2 AC2 8 THR A 333 SER A 334 HOH A 666 HOH A 743 SITE 1 AC3 6 SER A 12 HOH A 690 HOH A 779 HOH A 825 SITE 2 AC3 6 HOH A 928 HOH A1050 SITE 1 AC4 8 ARG A 58 SER A 61 MET A 62 LYS A 63 SITE 2 AC4 8 HIS A 343 HOH A 586 HOH A 609 HOH A 709 SITE 1 AC5 4 ARG A 386 TZF A 406 HOH A 530 HOH A1093 SITE 1 AC6 11 THR A 77 VAL A 78 ASN A 85 ALA A 167 SITE 2 AC6 11 PHE A 168 VAL A 228 GLN A 385 SO4 A 405 SITE 3 AC6 11 HOH A 528 HOH A 581 HOH A 616 CRYST1 77.450 77.450 263.600 90.00 90.00 120.00 P 65 2 2 12 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 0.012912 0.007454 0.000000 0.00000 SCALE2 0.000000 0.014909 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003794 0.00000