HEADER TRANSFERASE 30-SEP-21 7VKO TITLE CRYSTAL STRUCTURE OF TRKA KINASE WITH REPOTRECTINIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.10.1; COMPND 5 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: NTRK1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS TRK, NTRK, MACROCYCLIC INHIBITOR, DRUG RESISTANCE, REPOTRECTINIB, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.W.MURRAY,E.ROGERS,D.ZHAI,W.DENG,X.CHEN,P.A.SPRENGELER,X.ZHANG, AUTHOR 2 A.GRABER,S.H.REICH,S.STOPATSCHINSKAJA,B.SOLOMON,B.BESSE,A.DRILON REVDAT 3 29-NOV-23 7VKO 1 REMARK REVDAT 2 23-FEB-22 7VKO 1 JRNL REVDAT 1 13-OCT-21 7VKO 0 JRNL AUTH B.W.MURRAY,E.ROGERS,D.ZHAI,W.DENG,X.CHEN,P.A.SPRENGELER, JRNL AUTH 2 X.ZHANG,A.GRABER,S.H.REICH,S.STOPATSCHINSKAJA,B.SOLOMON, JRNL AUTH 3 B.BESSE,A.DRILON JRNL TITL MOLECULAR CHARACTERISTICS OF REPOTRECTINIB THAT ENABLE JRNL TITL 2 POTENT INHIBITION OF TRK FUSION PROTEINS AND RESISTANT JRNL TITL 3 MUTATIONS. JRNL REF MOL.CANCER THER. V. 20 2446 2021 JRNL REFN ESSN 1538-8514 JRNL PMID 34625502 JRNL DOI 10.1158/1535-7163.MCT-21-0632 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 9242 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 491 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 674 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.3770 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.4400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2363 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 95.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.74000 REMARK 3 B22 (A**2) : 2.74000 REMARK 3 B33 (A**2) : -8.89000 REMARK 3 B12 (A**2) : 1.37000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.407 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.343 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.961 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2471 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2275 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3352 ; 1.704 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5241 ; 1.259 ; 1.585 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ; 7.873 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;31.904 ;20.357 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 405 ;23.845 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.165 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 296 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2761 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 567 ; 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): 1189 ; 9.134 ; 9.859 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1190 ; 9.131 ; 9.857 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1483 ;13.452 ;14.781 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1484 ;13.447 ;14.779 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1279 ; 9.409 ;10.598 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1260 ; 9.039 ;10.483 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1839 ;13.625 ;15.403 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2800 ;18.124 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2801 ;18.120 ; 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7VKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-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 : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9735 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4YNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRIC ACID PH 5.0, 8M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 52.38050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.24190 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 68.16867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 52.38050 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.24190 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 68.16867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 52.38050 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.24190 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 68.16867 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 52.38050 