HEADER TRANSFERASE 08-JAN-21 7DU8 TITLE CRYSTAL STRUCTURE OF HUMAN PROTO-ONCOGENE TYROSINE-PROTEIN KINASE TITLE 2 RECEPTOR RET IN COMPLEX WITH SELPERCATINIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: CADHERIN FAMILY MEMBER 12,PROTO-ONCOGENE C-RET; COMPND 6 EC: 2.7.10.1; 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 GENE: RET, CDHF12, CDHR16, PTC, RET51; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS TYROSINE-PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR I.MIYAZAKI,K.ISHIDA,T.SUZUKI REVDAT 2 29-MAY-24 7DU8 1 REMARK REVDAT 1 02-FEB-22 7DU8 0 JRNL AUTH I.MIYAZAKI,K.ISHIDA,T.SUZUKI JRNL TITL SELECTIVE RET INHIBITOR TAS0953/HM06 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 78.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 14927 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 680 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1130 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4540 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.62000 REMARK 3 B22 (A**2) : -1.13000 REMARK 3 B33 (A**2) : -0.85000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.438 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.350 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 36.776 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.868 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4648 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4497 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6288 ; 1.461 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10299 ; 1.179 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 5.970 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 191 ;35.132 ;22.670 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 826 ;13.148 ;15.133 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;14.760 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 675 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5153 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1071 ; 0.002 ; 0.020 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 714 A 807 REMARK 3 ORIGIN FOR THE GROUP (A): 4.433 -7.334 -6.462 REMARK 3 T TENSOR REMARK 3 T11: 0.1888 T22: 0.0621 REMARK 3 T33: 0.2036 T12: 0.0062 REMARK 3 T13: 0.1016 T23: -0.0622 REMARK 3 L TENSOR REMARK 3 L11: 4.7146 L22: 0.6346 REMARK 3 L33: 1.7532 L12: -0.2563 REMARK 3 L13: 2.5718 L23: 0.2816 REMARK 3 S TENSOR REMARK 3 S11: 0.0807 S12: 0.2088 S13: -0.4272 REMARK 3 S21: -0.1499 S22: 0.1103 S23: -0.0474 REMARK 3 S31: -0.0389 S32: 0.1616 S33: -0.1911 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 808 A 1012 REMARK 3 ORIGIN FOR THE GROUP (A): 21.185 4.718 7.867 REMARK 3 T TENSOR REMARK 3 T11: 0.1391 T22: 0.0067 REMARK 3 T33: 0.0232 T12: -0.0148 REMARK 3 T13: 0.0356 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 3.9996 L22: 1.9613 REMARK 3 L33: 2.1838 L12: 0.0989 REMARK 3 L13: -0.6252 L23: 0.4310 REMARK 3 S TENSOR REMARK 3 S11: -0.0442 S12: -0.0355 S13: 0.1346 REMARK 3 S21: 0.1501 S22: -0.0059 S23: -0.0185 REMARK 3 