HEADER TRANSFERASE 08-NOV-18 6IQN TITLE CRYSTAL STRUCTURE OF TRKA KINASE WITH LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 1,TRK1- COMPND 5 TRANSFORMING TYROSINE KINASE PROTEIN,TROPOMYOSIN-RELATED KINASE A, COMPND 6 TYROSINE KINASE RECEPTOR,TYROSINE KINASE RECEPTOR A,TRK-A,GP140TRK, COMPND 7 P140-TRKA; COMPND 8 EC: 2.7.10.1; COMPND 9 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, MTC, TRK, TRKA; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS INHIBITOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.NORITAKA REVDAT 2 22-NOV-23 6IQN 1 REMARK REVDAT 1 22-JAN-20 6IQN 0 JRNL AUTH N.FURUYA,T.MOMOSE,K.KATSUNO,N.FUSHIMI,H.MURANAKA,C.HANDA, JRNL AUTH 2 M.SAWA,T.OZAWA,T.KINOSHITA JRNL TITL AN ISOFORM-SELECTIVE INHIBITOR OF TROPOMYOSIN RECEPTOR JRNL TITL 2 KINASE A BEHAVES AS MOLECULAR GLUE. JRNL REF BIOORG.MED.CHEM.LETT. V. 30 26775 2020 JRNL REFN ESSN 1464-3405 JRNL PMID 31699609 JRNL DOI 10.1016/J.BMCL.2019.126775 REMARK 2 REMARK 2 RESOLUTION. 2.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 26588 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1369 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1902 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.4010 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.4600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4222 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -1.42000 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): 0.406 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.302 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.292 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.408 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4413 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4259 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5976 ; 1.948 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9738 ; 1.236 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 521 ; 7.930 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 201 ;32.223 ;22.537 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 727 ;16.771 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;16.813 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4908 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1083 ; 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): 2111 ; 1.871 ; 2.712 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2110 ; 1.869 ; 2.711 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2623 ; 3.138 ; 4.054 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2624 ; 3.138 ; 4.055 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2302 ; 1.982 ; 2.897 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2303 ; 1.981 ; 2.897 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3354 ; 3.357 ; 4.248 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 18305 ; 6.771 ;25.075 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 18268 ; 6.760 ;25.020 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 : 2 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 501 A 790 REMARK 3 ORIGIN FOR THE GROUP (A): -9.0018 14.1106 -13.0453 REMARK 3 T TENSOR REMARK 3 T11: 0.4049 T22: 0.3894 REMARK 3 T33: 0.0273 T12: 0.0143 REMARK 3 T13: 0.0090 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 2.6269 L22: 1.5335 REMARK 3 L33: 2.1168 L12: 0.0251 REMARK 3 L13: -0.3042 L23: 0.1314 REMARK 3 S TENSOR REMARK 3 S11: 0.0198 S12: -0.0878 S13: 0.2474 REMARK 3 S21: 0.0229 S22: 0.0606 S23: 0.0631 REMARK 3 S31: -0.2660 S32: 0.0679 S33: -0.0803 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 : B 501 B 788 REMARK 3 ORIGIN FOR THE GROUP (A): -13.4131 -7.6542 -34.8992 REMARK 3 T TENSOR REMARK 3 T11: 0.5182 T22: 0.2516 REMARK 3 T33: 0.1250 T12: 0.0329 REMARK 3 T13: -0.0479 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 2.6696 L22: 2.2033 REMARK 3 L33: 2.6972 L12: -0.2225 REMARK 3 L13: -0.6051 L23: 1.0132 REMARK 3 S TENSOR REMARK 3 S11: -0.0722 S12: 0.0716 S13: -0.4327 REMARK 3 S21: -0.2891 S22: -0.1238 S23: 0.3779 REMARK 3 S31: 0.2005 S32: -0.0470 S33: 0.1959 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6IQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009652. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28231 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 66.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.34800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 2.87200 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: MOLREP REMARK 200 STARTING MODEL: 5H3Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH6.5, 18% PEG 8000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.55350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.41900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.41900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.27675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.41900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.41900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 147.83025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.41900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.41900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 49.27675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.41900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.41900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 147.83025 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 98.55350 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: 2770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 B 925 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 GLU A 535 REMARK 465 GLN A 536 REMARK 465 ASP A 537 REMARK 465 ALA A 549 REMARK 465 SER A 550 REMARK 465 GLU A 551 REMARK 465 GLY A 670 REMARK 465 MET A 671 REMARK 465 SER A 672 REMARK 465 ARG A 673 REMARK 465 ASP A 674 REMARK 465 ILE A 675 REMARK 465 TYR A 676 REMARK 465 SER A 677 REMARK 465 VAL A 683 REMARK 465 GLY A 684 REMARK 465 GLY A 685 REMARK 465 ARG A 686 REMARK 465 TYR A 791 REMARK 465 LEU A 792 REMARK 465 ASP A 793 REMARK 465 VAL A 794 REMARK 465 LEU A 795 REMARK 465 GLY A 796 REMARK 465 PRO B 534 REMARK 465 GLU B 535 REMARK 465 GLN B 536 REMARK 465 LYS B 547 REMARK 465 GLU B 548 REMARK 465 ALA B 549 REMARK 465 SER B 550 REMARK 465 GLU B 551 REMARK 465 SER B 552 REMARK 465 ALA B 553 REMARK 465 ARG B 554 REMARK 465 GLN B 555 REMARK 465 MET B 671 REMARK 465 SER B 672 REMARK 465 ARG B 673 REMARK 465 ASP B 674 REMARK 465 ILE B 675 REMARK 465 TYR B 676 REMARK 465 SER B 677 REMARK 465 THR B 678 REMARK 465 ASP B 679 REMARK 465 TYR B 680 REMARK 465 TYR B 681 REMARK 465 ARG B 682 REMARK 465 VAL B 683 REMARK 465 GLY B 684 REMARK 465 GLY B 685 REMARK 465 ARG B 686 REMARK 465 THR B 687 REMARK 465 MET B 688 REMARK 465 PRO B 789 REMARK 465 VAL B 790 REMARK 465 TYR B 791 REMARK 465 LEU B 792 REMARK 465 ASP B 793 REMARK 465 VAL B 794 REMARK 465 LEU B 795 REMARK 465 GLY B 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 GLU A 548 CG CD OE1 OE2 REMARK 470 ARG A 682 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 556 CG OD1 OD2 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 593 OE2 