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 30.24190 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 68.16867 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 52.38050 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 30.24190 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 68.16867 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 52.38050 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 30.24190 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 68.16867 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 60.48379 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 136.33733 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 60.48379 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 136.33733 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 60.48379 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 136.33733 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 60.48379 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 136.33733 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 60.48379 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 136.33733 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 60.48379 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 136.33733 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 A 915 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 921 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 471 REMARK 465 SER A 472 REMARK 465 TYR A 473 REMARK 465 TYR A 474 REMARK 465 HIS A 475 REMARK 465 HIS A 476 REMARK 465 HIS A 477 REMARK 465 HIS A 478 REMARK 465 HIS A 479 REMARK 465 HIS A 480 REMARK 465 ASP A 481 REMARK 465 TYR A 482 REMARK 465 ASP A 483 REMARK 465 ILE A 484 REMARK 465 PRO A 485 REMARK 465 THR A 486 REMARK 465 THR A 487 REMARK 465 GLU A 488 REMARK 465 ASN A 489 REMARK 465 LEU A 490 REMARK 465 TYR A 491 REMARK 465 PHE A 492 REMARK 465 GLN A 493 REMARK 465 GLY A 494 REMARK 465 ALA A 495 REMARK 465 MET A 496 REMARK 465 VAL A 794 REMARK 465 LEU A 795 REMARK 465 GLY A 796 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 LYS A 538 CG CD CE NZ REMARK 470 LYS A 547 CG CD 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 NH2 ARG A 599 O HOH A 901 1.76 REMARK 500 OD2 ASP A 650 OH TYR A 680 1.78 REMARK 500 OE1 GLU A 745 NH2 ARG A 761 2.05 REMARK 500 O THR A 705 N SER A 708 2.09 REMARK 500 O THR A 741 NH2 ARG A 766 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 702 NH2 ARG A 702 17434 1.41 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 VAL A 573 122.55 -33.13 REMARK 500 VAL A 578 -164.26 -113.85 REMARK 500 CYS A 579 114.04 -162.61 REMARK 500 ARG A 583 101.06 -163.39 REMARK 500 HIS A 645 42.71 39.61 REMARK 500 ASP A 650 52.60 -141.99 REMARK 500 LEU A 662 35.51 71.90 REMARK 500 PHE A 669 -91.62 -131.43 REMARK 500 MET A 671 77.87 58.31 REMARK 500 ARG A 673 -78.25 -61.95 REMARK 500 LEU A 700 -75.06 -77.98 REMARK 500 THR A 706 -30.08 -26.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 583 PRO A 584 60.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 921 DISTANCE = 10.18 ANGSTROMS DBREF 7VKO A 502 796 UNP J3KP20 J3KP20_HUMAN 499 793 SEQADV 7VKO MET A 471 UNP J3KP20 INITIATING METHIONINE SEQADV 7VKO SER A 472 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO TYR A 473 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO TYR A 474 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO HIS A 475 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO HIS A 476 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO HIS A 477 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO HIS A 478 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO HIS A 479 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO HIS A 480 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO ASP A 481 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO TYR A 482 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO ASP A 483 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO ILE A 484 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO PRO A 485 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO THR A 486 