PDB Short entry for 3V5Q HEADER TRANSFERASE/TRANSFERASE INHIBITOR 16-DEC-11 3V5Q TITLE DISCOVERY OF A SELECTIVE TRK INHIBITOR WITH EFFICACY IN RODENT CANCER TITLE 2 TUMOR MODELS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NT-3 GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE DOMAIN (UNP RESIDUES 530-818); COMPND 5 SYNONYM: GP145-TRKC, TRK-C, NEUROTROPHIC TYROSINE KINASE RECEPTOR COMPND 6 TYPE 3, TRKC TYROSINE KINASE; COMPND 7 EC: 2.7.10.1; COMPND 8 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: NTRK3, TRKC; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS KINASE DOMAIN, KINASE, PHOSPHORYLATION, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.KREUSCH REVDAT 3 28-FEB-24 3V5Q 1 REMARK SEQADV REVDAT 2 24-JAN-18 3V5Q 1 JRNL REVDAT 1 08-FEB-12 3V5Q 0 JRNL AUTH P.ALBAUGH,Y.FAN,Y.MI,F.SUN,F.ADRIAN,N.LI,Y.JIA,Y.SARKISOVA, JRNL AUTH 2 A.KREUSCH,T.HOOD,M.LU,G.LIU,S.HUANG,Z.LIU,J.LOREN, JRNL AUTH 3 T.TUNTLAND,D.S.KARANEWSKY,H.M.SEIDEL,V.MOLTENI JRNL TITL DISCOVERY OF GNF-5837, A SELECTIVE TRK INHIBITOR WITH JRNL TITL 2 EFFICACY IN RODENT CANCER TUMOR MODELS. JRNL REF ACS MED CHEM LETT V. 3 140 2012 JRNL REFN ISSN 1948-5875 JRNL PMID 24900443 JRNL DOI 10.1021/ML200261D REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 3 NUMBER OF REFLECTIONS : 36886 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1865 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.9521 - 5.1699 0.87 2753 138 0.2250 0.2611 REMARK 3 2 5.1699 - 4.1047 0.90 2795 162 0.1706 0.2085 REMARK 3 3 4.1047 - 3.5862 0.89 2869 132 0.1791 0.2337 REMARK 3 4 3.5862 - 3.2585 0.90 2826 134 0.1895 0.2213 REMARK 3 5 3.2585 - 3.0250 0.90 2865 155 0.1996 0.2723 REMARK 3 6 3.0250 - 2.8467 0.86 2667 141 0.2317 0.3289 REMARK 3 7 2.8467 - 2.7041 0.87 2763 142 0.2400 0.3190 REMARK 3 8 2.7041 - 2.5865 0.89 2844 169 0.2392 0.2690 REMARK 3 9 2.5865 - 2.4869 0.84 2647 135 0.2613 0.3553 REMARK 3 10 2.4869 - 2.4011 0.88 2794 146 0.2791 0.3493 REMARK 3 11 2.4011 - 2.3260 0.84 2669 131 0.2792 0.3368 REMARK 3 12 2.3260 - 2.2595 0.74 2333 149 0.2989 0.3486 REMARK 3 13 2.2595 - 2.2001 0.70 2196 131 0.3106 0.3687 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 67.80 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.850 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.83370 REMARK 3 B22 (A**2) : 1.83370 REMARK 3 B33 (A**2) : -3.66740 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 4406 REMARK 3 ANGLE : 1.368 5960 REMARK 3 CHIRALITY : 0.077 652 REMARK 3 PLANARITY : 0.005 737 REMARK 3 DIHEDRAL : 19.545 1594 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3V5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37248 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000 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) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.43600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M NACL, 0.1 M NA/K PHOSPHATE, PH REMARK 280 6.