HEADER TRANSFERASE 13-JAN-10 2X2M TITLE CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN WITH TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: TYROSINE KINASE DOMAIN, RESIDUES 705-1013; COMPND 5 SYNONYM: RET TYROSINE KINASE RECEPTOR, C-RET; COMPND 6 EC: 2.7.10.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBACPAK-HIS3 (CLONTECH) MODIFIED KEYWDS HIRSCHSPRUNG DISEASE, GDNF RECEPTOR, TRANSMEMBRANE, PROTO-ONCOGENE, KEYWDS 2 PHOSPHOPROTEIN, DISEASE MUTATION, PHOSPHOTRANSFERASE, RET, KINASE, KEYWDS 3 MEMBRANE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.P.KNOWLES,J.MURRAY-RUST,S.KJAER,N.Q.MCDONALD REVDAT 8 20-DEC-23 2X2M 1 REMARK REVDAT 7 08-MAY-19 2X2M 1 REMARK LINK REVDAT 6 30-JAN-19 2X2M 1 REMARK REVDAT 5 28-FEB-18 2X2M 1 JRNL REVDAT 4 28-JUN-17 2X2M 1 REMARK REVDAT 3 29-MAR-17 2X2M 1 REMARK REVDAT 2 02-MAR-10 2X2M 1 JRNL REMARK REVDAT 1 09-FEB-10 2X2M 0 JRNL AUTH L.MOLOGNI,R.ROSTAGNO,S.BRUSSOLO,P.P.KNOWLES,S.KJAER, JRNL AUTH 2 J.MURRAY-RUST,E.ROSSO,A.ZAMBON,L.SCAPOZZA,N.Q.MCDONALD, JRNL AUTH 3 V.LUCCHINI,C.GAMBACORTI-PASSERINI JRNL TITL SYNTHESIS, STRUCTURE-ACTIVITY RELATIONSHIP AND JRNL TITL 2 CRYSTALLOGRAPHIC STUDIES OF 3-SUBSTITUTED INDOLIN-2-ONE RET JRNL TITL 3 INHIBITORS. JRNL REF BIOORG. MED. CHEM. V. 18 1482 2010 JRNL REFN ESSN 1464-3391 JRNL PMID 20117004 JRNL DOI 10.1016/J.BMC.2010.01.011 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 22326 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1197 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1626 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4327 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.43000 REMARK 3 B13 (A**2) : 0.63000 REMARK 3 B23 (A**2) : 1.02000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.508 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.278 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.194 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.581 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4471 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6049 ; 1.562 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 559 ; 5.533 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;37.612 ;22.911 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 742 ;16.289 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.952 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 679 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3264 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1951 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3042 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 169 ; 0.244 ; 0.200 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): 32 ; 0.308 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.201 ; 0.200 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): 2897 ; 0.790 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4490 ; 1.365 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1844 ; 1.856 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1559 ; 2.928 ; 4.500 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 : 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 2X2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1290036341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23524 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 18.