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO THR A 487 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO GLU A 488 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO ASN A 489 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO LEU A 490 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO TYR A 491 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO PHE A 492 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO GLN A 493 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO GLY A 494 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO ALA A 495 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO MET A 496 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO GLY A 497 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO SER A 498 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO GLY A 499 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO ILE A 500 UNP J3KP20 EXPRESSION TAG SEQADV 7VKO ARG A 501 UNP J3KP20 EXPRESSION TAG SEQRES 1 A 326 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 A 326 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY ALA MET SEQRES 3 A 326 GLY SER GLY ILE ARG VAL HIS HIS ILE LYS ARG ARG ASP SEQRES 4 A 326 ILE VAL LEU LYS TRP GLU LEU GLY GLU GLY ALA PHE GLY SEQRES 5 A 326 LYS VAL PHE LEU ALA GLU CYS HIS ASN LEU LEU PRO GLU SEQRES 6 A 326 GLN ASP LYS MET LEU VAL ALA VAL LYS ALA LEU LYS GLU SEQRES 7 A 326 ALA SER GLU SER ALA ARG GLN ASP PHE GLN ARG GLU ALA SEQRES 8 A 326 GLU LEU LEU THR MET LEU GLN HIS GLN HIS ILE VAL ARG SEQRES 9 A 326 PHE PHE GLY VAL CYS THR GLU GLY ARG PRO LEU LEU MET SEQRES 10 A 326 VAL PHE GLU TYR MET ARG HIS GLY ASP LEU ASN ARG PHE SEQRES 11 A 326 LEU ARG SER HIS GLY PRO ASP ALA LYS LEU LEU ALA GLY SEQRES 12 A 326 GLY GLU ASP VAL ALA PRO GLY PRO LEU GLY LEU GLY GLN SEQRES 13 A 326 LEU LEU ALA VAL ALA SER GLN VAL ALA ALA GLY MET VAL SEQRES 14 A 326 TYR LEU ALA GLY LEU HIS PHE VAL HIS ARG ASP LEU ALA SEQRES 15 A 326 THR ARG ASN CYS LEU VAL GLY GLN GLY LEU VAL VAL LYS SEQRES 16 A 326 ILE GLY ASP PHE GLY MET SER ARG ASP ILE TYR SER THR SEQRES 17 A 326 ASP TYR TYR ARG VAL GLY GLY ARG THR MET LEU PRO ILE SEQRES 18 A 326 ARG TRP MET PRO PRO GLU SER ILE LEU TYR ARG LYS PHE SEQRES 19 A 326 THR THR GLU SER ASP VAL TRP SER PHE GLY VAL VAL LEU SEQRES 20 A 326 TRP GLU ILE PHE THR TYR GLY LYS GLN PRO TRP TYR GLN SEQRES 21 A 326 LEU SER ASN THR GLU ALA ILE ASP CYS ILE THR GLN GLY SEQRES 22 A 326 ARG GLU LEU GLU ARG PRO ARG ALA CYS PRO PRO GLU VAL SEQRES 23 A 326 TYR ALA ILE MET ARG GLY CYS TRP GLN ARG GLU PRO GLN SEQRES 24 A 326 GLN ARG HIS SER ILE LYS ASP VAL HIS ALA ARG LEU GLN SEQRES 25 A 326 ALA LEU ALA GLN ALA PRO PRO VAL TYR LEU ASP VAL LEU SEQRES 26 A 326 GLY HET 7GI A 801 26 HET SO4 A 802 5 HET SO4 A 803 5 HET SO4 A 804 5 HET SO4 A 805 5 HET SO4 A 806 5 HETNAM 7GI REPOTRECTINIB HETNAM SO4 SULFATE ION HETSYN 7GI TPX-0005 FORMUL 2 7GI C18 H18 F N5 O2 FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *21(H2 O) HELIX 1 AA1 LYS A 506 ARG A 508 5 3 HELIX 2 AA2 SER A 550 LEU A 567 1 18 HELIX 3 AA3 ASP A 596 HIS A 604 1 9 HELIX 4 AA4 GLY A 623 LEU A 644 1 22 HELIX 5 AA5 ALA A 652 ARG A 654 5 3 HELIX 6 AA6 GLN A 660 LEU A 662 5 3 HELIX 7 AA7 PRO A 690 MET A 694 5 5 HELIX 8 AA8 PRO A 695 LEU A 700 1 6 HELIX 9 AA9 THR A 705 PHE A 721 1 17 HELIX 10 AB1 SER A 732 GLY A 743 1 12 HELIX 11 AB2 PRO A 753 TRP A 764 1 12 HELIX 12 AB3 GLU A 767 ARG A 771 5 5 HELIX 13 AB4 SER A 773 ALA A 787 1 15 SHEET 1 AA1 5 ILE A 510 GLU A 518 0 SHEET 2 AA1 5 LYS A 523 LEU A 533 -1 O VAL A 524 N GLY A 517 SHEET 3 AA1 5 GLN A 536 LYS A 544 -1 O MET A 539 N CYS A 529 SHEET 4 AA1 5 LEU A 586 GLU A 590 -1 O PHE A 589 N ALA A 542 SHEET 5 AA1 5 PHE A 575 CYS A 579 -1 N PHE A 576 O VAL A 588 SHEET 1 AA2 2 CYS A 656 GLY A 659 0 SHEET 2 AA2 2 VAL A 663 ILE A 666 -1 O VAL A 663 N GLY A 659 SHEET 1 AA3 2 TYR A 681 ARG A 682 0 SHEET 2 AA3 2 MET A 688 LEU A 689 -1 O LEU A 689 N TYR A 681 CRYST1 104.761 104.761 204.506 90.00 90.00 120.00 H 3 2 18 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 0.009546 0.005511 0.000000 0.00000 SCALE2 0.000000 0.011022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004890 0.00000