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 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 118.16800 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 59.08400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 -8 REMARK 465 ALA A -7 REMARK 465 MET A -6 REMARK 465 HIS A -5 REMARK 465 SER A -4 REMARK 465 GLY A 545 REMARK 465 GLU A 546 REMARK 465 GLY A 547 REMARK 465 ALA A 548 REMARK 465 PHE A 549 REMARK 465 GLY A 550 REMARK 465 LYS A 575 REMARK 465 ASP A 576 REMARK 465 ASP A 635 REMARK 465 ALA A 636 REMARK 465 MET A 637 REMARK 465 ILE A 638 REMARK 465 LEU A 639 REMARK 465 VAL A 640 REMARK 465 ASP A 641 REMARK 465 GLY A 642 REMARK 465 GLN A 643 REMARK 465 PRO A 644 REMARK 465 ARG A 645 REMARK 465 GLN A 646 REMARK 465 ALA A 647 REMARK 465 LYS A 648 REMARK 465 GLY A 649 REMARK 465 SER A 701 REMARK 465 ARG A 702 REMARK 465 VAL A 726 REMARK 465 GLY A 727 REMARK 465 GLY A 728 REMARK 465 HIS A 729 REMARK 465 GLY B -8 REMARK 465 ALA B -7 REMARK 465 MET B -6 REMARK 465 HIS B -5 REMARK 465 SER B -4 REMARK 465 GLU B 547 REMARK 465 GLY B 548 REMARK 465 ALA B 549 REMARK 465 GLY B 550A REMARK 465 GLY B 607A REMARK 465 ASP B 607B REMARK 465 ASP B 635 REMARK 465 ALA B 636 REMARK 465 MET B 637 REMARK 465 ILE B 638 REMARK 465 LEU B 639 REMARK 465 VAL B 640 REMARK 465 ASP B 641 REMARK 465 GLY B 642 REMARK 465 GLN B 643 REMARK 465 PRO B 644 REMARK 465 ARG B 645 REMARK 465 GLN B 646 REMARK 465 ALA B 647 REMARK 465 LYS B 648 REMARK 465 GLY B 649 REMARK 465 SER B 701 REMARK 465 ARG B 702 REMARK 465 VAL B 726 REMARK 465 GLY B 727 REMARK 465 GLY B 728 REMARK 465 HIS B 729 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 551 CG CD CE NZ REMARK 470 LYS A 564 CG CD CE NZ REMARK 470 ASP A 565 CG OD1 OD2 REMARK 470 LEU A 579 CG CD1 CD2 REMARK 470 ARG A 582 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 583 CG CD CE NZ REMARK 470 ASP A 609 CG OD1 OD2 REMARK 470 ASP A 611 CG OD1 OD2 REMARK 470 ASP A 703 CG OD1 OD2 REMARK 470 ARG A 793 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 813 CG CD OE1 NE2 REMARK 470 PHE B 550 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 551 CG CD CE NZ REMARK 470 ASP B 565 CG OD1 OD2 REMARK 470 LEU B 574 CG CD1 CD2 REMARK 470 LYS B 575 CG CD CE NZ REMARK 470 ARG B 587 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 609 CG OD1 OD2 REMARK 470 ASP B 703 CG OD1 OD2 REMARK 470 ARG B 793 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 812 CG CD OE1 NE2 REMARK 470 GLN B 813 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 1015 O HOH B 1033 2.03 REMARK 500 O HOH B 1021 O HOH B 