HEADER TRANSFERASE 01-JUL-19 6PMC TITLE TRK-A IN COMPLEX WITH LIGAND 1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A; 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRK-A KINASE DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.SUBRAMANIAN,D.G.BROWN REVDAT 2 03-FEB-21 6PMC 1 JRNL REVDAT 1 26-FEB-20 6PMC 0 JRNL AUTH G.SUBRAMANIAN,R.VAIRAGOUNDAR,S.J.BOWEN,N.ROUSH,T.ZACHARY, JRNL AUTH 2 C.JAVENS,T.WILLIAMS,A.JANSSEN,A.GONZALES JRNL TITL SYNTHETIC INHIBITOR LEADS OF HUMAN TROPOMYOSIN RECEPTOR JRNL TITL 2 KINASE A ( H TRKA). JRNL REF RSC MED CHEM V. 11 370 2020 JRNL REFN ESSN 2632-8682 JRNL PMID 33479642 JRNL DOI 10.1039/C9MD00554D REMARK 2 REMARK 2 RESOLUTION. 2.19 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 17176 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) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1467 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1228 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.3970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2318 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.78000 REMARK 3 B22 (A**2) : 0.78000 REMARK 3 B33 (A**2) : -2.55000 REMARK 3 B12 (A**2) : 0.39000 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): 0.304 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.251 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2338 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2133 ; 0.035 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3177 ; 1.901 ; 1.638 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4906 ; 2.427 ; 1.569 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 287 ; 7.296 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;33.217 ;21.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 355 ;17.380 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.744 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 287 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2644 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 520 ; 0.013 ; 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): 1154 ; 2.923 ; 3.842 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1153 ; 2.922 ; 3.840 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1439 ; 4.609 ; 5.745 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6PMC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-16 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 : 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) : 0.9282 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18645 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 77.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.10M KH2PO4/ 0.10M NAH2PO4/ 0.1M REMARK 280 MES/NAOH PH = 6.00 AND 1.9M NACL (CRYO: 25% GLYCEROL IN REMARK 280 RESERVOIR), OR 18% (W/V) PEG 3350, 0.2M CACL2, 0.10M, MES PH = REMARK 280 6.50 (CRYO: DIRECT), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 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 77.84800 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 155.69600 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 155.69600 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 77.84800 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 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 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 