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.21 REMARK 200 R MERGE FOR SHELL (I) : 0.11000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.600 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: PDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN 4.5 MG/ML IN 20 MM TRIS-HCL PH REMARK 280 8, 100MM NACL, 1MM DTT, 1MM EDTA RESERVOIR 1.75 M SODIUM FORMATE, REMARK 280 0.1 SODIUM CITRATE PH 5.5, 0.15 M POTASSIUM THIOCYANATE VAPOUR REMARK 280 DIFFUSION, SITTING DROP, 289 K, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 713 REMARK 465 GLY A 733 REMARK 465 GLU A 734 REMARK 465 LYS A 821 REMARK 465 VAL A 822 REMARK 465 GLY A 823 REMARK 465 PRO A 824 REMARK 465 GLY A 825 REMARK 465 TYR A 826 REMARK 465 LEU A 827 REMARK 465 GLY A 828 REMARK 465 SER A 829 REMARK 465 GLY A 830 REMARK 465 GLY A 831 REMARK 465 SER A 832 REMARK 465 ARG A 833 REMARK 465 ASN A 834 REMARK 465 SER A 835 REMARK 465 SER A 836 REMARK 465 SER A 837 REMARK 465 LEU A 838 REMARK 465 ASP A 839 REMARK 465 HIS A 840 REMARK 465 PRO A 841 REMARK 465 ASP A 842 REMARK 465 GLU A 843 REMARK 465 ARG A 844 REMARK 465 LEU B 712 REMARK 465 GLU B 713 REMARK 465 ASP B 714 REMARK 465 GLY B 733 REMARK 465 GLU B 734 REMARK 465 PHE B 735 REMARK 465 GLY B 736 REMARK 465 ARG B 820 REMARK 465 LYS B 821 REMARK 465 VAL B 822 REMARK 465 GLY B 823 REMARK 465 PRO B 824 REMARK 465 GLY B 825 REMARK 465 TYR B 826 REMARK 465 LEU B 827 REMARK 465 GLY B 828 REMARK 465 SER B 829 REMARK 465 GLY B 830 REMARK 465 GLY B 831 REMARK 465 SER B 832 REMARK 465 ARG B 833 REMARK 465 ASN B 834 REMARK 465 SER B 835 REMARK 465 SER B 836 REMARK 465 SER B 837 REMARK 465 LEU B 838 REMARK 465 ASP B 839 REMARK 465 HIS B 840 REMARK 465 PRO B 841 REMARK 465 ASP B 842 REMARK 465 GLU B 843 REMARK 465 ARG B 844 REMARK 465 ARG B 1012 REMARK 465 ARG B 1013 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 ALA A 708 O REMARK 470 LYS A 710 CG CD CE NZ REMARK 470 ILE A 711 CG1 CG2 CD1 REMARK 470 ASP A 714 CG OD1 OD2 REMARK 470 ARG A 721 CD NE CZ NH1 NH2 REMARK 470 LYS A 722 CD CE NZ REMARK 470 GLU A 732 CD OE1 OE2 REMARK 470 PHE A 735 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 762 CD OE1 OE2 REMARK 470 GLN A 796 CG CD OE1 NE2 REMARK 470 ASP A 797 CG OD1 OD2 REMARK 470 ARG A 820 CG CD NE CZ NH1 NH2 REMARK 470 MET A 848 CG SD CE REMARK 470 GLU A 867 CD OE1 OE2 REMARK 470 GLU A 884 CG CD OE1 OE2 REMARK 470 ASP A 892 OD1 OD2 REMARK 470 TYR A 900 CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 901 CG CD OE2 REMARK 470 ARG A 908 NE CZ NH1 NH2 REMARK 470 ARG A 959 CD NE CZ NH1 NH2 REMARK 470 LYS A 965 CE NZ REMARK 470 GLU A 971 CG CD OE1 OE2 REMARK 470 GLU A 978 CG CD OE1 OE2 REMARK 470 GLU A 979 CG CD OE1 OE2 REMARK 470 ARG A 982 CD NE CZ NH1 NH2 REMARK 470 LYS A 989 CE NZ REMARK 470 GLN A 990 CD OE1 NE2 REMARK 470 GLU A 991 CG CD OE1 OE2 REMARK 470 ASP A 993 CG OD1 OD2 REMARK 470 LYS A 994 CD CE NZ REMARK 470 LYS A1003 CD CE NZ REMARK 470 GLU A1006 CD OE1 OE2 REMARK 470 LYS A1007 CG CD CE NZ REMARK 470 LYS A1011 CG CD CE NZ REMARK 470 ARG A1012 CD NE CZ NH1 NH2 REMARK 470 ARG A1013 CG CD NE CZ NH1 NH2 REMARK 470 ALA B 708 O REMARK 470 LYS B 710 CG CD CE NZ REMARK 470 ILE B 711 CG1 CG2 CD1 REMARK 470 LYS B 722 CD CE NZ REMARK 470 GLU B 732 CD OE1 OE2 REMARK 470 GLU B 762 CD OE1 OE2 REMARK 470 LYS B 780 NZ REMARK 470 GLN B 796 CG CD OE1 NE2 REMARK 470 ASP B 797 CG OD1 OD2 REMARK 470 ARG B 813 CZ NH1 NH2 REMARK 470 GLU B 867 CD OE1 OE2 REMARK 470 MET B 868 CG SD CE REMARK 470 LYS B 869 CE NZ REMARK 470 GLU B 884 CG CD OE1 OE2 REMARK 470 TYR B 900 CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 901 CG CD OE2 REMARK 470 GLU B 902 