1086 2.11 REMARK 500 O PRO B 577 NH1 ARG B 582 2.17 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 O HOH A 1051 O HOH B 1006 2544 2.17 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 PRO A 634 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 ASP B 576 N - CA - C ANGL. DEV. = -20.2 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 542 137.68 -176.82 REMARK 500 LEU A 560 -66.10 -137.86 REMARK 500 THR A 563 -97.18 -75.88 REMARK 500 ARG A 678 -19.30 82.08 REMARK 500 LYS B 541 -55.04 -120.13 REMARK 500 LEU B 560 -58.60 -129.95 REMARK 500 PRO B 577 -156.89 -82.94 REMARK 500 ARG B 678 -15.71 75.36 REMARK 500 VAL B 704 -25.95 65.61 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 ASP B 576 PRO B 577 -123.23 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 CL A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0F4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0F4 B 901 DBREF 3V5Q A 530 832 UNP Q16288 NTRK3_HUMAN 530 818 DBREF 3V5Q B 530 832 UNP Q16288 NTRK3_HUMAN 530 818 SEQADV 3V5Q GLY A -8 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q ALA A -7 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q MET A -6 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q HIS A -5 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q SER A -4 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q GLY A -3 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q ILE A -2 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q HIS A -1 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q GLY B -8 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q ALA B -7 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q MET B -6 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q HIS B -5 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q SER B -4 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q GLY B -3 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q ILE B -2 UNP Q16288 CLONING ARTIFACT SEQADV 3V5Q HIS B -1 UNP Q16288 CLONING ARTIFACT SEQRES 1 A 297 GLY ALA MET HIS SER GLY ILE HIS VAL GLN HIS ILE LYS SEQRES 2 A 297 ARG ARG ASP ILE VAL LEU LYS ARG GLU LEU GLY GLU GLY SEQRES 3 A 297 ALA PHE GLY LYS VAL PHE LEU ALA GLU CYS TYR ASN LEU SEQRES 4 A 297 SER PRO THR LYS ASP LYS MET LEU VAL ALA VAL LYS ALA SEQRES 5 A 297 LEU LYS ASP PRO THR LEU ALA ALA ARG LYS ASP PHE GLN SEQRES 6 A 297 ARG GLU ALA GLU LEU LEU THR ASN LEU GLN HIS GLU HIS SEQRES 7 A 297 ILE VAL LYS PHE TYR GLY VAL CYS GLY ASP GLY ASP PRO SEQRES 8 A 297 LEU ILE MET VAL PHE GLU TYR MET LYS HIS GLY ASP LEU SEQRES 9 A 297 ASN LYS PHE LEU ARG ALA HIS GLY PRO ASP ALA MET ILE SEQRES 10 A 297 LEU VAL ASP GLY GLN PRO ARG GLN ALA LYS GLY GLU LEU SEQRES 11 A 297 GLY LEU SER GLN MET LEU HIS ILE ALA SER GLN ILE