S31: -0.0453 S32: 0.0296 S33: 0.0501 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 700 B 807 REMARK 3 ORIGIN FOR THE GROUP (A): 33.780 15.296 -20.261 REMARK 3 T TENSOR REMARK 3 T11: 0.1529 T22: 0.2043 REMARK 3 T33: 0.1705 T12: 0.0168 REMARK 3 T13: 0.1113 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.1152 L22: 3.3374 REMARK 3 L33: 2.5388 L12: -0.5824 REMARK 3 L13: 0.2907 L23: -1.7011 REMARK 3 S TENSOR REMARK 3 S11: -0.0105 S12: -0.0148 S13: 0.0130 REMARK 3 S21: -0.0846 S22: -0.1451 S23: -0.2237 REMARK 3 S31: -0.0239 S32: 0.0086 S33: 0.1555 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 808 B 1012 REMARK 3 ORIGIN FOR THE GROUP (A): 20.764 -2.046 -34.911 REMARK 3 T TENSOR REMARK 3 T11: 0.1803 T22: 0.1145 REMARK 3 T33: 0.0867 T12: 0.0182 REMARK 3 T13: 0.0232 T23: -0.0553 REMARK 3 L TENSOR REMARK 3 L11: 2.4829 L22: 4.6172 REMARK 3 L33: 3.5205 L12: 1.5118 REMARK 3 L13: -0.2449 L23: 0.4403 REMARK 3 S TENSOR REMARK 3 S11: -0.0613 S12: 0.0068 S13: -0.0070 REMARK 3 S21: -0.2841 S22: -0.1287 S23: 0.4385 REMARK 3 S31: 0.0296 S32: -0.3039 S33: 0.1900 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 7DU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300019356. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15607 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 78.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10600 REMARK 200 FOR THE DATA SET : 9.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44600 REMARK 200 FOR SHELL : 2.770 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.20 M LICL, 0.10 M NA ACETATE, PH REMARK 280 4.50, 2.5 M NA FORMATE, 5 MM MGCL2, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.13250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: 3010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 GLY A 700 REMARK 465 PRO A 701 REMARK 465 LEU A 702 REMARK 465 SER A 703 REMARK 465 LEU A 704 REMARK 465 SER A 705 REMARK 465 VAL A 706 REMARK 465 ASP A 707 REMARK 465 ALA A 708 REMARK 465 PHE A 709 REMARK 465 LYS A 710 REMARK 465 ILE A 711 REMARK 465 LEU A 712 REMARK 465 GLU A 713 REMARK 465 SER A 829 REMARK 465 GLY A 830 REMARK 465 GLY A 831 REMARK 465 SER A 832 REMARK 465 ARG A 833 REMARK 465 ASN A 834 REMARK 465 SER A 835 REMARK 465 SER A 836 REMARK 465 SER A 837 REMARK 465 LEU A 838 REMARK 465 ASP A 839 REMARK 465 HIS A 840 REMARK 465 PRO A 841 REMARK 465 ARG A 1013 REMARK 465 LEU B 712 REMARK 465 GLU B 713 REMARK 465 ASP B 714 REMARK 465 GLY B 823 REMARK 465 PRO B 824 REMARK 465 GLY B 825 REMARK 465 TYR B 826 REMARK 465 LEU B 827 REMARK 465 GLY B 828 REMARK 465 SER B 829 REMARK 465 GLY B 830 REMARK 465 GLY B 831 REMARK 465 SER B 832 REMARK 465 ARG B 833 REMARK 465 ASN B 834 REMARK 465 SER B 835 REMARK 465 SER B 836 REMARK 465 SER B 837 REMARK 465 LEU B 838 REMARK 465 ASP B 839 REMARK 465 HIS B 840 REMARK 465 PRO B 841 REMARK 465 ASP B 842 REMARK 465 GLU B 843 REMARK 465 TYR B 900 REMARK 465 GLU B 901 REMARK 465 GLU B 902 REMARK 465 ASP B 903 REMARK 465 SER B 904 REMARK 465 TYR B 905 REMARK 465 VAL