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 485 REMARK 465 LEU A 486 REMARK 465 GLN A 487 REMARK 465 GLY A 488 REMARK 465 HIS A 489 REMARK 465 ILE A 490 REMARK 465 ILE A 491 REMARK 465 GLU A 492 REMARK 465 ASN A 493 REMARK 465 PRO A 494 REMARK 465 GLN A 495 REMARK 465 TYR A 496 REMARK 465 PHE A 497 REMARK 465 SER A 498 REMARK 465 ASP A 499 REMARK 465 PRO A 606 REMARK 465 ASP A 607 REMARK 465 ALA A 608 REMARK 465 LYS A 609 REMARK 465 LEU A 610 REMARK 465 LEU A 611 REMARK 465 ALA A 612 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 CYS A 501 SG REMARK 480 ARG A 508 CZ NH1 NH2 REMARK 480 ILE A 510 CD1 REMARK 480 PHE A 521 CG CD1 CD2 CE1 CE2 CZ REMARK 480 LYS A 538 CE NZ REMARK 480 LEU A 546 CD1 CD2 REMARK 480 LYS A 547 CD CE NZ REMARK 480 GLU A 551 CG CD OE1 OE2 REMARK 480 SER A 552 OG REMARK 480 ARG A 554 CD NE CZ NH1 NH2 REMARK 480 GLN A 555 CG CD OE1 NE2 REMARK 480 GLN A 558 CD OE1 NE2 REMARK 480 ARG A 559 CG CD NE CZ NH1 NH2 REMARK 480 MET A 566 CG SD CE REMARK 480 ARG A 599 CD NE CZ NH1 NH2 REMARK 480 MET A 638 CE REMARK 480 LEU A 644 CD1 CD2 REMARK 480 MET A 671 CE REMARK 480 ARG A 686 CG CD NE CZ NH1 NH2 REMARK 480 MET A 688 CE REMARK 480 LYS A 725 CD CE NZ REMARK 480 ARG A 750 NE CZ NH1 NH2 REMARK 480 ARG A 761 CZ NH1 NH2 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 CYS A 501 CB CYS A 501 SG -0.160 REMARK 500 ARG A 508 NE ARG A 508 CZ -0.406 REMARK 500 PHE A 521 CB PHE A 521 CG -0.206 REMARK 500 GLU A 551 CB GLU A 551 CG -0.532 REMARK 500 SER A 552 CB SER A 552 OG -0.268 REMARK 500 GLN A 555 CB GLN A 555 CG -0.309 REMARK 500 GLN A 558 CG GLN A 558 CD -0.146 REMARK 500 MET A 566 CB MET A 566 CG -0.296 REMARK 500 LEU A 644 CG LEU A 644 CD2 -0.234 REMARK 500 ARG A 686 CB ARG A 686 CG -0.357 REMARK 500 ARG A 750 CD ARG A 750 NE -0.327 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 508 CD - NE - CZ ANGL. DEV. = 40.6 DEGREES REMARK 500 ARG A 508 NE - CZ - NH1 ANGL. DEV. = -26.3 DEGREES REMARK 500 ARG A 508 NE - CZ - NH2 ANGL. DEV. = 24.1 DEGREES REMARK 500 GLU A 551 CA - CB - CG ANGL. DEV. = 16.2 DEGREES REMARK 500 GLU A 551 CB - CG - CD ANGL. DEV. = -25.3 DEGREES REMARK 500 ARG A 559 CA - CB - CG ANGL. DEV. = 28.6 DEGREES REMARK 500 ARG A 559 CB - CG - CD ANGL. DEV. = 15.6 DEGREES REMARK 500 MET A 566 CA - CB - CG ANGL. DEV. = 27.7 DEGREES REMARK 500 LEU A 644 CB - CG - CD2 ANGL. DEV. = 16.4 DEGREES REMARK 500 ARG A 686 CA - CB - CG ANGL. DEV. = 25.0 DEGREES REMARK 500 MET A 688 CG - SD - CE ANGL. DEV. = 25.7 DEGREES REMARK 500 LYS A 725 CB - CG - CD ANGL. DEV. = 16.6 DEGREES REMARK 500 ARG A 750 CG - CD - NE ANGL. DEV. = -19.4 DEGREES REMARK 500 ARG A 750 CD - NE - CZ ANGL. DEV. = -15.6 DEGREES REMARK 500 ARG A 761 CD - NE - CZ ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG A 761 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 761 NE - CZ - NH2 ANGL. DEV. = -7.7 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 LYS A 547 -76.15 -55.65 REMARK 500 SER A 550 -144.90 -84.80 REMARK 500 ARG A 649 -24.57 89.25 REMARK 500 ALA A 751 1.14 -64.93 REMARK 500 VAL A 790 -32.70 -39.71 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 750 0.20 SIDE CHAIN REMARK 500 ARG A 761 0.18 SIDE CHAIN 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 OQJ A 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6PMA RELATED DB: PDB REMARK 900 RELATED ID: 6PMB