ALA SEQRES 12 A 297 SER GLY MET VAL TYR LEU ALA SER GLN HIS PHE VAL HIS SEQRES 13 A 297 ARG ASP LEU ALA THR ARG ASN CYS LEU VAL GLY ALA ASN SEQRES 14 A 297 LEU LEU VAL LYS ILE GLY ASP PHE GLY MET SER ARG ASP SEQRES 15 A 297 VAL TYR SER THR ASP TYR TYR ARG VAL GLY GLY HIS THR SEQRES 16 A 297 MET LEU PRO ILE ARG TRP MET PRO PRO GLU SER ILE MET SEQRES 17 A 297 TYR ARG LYS PHE THR THR GLU SER ASP VAL TRP SER PHE SEQRES 18 A 297 GLY VAL ILE LEU TRP GLU ILE PHE THR TYR GLY LYS GLN SEQRES 19 A 297 PRO TRP PHE GLN LEU SER ASN THR GLU VAL ILE GLU CYS SEQRES 20 A 297 ILE THR GLN GLY ARG VAL LEU GLU ARG PRO ARG VAL CYS SEQRES 21 A 297 PRO LYS GLU VAL TYR ASP VAL MET LEU GLY CYS TRP GLN SEQRES 22 A 297 ARG GLU PRO GLN GLN ARG LEU ASN ILE LYS GLU ILE TYR SEQRES 23 A 297 LYS ILE LEU HIS ALA LEU GLY LYS ALA THR PRO SEQRES 1 B 297 GLY ALA MET HIS SER GLY ILE HIS VAL GLN HIS ILE LYS SEQRES 2 B 297 ARG ARG ASP ILE VAL LEU LYS ARG GLU LEU GLY GLU GLY SEQRES 3 B 297 ALA PHE GLY LYS VAL PHE LEU ALA GLU CYS TYR ASN LEU SEQRES 4 B 297 SER PRO THR LYS ASP LYS MET LEU VAL ALA VAL LYS ALA SEQRES 5 B 297 LEU LYS ASP PRO THR LEU ALA ALA ARG LYS ASP PHE GLN SEQRES 6 B 297 ARG GLU ALA GLU LEU LEU THR ASN LEU GLN HIS GLU HIS SEQRES 7 B 297 ILE VAL LYS PHE TYR GLY VAL CYS GLY ASP GLY ASP PRO SEQRES 8 B 297 LEU ILE MET VAL PHE GLU TYR MET LYS HIS GLY ASP LEU SEQRES 9 B 297 ASN LYS PHE LEU ARG ALA HIS GLY PRO ASP ALA MET ILE SEQRES 10 B 297 LEU VAL ASP GLY GLN PRO ARG GLN ALA LYS GLY GLU LEU SEQRES 11 B 297 GLY LEU SER GLN MET LEU HIS ILE ALA SER GLN ILE ALA SEQRES 12 B 297 SER GLY MET VAL TYR LEU ALA SER GLN HIS PHE VAL HIS SEQRES 13 B 297 ARG ASP LEU ALA THR ARG ASN CYS LEU VAL GLY ALA ASN SEQRES 14 B 297 LEU LEU VAL LYS ILE GLY ASP PHE GLY MET SER ARG ASP SEQRES 15 B 297 VAL TYR SER THR ASP TYR TYR ARG VAL GLY GLY HIS THR SEQRES 16 B 297 MET LEU PRO ILE ARG TRP MET PRO PRO GLU SER ILE MET SEQRES 17 B 297 TYR ARG LYS PHE THR THR GLU SER ASP VAL TRP SER PHE SEQRES 18 B 297 GLY VAL ILE LEU TRP GLU ILE PHE THR TYR GLY LYS GLN SEQRES 19 B 297 PRO TRP PHE GLN LEU SER ASN THR GLU VAL ILE GLU CYS SEQRES 20 B 297 ILE THR GLN GLY ARG VAL LEU GLU ARG PRO ARG VAL CYS SEQRES 21 B 297 PRO LYS GLU VAL TYR ASP VAL MET LEU GLY CYS TRP GLN SEQRES 22 B 297 ARG GLU PRO GLN GLN ARG LEU ASN ILE LYS GLU ILE TYR SEQRES 23 B 297 LYS ILE LEU HIS ALA LEU GLY LYS ALA THR PRO HET CL A 901 1 HET 0F4 A 902 37 HET 0F4 B 901 37 HETNAM CL CHLORIDE ION HETNAM 0F4 1-(3-{[(3Z)-2-OXO-3-(1H-PYRROL-2-YLMETHYLIDENE)-2,3- HETNAM 2 0F4 DIHYDRO-1H-INDOL-6-YL]AMINO}PHENYL)-3-[3- HETNAM 3 0F4 (TRIFLUOROMETHYL)PHENYL]UREA FORMUL 3 CL CL 1- FORMUL 4 0F4 2(C27 H20 F3 N5 O2) FORMUL 6 HOH *189(H2 O) HELIX 1 1 LYS A 534 ARG A 536 5 3 HELIX 2 2 THR A 578 LEU A 595 1 18 HELIX 3 3 