B 906 REMARK 465 LYS B 907 REMARK 465 ARG B 908 REMARK 465 SER B 909 REMARK 465 ARG B 1013 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 716 NZ REMARK 480 GLU A 734 CG CD OE1 OE2 REMARK 480 LYS A 747 CE NZ REMARK 480 LYS A 761 CE NZ REMARK 480 GLN A 781 CD OE1 NE2 REMARK 480 LYS A 789 CE NZ REMARK 480 ASP A 797 CG OD1 OD2 REMARK 480 LYS A 821 CE NZ REMARK 480 GLU A 901 CG CD OE1 OE2 REMARK 480 ARG A 959 CD NE CZ NH1 NH2 REMARK 480 LEU A 963 CD1 CD2 REMARK 480 LYS A 965 NZ REMARK 480 GLU A 978 CD OE1 OE2 REMARK 480 ARG A 982 CD NE CZ NH1 NH2 REMARK 480 GLU A 991 CD OE1 OE2 REMARK 480 ASP A 993 CG OD1 OD2 REMARK 480 LYS A 994 CE NZ REMARK 480 LYS A 1003 CD CE NZ REMARK 480 LYS A 1007 CE NZ REMARK 480 ARG A 1012 NE CZ NH1 NH2 REMARK 480 LYS B 710 NZ REMARK 480 LYS B 716 NZ REMARK 480 GLU B 734 CD OE1 OE2 REMARK 480 LYS B 737 CE NZ REMARK 480 LYS B 761 CE NZ REMARK 480 GLU B 762 CD OE1 OE2 REMARK 480 LYS B 780 NZ REMARK 480 LEU B 800 CD1 CD2 REMARK 480 GLU B 818 CG CD OE1 OE2 REMARK 480 ARG B 820 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 821 CG CD CE NZ REMARK 480 VAL B 822 CG1 CG2 REMARK 480 GLU B 867 CD OE1 OE2 REMARK 480 LYS B 869 CD CE NZ REMARK 480 LYS B 887 NZ REMARK 480 ASP B 898 CG OD1 OD2 REMARK 480 VAL B 899 CG1 CG2 REMARK 480 LYS B 965 CG CD CE NZ REMARK 480 GLU B 978 CG CD OE1 OE2 REMARK 480 GLU B 979 CG CD OE1 OE2 REMARK 480 ARG B 982 CG CD NE CZ NH1 NH2 REMARK 480 GLU B 991 CD OE1 OE2 REMARK 480 LYS B 994 CE NZ REMARK 480 LYS B 1003 NZ 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 763 31.46 -95.45 REMARK 500 ARG A 873 -46.10 76.18 REMARK 500 ASP A 874 50.28 -106.19 REMARK 500 ASP A 892 71.22 61.28 REMARK 500 ASP A 892 71.12 61.93 REMARK 500 VAL A 899 50.64 -142.46 REMARK 500 GLU A 902 -5.99 70.85 REMARK 500 ASN B 763 31.64 -95.06 REMARK 500 ARG B 873 -46.88 77.27 REMARK 500 ASP B 874 50.78 -106.80 REMARK 500 ASP B 892 72.86 63.40 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 Q6G A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Q6G B 1101 DBREF 7DU8 A 705 1013 UNP P07949 RET_HUMAN 705 1013 DBREF 7DU8 B 705 1013 UNP P07949 RET_HUMAN 705 1013 SEQADV 7DU8 GLY A 700 UNP P07949 EXPRESSION TAG SEQADV 7DU8 PRO A 701 UNP P07949 EXPRESSION TAG SEQADV 7DU8 LEU A 702 UNP P07949 EXPRESSION TAG SEQADV 7DU8 SER A 703 UNP P07949 EXPRESSION TAG SEQADV 7DU8 LEU A 704 UNP P07949 EXPRESSION TAG SEQADV 7DU8 GLY B 700 UNP P07949 EXPRESSION TAG SEQADV 7DU8 PRO B 701 UNP P07949 EXPRESSION TAG SEQADV 7DU8 LEU B 702 UNP P07949 EXPRESSION TAG SEQADV 7DU8 SER B 703 UNP P07949 EXPRESSION TAG SEQADV 7DU8 LEU B 704 UNP P07949 EXPRESSION TAG SEQRES 1 A 314 GLY PRO LEU SER LEU SER VAL ASP ALA PHE LYS ILE LEU SEQRES 2 A 314 GLU ASP PRO LYS TRP GLU PHE PRO ARG LYS ASN LEU VAL SEQRES 3 A 314 LEU GLY LYS THR LEU GLY GLU GLY GLU PHE GLY LYS VAL SEQRES 4 A 314 VAL LYS ALA THR ALA PHE HIS LEU LYS GLY ARG ALA GLY SEQRES 5 A 314 TYR THR THR VAL ALA VAL LYS MET LEU LYS GLU ASN ALA SEQRES 6 A 314 SER PRO SER GLU LEU ARG ASP LEU LEU SER GLU PHE ASN SEQRES 7 A 