GLU A 615 2.11 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 599 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 599 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 607 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 VAL A 790 CA - C - O ANGL. DEV. = 14.3 DEGREES REMARK 500 MET B 587 CG - SD - CE ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG B 593 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 HIS B 604 N - CA - C ANGL. DEV. = -21.1 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 ARG A 649 -25.89 85.54 REMARK 500 ASP A 668 -70.49 -117.20 REMARK 500 PRO A 789 -177.47 -57.99 REMARK 500 ALA B 545 -159.65 -126.93 REMARK 500 HIS B 604 -160.58 -103.37 REMARK 500 PRO B 606 -80.96 -29.05 REMARK 500 ASP B 607 40.66 -100.23 REMARK 500 ARG B 649 -12.37 82.75 REMARK 500 ASP B 650 45.21 -154.53 REMARK 500 PHE B 669 -62.07 -121.75 REMARK 500 ALA B 787 75.92 40.55 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 ALA B 751 CYS B 752 -147.48 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 954 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 955 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 956 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A 957 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 958 DISTANCE = 6.70 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AQ6 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AQ6 B 801 DBREF 6IQN A 502 796 UNP P04629 NTRK1_HUMAN 502 796 DBREF 6IQN B 502 796 UNP P04629 NTRK1_HUMAN 502 796 SEQADV 6IQN SER A 501 UNP P04629 EXPRESSION TAG SEQADV 6IQN SER B 501 UNP P04629 EXPRESSION TAG SEQRES 1 A 296 SER VAL HIS HIS ILE LYS ARG ARG ASP ILE VAL LEU LYS SEQRES 2 A 296 TRP GLU LEU GLY GLU GLY ALA PHE GLY LYS VAL PHE LEU SEQRES 3 A 296 ALA GLU CYS HIS ASN LEU LEU PRO GLU GLN ASP LYS MET SEQRES 4 A 296 LEU VAL ALA VAL LYS ALA LEU LYS GLU ALA SER GLU SER SEQRES 5 A 296 ALA ARG GLN ASP PHE GLN ARG GLU ALA GLU LEU LEU THR SEQRES 6 A 296 MET LEU GLN HIS GLN HIS ILE VAL ARG PHE PHE GLY VAL SEQRES 7 A 296 CYS THR GLU GLY ARG PRO LEU LEU MET VAL PHE GLU TYR SEQRES 8 A 296 MET ARG HIS GLY ASP LEU ASN ARG PHE LEU ARG SER HIS SEQRES 9 A 296 GLY PRO ASP ALA LYS LEU LEU ALA GLY GLY GLU ASP VAL SEQRES 10 A 296 ALA PRO GLY PRO LEU GLY LEU GLY GLN LEU LEU ALA VAL SEQRES 11 A 296 ALA SER GLN VAL ALA ALA GLY MET VAL TYR LEU ALA GLY SEQRES 12 A 296 LEU HIS PHE VAL HIS ARG ASP LEU ALA THR ARG ASN CYS SEQRES 13 A 296 LEU VAL GLY GLN GLY LEU VAL VAL LYS ILE GLY ASP PHE SEQRES 14 A 296 GLY MET SER ARG ASP ILE TYR SER THR ASP TYR TYR ARG SEQRES 15 A 296 VAL GLY GLY ARG THR MET LEU PRO ILE ARG TRP MET PRO SEQRES 16 A 296 PRO GLU SER ILE LEU TYR ARG LYS PHE THR THR GLU SER SEQRES 17 A 296 ASP VAL TRP SER PHE GLY VAL VAL LEU TRP GLU ILE PHE SEQRES 18 A 296 THR TYR GLY LYS GLN PRO TRP TYR GLN LEU SER ASN THR SEQRES 19 A 296 GLU ALA ILE ASP CYS ILE THR GLN GLY ARG GLU LEU GLU SEQRES 20 A 296 ARG PRO ARG ALA CYS PRO PRO GLU VAL TYR ALA ILE MET SEQRES 21 A 296 ARG GLY CYS TRP GLN ARG GLU PRO GLN GLN ARG HIS SER SEQRES 22 A 296 ILE LYS ASP VAL HIS ALA ARG LEU GLN ALA LEU ALA GLN SEQRES 23 A 296 ALA PRO PRO VAL TYR LEU ASP VAL LEU GLY SEQRES 1 B 296 SER VAL HIS HIS ILE LYS ARG ARG ASP ILE VAL LEU LYS SEQRES 2 B 296 TRP GLU LEU GLY GLU GLY ALA PHE GLY LYS VAL PHE LEU SEQRES 3 B 296 ALA GLU CYS HIS ASN LEU LEU PRO GLU GLN ASP LYS MET SEQRES 4 B 296 LEU VAL ALA VAL LYS ALA LEU LYS GLU ALA SER GLU SER SEQRES 5 B 296 ALA ARG GLN ASP PHE GLN ARG GLU ALA GLU LEU LEU THR SEQRES 6 B 296 MET LEU GLN HIS GLN HIS ILE VAL ARG