ASP A 624 HIS A 632 1 9 HELIX 4 4 GLY A 652 GLN A 673 1 22 HELIX 5 5 ALA A 681 ARG A 683 5 3 HELIX 6 6 ALA A 689 LEU A 691 5 3 HELIX 7 7 TYR A 705 TYR A 709 5 5 HELIX 8 8 PRO A 733 MET A 737 5 5 HELIX 9 9 PRO A 738 ARG A 745 1 8 HELIX 10 10 THR A 748 PHE A 764 1 17 HELIX 11 11 SER A 775 GLY A 786 1 12 HELIX 12 12 PRO A 796 TRP A 807 1 12 HELIX 13 13 GLU A 810 ARG A 814 5 5 HELIX 14 14 ASN A 816 ALA A 830 1 15 HELIX 15 15 LYS B 534 ARG B 536 5 3 HELIX 16 16 THR B 578 LEU B 595 1 18 HELIX 17 17 LEU B 625 ALA B 631 1 7 HELIX 18 18 GLY B 652 GLN B 673 1 22 HELIX 19 19 ALA B 681 ARG B 683 5 3 HELIX 20 20 ALA B 689 LEU B 691 5 3 HELIX 21 21 TYR B 705 TYR B 709 5 5 HELIX 22 22 PRO B 733 MET B 737 5 5 HELIX 23 23 PRO B 738 ARG B 745 1 8 HELIX 24 24 THR B 748 PHE B 764 1 17 HELIX 25 25 SER B 775 GLY B 786 1 12 HELIX 26 26 PRO B 796 TRP B 807 1 12 HELIX 27 27 GLU B 810 ARG B 814 5 5 HELIX 28 28 ASN B 816 ALA B 830 1 15 SHEET 1 A 6 HIS A 532 ILE A 533 0 SHEET 2 A 6 PHE A 603 CYS A 607 1 O VAL A 606 N ILE A 533 SHEET 3 A 6 ILE A 614 GLU A 618 -1 O VAL A 616 N TYR A 604 SHEET 4 A 6 LYS A 566 ALA A 573 -1 N ALA A 570 O PHE A 617 SHEET 5 A 6 VAL A 552 TYR A 558 -1 N PHE A 553 O VAL A 571 SHEET 6 A 6 ILE A 538 GLU A 543 -1 N ARG A 542 O LEU A 554 SHEET 1 B 2 CYS A 685 VAL A 687 0 SHEET 2 B 2 VAL A 693 ILE A 695 -1 O LYS A 694 N LEU A 686 SHEET 1 C 6 HIS B 532 ILE B 533 0 SHEET 2 C 6 PHE B 603 CYS B 607 1 O VAL B 606 N ILE B 533 SHEET 3 C 6 ILE B 614 GLU B 618 -1 O VAL B 616 N GLY B 605 SHEET 4 C 6 LYS B 566 ALA B 573 -1 N ALA B 570 O PHE B 617 SHEET 5 C 6 LYS B 551 TYR B 558 -1 N PHE B 553 O VAL B 571 SHEET 6 C 6 ILE B 538 GLU B 543 -1 N VAL B 539 O GLU B 556 SHEET 1 D 3 GLY B 623 ASP B 624 0 SHEET 2 D 3 CYS B 685 VAL B 687 -1 O VAL B 687 N GLY B 623 SHEET 3 D 3 VAL B 693 ILE B 695 -1 O LYS B 694 N LEU B 686 CISPEP 1 ASP A 611 PRO A 612 0 2.60 CISPEP 2 LYS B 575 ASP B 576 0 -18.57 SITE 1 AC1 6 ARG A 535 ILE A 538 LEU A 540 ARG B 535 SITE 2 AC1 6 ILE B 538 LEU B 540 SITE 1 AC2 19 ALA A 570 LYS A 572 GLU A 588 LEU A 591 SITE 2 AC2 19 LEU A 592 ILE A 600 PHE A 617 GLU A 618 SITE 3 AC2 19 TYR A 619 MET A 620 GLY A 623 LEU A 670 SITE 4 AC2 19 PHE A 675 HIS A 677 LEU A 686 ILE A 695 SITE 5 AC2 19 GLY A 696 ASP A 697 PHE A 698 SITE 1 AC3 20 LEU B 544 ALA B 570 LYS B 572 GLU B 588 SITE 2 AC3 20 LEU B 592 LEU B 595 ILE B 600 PHE B 617 SITE 3 AC3 20 GLU B 618 TYR B 619 MET B 620 GLY B 623 SITE 4 AC3 20 LEU B 670 PHE B 675 HIS B 677 LEU B 686 SITE 5 AC3 20 ILE B 695 GLY B 696 ASP B 697 PHE B 698 CRYST1 65.580 65.580 177.252 90.00 90.00 120.00 P 32 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 0.015249 0.008804 0.000000 0.00000 SCALE2 0.000000 0.017608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005642 0.00000