314 VAL LEU LYS GLN VAL ASN HIS PRO HIS VAL ILE LYS LEU SEQRES 8 A 314 TYR GLY ALA CYS SER GLN ASP GLY PRO LEU LEU LEU ILE SEQRES 9 A 314 VAL GLU TYR ALA LYS TYR GLY SER LEU ARG GLY PHE LEU SEQRES 10 A 314 ARG GLU SER ARG LYS VAL GLY PRO GLY TYR LEU GLY SER SEQRES 11 A 314 GLY GLY SER ARG ASN SER SER SER LEU ASP HIS PRO ASP SEQRES 12 A 314 GLU ARG ALA LEU THR MET GLY ASP LEU ILE SER PHE ALA SEQRES 13 A 314 TRP GLN ILE SER GLN GLY MET GLN TYR LEU ALA GLU MET SEQRES 14 A 314 LYS LEU VAL HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU SEQRES 15 A 314 VAL ALA GLU GLY ARG LYS MET LYS ILE SER ASP PHE GLY SEQRES 16 A 314 LEU SER ARG ASP VAL TYR GLU GLU ASP SER TYR VAL LYS SEQRES 17 A 314 ARG SER GLN GLY ARG ILE PRO VAL LYS TRP MET ALA ILE SEQRES 18 A 314 GLU SER LEU PHE ASP HIS ILE TYR THR THR GLN SER ASP SEQRES 19 A 314 VAL TRP SER PHE GLY VAL LEU LEU TRP GLU ILE VAL THR SEQRES 20 A 314 LEU GLY GLY ASN PRO TYR PRO GLY ILE PRO PRO GLU ARG SEQRES 21 A 314 LEU PHE ASN LEU LEU LYS THR GLY HIS ARG MET GLU ARG SEQRES 22 A 314 PRO ASP ASN CYS SER GLU GLU MET TYR ARG LEU MET LEU SEQRES 23 A 314 GLN CYS TRP LYS GLN GLU PRO ASP LYS ARG PRO VAL PHE SEQRES 24 A 314 ALA ASP ILE SER LYS ASP LEU GLU LYS MET MET VAL LYS SEQRES 25 A 314 ARG ARG SEQRES 1 B 314 GLY PRO LEU SER LEU SER VAL ASP ALA PHE LYS ILE LEU SEQRES 2 B 314 GLU ASP PRO LYS TRP GLU PHE PRO ARG LYS ASN LEU VAL SEQRES 3 B 314 LEU GLY LYS THR LEU GLY GLU GLY GLU PHE GLY LYS VAL SEQRES 4 B 314 VAL LYS ALA THR ALA PHE HIS LEU LYS GLY ARG ALA GLY SEQRES 5 B 314 TYR THR THR VAL ALA VAL LYS MET LEU LYS GLU ASN ALA SEQRES 6 B 314 SER PRO SER GLU LEU ARG ASP LEU LEU SER GLU PHE ASN SEQRES 7 B 314 VAL LEU LYS GLN VAL ASN HIS PRO HIS VAL ILE LYS LEU SEQRES 8 B 314 TYR GLY ALA CYS SER GLN ASP GLY PRO LEU LEU LEU ILE SEQRES 9 B 314 VAL GLU TYR ALA LYS TYR GLY SER LEU ARG GLY PHE LEU SEQRES 10 B 314 ARG GLU SER ARG LYS VAL GLY PRO GLY TYR LEU GLY SER SEQRES 11 B 314 GLY GLY SER ARG ASN SER SER SER LEU ASP HIS PRO ASP SEQRES 12 B 314 GLU ARG ALA LEU THR MET GLY ASP LEU ILE SER PHE ALA SEQRES 13 B 314 TRP GLN ILE SER GLN GLY MET GLN TYR LEU ALA GLU MET SEQRES 14 B 314 LYS LEU VAL HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU SEQRES 15 B 314 VAL ALA GLU GLY ARG LYS MET LYS ILE SER ASP PHE GLY SEQRES 16 B 314 LEU SER ARG ASP VAL TYR GLU GLU ASP SER TYR VAL LYS SEQRES 17 B 314 ARG SER GLN GLY ARG ILE PRO VAL LYS TRP MET ALA ILE SEQRES 18 B 314 GLU SER LEU PHE ASP HIS ILE TYR THR THR GLN SER ASP SEQRES 19 B 314 VAL TRP SER PHE GLY VAL LEU LEU TRP GLU ILE VAL THR SEQRES 20 B 314 LEU GLY GLY ASN PRO TYR PRO GLY ILE PRO PRO GLU ARG SEQRES 21 B 314 LEU PHE ASN LEU LEU LYS THR GLY HIS ARG MET GLU ARG SEQRES 22 B 314 PRO ASP ASN CYS SER GLU GLU MET TYR ARG LEU MET LEU SEQRES 23 B 314 GLN CYS TRP LYS GLN GLU PRO ASP LYS ARG PRO VAL PHE SEQRES 24 B 314 ALA ASP ILE SER LYS ASP LEU GLU LYS MET MET VAL LYS SEQRES 25 B 314 ARG ARG HET Q6G A1101 39 HET Q6G B1101 39 HETNAM Q6G SELPERCATINIB HETSYN Q6G 6-(2-HYDROXY-2-METHYLPROPOXY)-4-(6-{(1R,5S)-6-[(6- HETSYN 