PHE PHE GLY VAL SEQRES 7 B 296 CYS THR GLU GLY ARG PRO LEU LEU MET VAL PHE GLU TYR SEQRES 8 B 296 MET ARG HIS GLY ASP LEU ASN ARG PHE LEU ARG SER HIS SEQRES 9 B 296 GLY PRO ASP ALA LYS LEU LEU ALA GLY GLY GLU ASP VAL SEQRES 10 B 296 ALA PRO GLY PRO LEU GLY LEU GLY GLN LEU LEU ALA VAL SEQRES 11 B 296 ALA SER GLN VAL ALA ALA GLY MET VAL TYR LEU ALA GLY SEQRES 12 B 296 LEU HIS PHE VAL HIS ARG ASP LEU ALA THR ARG ASN CYS SEQRES 13 B 296 LEU VAL GLY GLN GLY LEU VAL VAL LYS ILE GLY ASP PHE SEQRES 14 B 296 GLY MET SER ARG ASP ILE TYR SER THR ASP TYR TYR ARG SEQRES 15 B 296 VAL GLY GLY ARG THR MET LEU PRO ILE ARG TRP MET PRO SEQRES 16 B 296 PRO GLU SER ILE LEU TYR ARG LYS PHE THR THR GLU SER SEQRES 17 B 296 ASP VAL TRP SER PHE GLY VAL VAL LEU TRP GLU ILE PHE SEQRES 18 B 296 THR TYR GLY LYS GLN PRO TRP TYR GLN LEU SER ASN THR SEQRES 19 B 296 GLU ALA ILE ASP CYS ILE THR GLN GLY ARG GLU LEU GLU SEQRES 20 B 296 ARG PRO ARG ALA CYS PRO PRO GLU VAL TYR ALA ILE MET SEQRES 21 B 296 ARG GLY CYS TRP GLN ARG GLU PRO GLN GLN ARG HIS SER SEQRES 22 B 296 ILE LYS ASP VAL HIS ALA ARG LEU GLN ALA LEU ALA GLN SEQRES 23 B 296 ALA PRO PRO VAL TYR LEU ASP VAL LEU GLY HET AQ6 A 801 39 HET AQ6 B 801 39 HETNAM AQ6 4-[[4-AZANYL-3-(4-CYCLOHEXYLPIPERAZIN-1-YL)-9,10- HETNAM 2 AQ6 BIS(OXIDANYLIDENE)ANTHRACEN-1-YL]AMINO]BENZOIC ACID FORMUL 3 AQ6 2(C31 H32 N4 O4) FORMUL 5 HOH *91(H2 O) HELIX 1 AA1 LYS A 506 ARG A 508 5 3 HELIX 2 AA2 ARG A 554 LEU A 567 1 14 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 PRO A 690 MET A 694 5 5 HELIX 7 AA7 PRO A 695 ARG A 702 1 8 HELIX 8 AA8 THR A 705 THR A 722 1 18 HELIX 9 AA9 SER A 732 GLN A 742 1 11 HELIX 10 AB1 PRO A 753 TRP A 764 1 12 HELIX 11 AB2 GLU A 767 ARG A 771 5 5 HELIX 12 AB3 SER A 773 ALA A 787 1 15 HELIX 13 AB4 PHE B 557 LEU B 567 1 11 HELIX 14 AB5 ASP B 596 HIS B 604 1 9 HELIX 15 AB6 LEU B 622 LEU B 644 1 23 HELIX 16 AB7 ALA B 652 ARG B 654 5 3 HELIX 17 AB8 PRO B 690 MET B 694 5 5 HELIX 18 AB9 PRO B 695 ARG B 702 1 8 HELIX 19 AC1 THR B 705 THR B 722 1 18 HELIX 20 AC2 SER B 732 GLN B 742 1 11 HELIX 21 AC3 PRO B 753 TRP B 764 1 12 HELIX 22 AC4 GLU B 767 ARG B 771 5 5 HELIX 23 AC5 SER B 773 GLN B 786 1 14 SHEET 1 AA1 5 ILE A 510 GLU A 518 0 SHEET 2 AA1 5 LYS A 523 CYS A 529 -1 O VAL A 524 N LEU A 516 SHEET 3 AA1 5 MET A 539 ALA A 545 -1 O ALA A 545 N LYS A 523 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 GLY A 577 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 5 ILE B 510 GLY B 519 0 SHEET 2 AA3 5 GLY B 522 CYS B 529 -1 O VAL B 524 N LEU B 516 SHEET 3 AA3 5 MET B 539 LYS B 544 -1 O MET B 539 N CYS B 529 SHEET 4 AA3 5 LEU B 586 GLU B 590 -1 O PHE B 589 N ALA B 542 SHEET 5 AA3 5 PHE B 575 CYS B 579 -1 N GLY B 577 O VAL B 588 SHEET 1 AA4 2 CYS B 656 GLY B 659 0 SHEET 2 AA4 2 VAL B 663 ILE B 666 -1 O VAL B 663 N GLY B 659 CISPEP 1 ARG A 583 PRO A 584 0 0.45 CISPEP 2 ARG B 583 PRO B 584 0 3.55 SITE 1 AC1 17 GLY A 517 GLU A 518 VAL A 524 ALA A 542 SITE 2 AC1 17 PHE A 589 GLU A 590 TYR A 591 MET A 592 SITE 3 AC1 17 HIS A 594 GLY A 595 ASP A 596 ARG A 599 SITE 4 AC1 17 HOH A 902 LEU B 731 SER B 732 ASN B 733 SITE 5 AC1 17 GLU B 735 SITE 1 AC2 18 LEU A 731 SER A 732 ASN A 733 GLU A 735 SITE 2 AC2 18 GLY B 517 VAL B 524 ALA B 542 PHE B 589 SITE 3 AC2 18 GLU B 590 TYR B 591 MET B 592 ARG B 593 SITE 4 AC2 18 HIS B 594 GLY B 595 ASP B 596 ARG B 599 SITE 5 AC2 18 LEU B 657 HOH B 906 CRYST1 90.838 90.838 197.107 90.00 90.00 90.00 P 41 21 2 16 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 0.011009 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005073 0.00000