RELATED DB: PDB DBREF 6PMC A 485 795 UNP P04629 NTRK1_HUMAN 387 697 SEQRES 1 A 311 GLY LEU GLN GLY HIS ILE ILE GLU ASN PRO GLN TYR PHE SEQRES 2 A 311 SER ASP ALA CYS VAL HIS HIS ILE LYS ARG ARG ASP ILE SEQRES 3 A 311 VAL LEU LYS TRP GLU LEU GLY GLU GLY ALA PHE GLY LYS SEQRES 4 A 311 VAL PHE LEU ALA GLU CYS HIS ASN LEU LEU PRO GLU GLN SEQRES 5 A 311 ASP LYS MET LEU VAL ALA VAL LYS ALA LEU LYS GLU ALA SEQRES 6 A 311 SER GLU SER ALA ARG GLN ASP PHE GLN ARG GLU ALA GLU SEQRES 7 A 311 LEU LEU THR MET LEU GLN HIS GLN HIS ILE VAL ARG PHE SEQRES 8 A 311 PHE GLY VAL CYS THR GLU GLY ARG PRO LEU LEU MET VAL SEQRES 9 A 311 PHE GLU TYR MET ARG HIS GLY ASP LEU ASN ARG PHE LEU SEQRES 10 A 311 ARG SER HIS GLY PRO ASP ALA LYS LEU LEU ALA GLY GLY SEQRES 11 A 311 GLU ASP VAL ALA PRO GLY PRO LEU GLY LEU GLY GLN LEU SEQRES 12 A 311 LEU ALA VAL ALA SER GLN VAL ALA ALA GLY MET VAL TYR SEQRES 13 A 311 LEU ALA GLY LEU HIS PHE VAL HIS ARG ASP LEU ALA THR SEQRES 14 A 311 ARG ASN CYS LEU VAL GLY GLN GLY LEU VAL VAL LYS ILE SEQRES 15 A 311 GLY ASP PHE GLY MET SER ARG ASP ILE TYR SEP THR ASP SEQRES 16 A 311 TYR TYR ARG VAL GLY GLY ARG THR MET LEU PRO ILE ARG SEQRES 17 A 311 TRP MET PRO PRO GLU SER ILE LEU TYR ARG LYS PHE THR SEQRES 18 A 311 THR GLU SER ASP VAL TRP SER PHE GLY VAL VAL LEU TRP SEQRES 19 A 311 GLU ILE PHE THR TYR GLY LYS GLN PRO TRP TYR GLN LEU SEQRES 20 A 311 SER ASN THR GLU ALA ILE ASP CYS ILE THR GLN GLY ARG SEQRES 21 A 311 GLU LEU GLU ARG PRO ARG ALA CYS PRO PRO GLU VAL TYR SEQRES 22 A 311 ALA ILE MET ARG GLY CYS TRP GLN ARG GLU PRO GLN GLN SEQRES 23 A 311 ARG HIS SER ILE LYS ASP VAL HIS ALA ARG LEU GLN ALA SEQRES 24 A 311 LEU ALA GLN ALA PRO PRO VAL TYR LEU ASP VAL LEU MODRES 6PMC SEP A 677 SER MODIFIED RESIDUE HET SEP A 677 10 HET OQJ A 801 31 HETNAM SEP PHOSPHOSERINE HETNAM OQJ N-(6-{[(5-CHLORO-2-METHOXYPHENYL)CARBAMOYL]AMINO}-1,3- HETNAM 2 OQJ BENZOTHIAZOL-2-YL)BENZAMIDE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 OQJ C22 H17 CL N4 O3 S FORMUL 3 HOH *35(H2 O) HELIX 1 AA1 LYS A 506 ARG A 508 5 3 HELIX 2 AA2 GLU A 551 LEU A 567 1 17 HELIX 3 AA3 ASP A 596 SER A 603 1 8 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 MET A 671 TYR A 676 1 6 HELIX 8 AA8 SEP A 677 TYR A 680 5 4 HELIX 9 AA9 PRO A 690 MET A 694 5 5 HELIX 10 AB1 PRO A 695 ARG A 702 1 8 HELIX 11 AB2 THR A 705 THR A 722 1 18 HELIX 12 AB3 SER A 732 GLY A 743 1 12 HELIX 13 AB4 PRO A 753 TRP A 764 1 12 HELIX 14 AB5 GLU A 767 ARG A 771 5 5 HELIX 15 AB6 SER A 773 GLN A 786 1 14 HELIX 16 AB7 PRO A 788 ASP A 793 1 6 SHEET 1 AA1 5 ILE A 510 GLU A 518 0 SHEET 2 AA1 5 GLY A 522 LEU A 533 -1 O LEU A 526 N LYS A 513 SHEET 3 AA1 5 GLN A 536 LEU A 546 -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 VAL A 658 0 SHEET 2 AA2 2 VAL A 664 ILE A 666 -1 O LYS A 665 N LEU A 657 SHEET 1 AA3 2 TYR A 681 VAL A 683 0 SHEET 2 AA3 2 THR A 687 LEU A 689 -1 O LEU A 689 N TYR A 681 LINK C TYR A 676 N SEP A 677 1555 1555 1.33 LINK C SEP A 677 N THR A 678 1555 1555 1.33 CISPEP 1 ARG A 583 PRO A 584 0 5.62 SITE 1 AC1 7 ALA A 542 GLU A 560 MET A 592 PHE A 646 SITE 2 AC1 7 GLY A 667 ASP A 668 PHE A 669 CRYST1 52.657 52.657 233.544 90.00 90.00 120.00 P 31 1 2 6 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 0.018991 0.010964 0.000000 0.00000 SCALE2 0.000000 0.021929 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004282 0.00000