2 Q6G METHOXYPYRIDIN-3-YL)METHYL]-3,6- HETSYN 3 Q6G DIAZABICYCLO[3.1.1]HEPTAN-3-YL}PYRIDIN-3-YL) HETSYN 4 Q6G PYRAZOLO[1,5-A]PYRIDINE-3-CARBONITRILE FORMUL 3 Q6G 2(C29 H31 N7 O3) FORMUL 5 HOH *58(H2 O) HELIX 1 AA1 PRO A 720 LYS A 722 5 3 HELIX 2 AA2 SER A 765 VAL A 782 1 18 HELIX 3 AA3 SER A 811 VAL A 822 1 12 HELIX 4 AA4 MET A 848 MET A 868 1 21 HELIX 5 AA5 GLU A 884 ARG A 886 5 3 HELIX 6 AA6 PRO A 914 MET A 918 5 5 HELIX 7 AA7 ALA A 919 HIS A 926 1 8 HELIX 8 AA8 THR A 929 THR A 946 1 18 HELIX 9 AA9 ARG A 959 GLY A 967 1 9 HELIX 10 AB1 SER A 977 TRP A 988 1 12 HELIX 11 AB2 GLU A 991 ARG A 995 5 5 HELIX 12 AB3 VAL A 997 ARG A 1012 1 16 HELIX 13 AB4 PRO B 701 ILE B 711 1 11 HELIX 14 AB5 PRO B 720 LYS B 722 5 3 HELIX 15 AB6 LEU B 746 ARG B 749 5 4 HELIX 16 AB7 SER B 765 VAL B 782 1 18 HELIX 17 AB8 SER B 811 SER B 819 1 9 HELIX 18 AB9 THR B 847 MET B 868 1 22 HELIX 19 AC1 GLU B 884 ARG B 886 5 3 HELIX 20 AC2 PRO B 914 MET B 918 5 5 HELIX 21 AC3 ALA B 919 HIS B 926 1 8 HELIX 22 AC4 THR B 929 THR B 946 1 18 HELIX 23 AC5 ARG B 959 GLY B 967 1 9 HELIX 24 AC6 SER B 977 TRP B 988 1 12 HELIX 25 AC7 GLU B 991 ARG B 995 5 5 HELIX 26 AC8 VAL B 997 ARG B 1012 1 16 SHEET 1 AA1 5 LEU A 724 GLU A 732 0 SHEET 2 AA1 5 GLY A 736 PHE A 744 -1 O LYS A 740 N LYS A 728 SHEET 3 AA1 5 TYR A 752 LEU A 760 -1 O VAL A 757 N VAL A 739 SHEET 4 AA1 5 LEU A 801 GLU A 805 -1 O VAL A 804 N ALA A 756 SHEET 5 AA1 5 LEU A 790 CYS A 794 -1 N TYR A 791 O ILE A 803 SHEET 1 AA2 2 TYR A 826 GLY A 828 0 SHEET 2 AA2 2 LEU A 846 THR A 847 1 O LEU A 846 N LEU A 827 SHEET 1 AA3 2 LEU A 870 VAL A 871 0 SHEET 2 AA3 2 ARG A 897 ASP A 898 -1 O ARG A 897 N VAL A 871 SHEET 1 AA4 2 ILE A 880 ALA A 883 0 SHEET 2 AA4 2 LYS A 887 ILE A 890 -1 O LYS A 889 N LEU A 881 SHEET 1 AA5 2 TYR A 905 VAL A 906 0 SHEET 2 AA5 2 ILE A 927 TYR A 928 -1 O TYR A 928 N TYR A 905 SHEET 1 AA6 5 LEU B 724 GLU B 732 0 SHEET 2 AA6 5 GLY B 736 PHE B 744 -1 O LYS B 740 N GLY B 727 SHEET 3 AA6 5 TYR B 752 LEU B 760 -1 O VAL B 757 N VAL B 739 SHEET 4 AA6 5 LEU B 801 GLU B 805 -1 O VAL B 804 N ALA B 756 SHEET 5 AA6 5 LEU B 790 CYS B 794 -1 N TYR B 791 O ILE B 803 SHEET 1 AA7 2 LEU B 870 VAL B 871 0 SHEET 2 AA7 2 ARG B 897 ASP B 898 -1 O ARG B 897 N VAL B 871 SHEET 1 AA8 2 ILE B 880 ALA B 883 0 SHEET 2 AA8 2 LYS B 887 ILE B 890 -1 O LYS B 889 N LEU B 881 CISPEP 1 GLY A 823 PRO A 824 0 -4.06 SITE 1 AC1 16 GLY A 731 PHE A 735 GLY A 736 LYS A 737 SITE 2 AC1 16 VAL A 738 ALA A 756 MET A 759 GLU A 768 SITE 3 AC1 16 LEU A 772 GLU A 805 TYR A 806 ALA A 807 SITE 4 AC1 16 LYS A 808 GLY A 810 LEU A 881 ASP A 892 SITE 1 AC2 15 LEU B 730 GLY B 731 PHE B 735 LYS B 737 SITE 2 AC2 15 VAL B 738 ALA B 756 MET B 759 GLU B 768 SITE 3 AC2 15 LEU B 772 GLU B 805 ALA B 807 LYS B 808 SITE 4 AC2 15 GLY B 810 LEU B 881 HOH B1215 CRYST1 50.771 80.265 79.910 90.00 99.61 90.00 P 1 21 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 0.019696 0.000000 0.003333 0.00000 SCALE2 0.000000 0.012459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012692 0.00000