CG CD OE1 OE2 REMARK 470 ARG B 912 CD NE CZ NH1 NH2 REMARK 470 ARG B 959 CD NE CZ NH1 NH2 REMARK 470 LYS B 965 CE NZ REMARK 470 GLU B 978 CG CD OE1 OE2 REMARK 470 GLU B 979 CG CD OE1 OE2 REMARK 470 ARG B 982 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 986 CD OE1 NE2 REMARK 470 LYS B 989 CE NZ REMARK 470 GLN B 990 CD OE1 NE2 REMARK 470 GLU B 991 CG CD OE1 OE2 REMARK 470 ASP B 993 CG OD1 OD2 REMARK 470 LYS B 994 CD CE NZ REMARK 470 ASP B1000 CG OD1 OD2 REMARK 470 LYS B1003 CG CD CE NZ REMARK 470 LYS B1007 CE NZ REMARK 470 LYS B1011 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 763 44.13 75.44 REMARK 500 ASP A 797 52.05 -143.72 REMARK 500 ARG A 873 -39.82 79.75 REMARK 500 ASP A 892 82.99 64.54 REMARK 500 ASN B 763 43.24 74.08 REMARK 500 ASN B 783 99.36 -162.35 REMARK 500 ASP B 797 -164.13 -120.70 REMARK 500 ARG B 873 -38.31 80.81 REMARK 500 ASP B 892 78.73 54.15 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 FMT B 2012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2014 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2015 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 2013 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 2014 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE X2M A 2016 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE X2M B 2015 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IVT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN REMARK 900 RELATED ID: 2IVU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN REMARK 900 COMPLEXED WITH THE INHIBITOR ZD6474 REMARK 900 RELATED ID: 2IVS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NON-PHOSPHORYLATED RET TYROSINE KINASE DOMAIN REMARK 900 RELATED ID: 2IVV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN REMARK 900 COMPLEXED WITH THE INHIBITOR PP1 REMARK 900 RELATED ID: 2X2K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN WITH REMARK 900 INHIBITOR REMARK 900 RELATED ID: 2X2L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN WITH REMARK 900 INHIBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 705-1013 CORRESPOND WITH P07949, 700-704 ARE VECTOR- REMARK 999 DERIVED DBREF 2X2M A 700 704 PDB 2X2M 2X2M 700 704 DBREF 2X2M A 705 1013 UNP P07949 RET_HUMAN 705 1013 DBREF 2X2M B 700 704 PDB 2X2M 2X2M 700 704 DBREF 2X2M B 705 1013 UNP P07949 RET_HUMAN 705 1013 SEQRES 1 A 314 GLY PRO LEU SER LEU SER VAL ASP ALA PHE LYS ILE LEU SEQRES 2 A 314 GLU ASP PRO LYS TRP GLU PHE PRO ARG LYS ASN LEU VAL SEQRES 3 A 314 LEU GLY LYS THR LEU GLY GLU GLY GLU PHE GLY LYS VAL SEQRES 4 A 314 VAL LYS ALA THR ALA PHE HIS LEU LYS GLY ARG ALA GLY SEQRES 5 A 314 TYR THR THR VAL ALA VAL LYS MET LEU LYS GLU ASN ALA SEQRES 6 A 314 SER PRO SER GLU LEU ARG ASP LEU LEU SER GLU PHE ASN SEQRES 7 A 314 VAL LEU LYS GLN VAL ASN HIS PRO HIS VAL ILE LYS LEU SEQRES 8 A 314 TYR GLY ALA CYS SER GLN ASP GLY PRO LEU LEU LEU ILE SEQRES 9 A 314 VAL GLU TYR ALA LYS TYR GLY SER LEU ARG GLY PHE LEU SEQRES 10 A 314 ARG GLU SER ARG LYS VAL GLY PRO GLY TYR LEU GLY SER SEQRES 11 A 314 GLY GLY SER ARG ASN SER SER SER LEU ASP HIS PRO ASP SEQRES 12 A 314 GLU ARG ALA LEU THR MET GLY ASP LEU ILE SER PHE ALA SEQRES 13 A 314 TRP GLN ILE SER GLN GLY MET GLN TYR LEU ALA GLU MET SEQRES 14 A 314 LYS LEU VAL HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU SEQRES 15 A 314 VAL ALA GLU GLY ARG LYS MET LYS ILE SER ASP PHE GLY SEQRES 16 A 314 LEU SER ARG ASP VAL TYR GLU GLU ASP SER PTR VAL LYS SEQRES 17 A 314 ARG SER GLN GLY ARG ILE PRO VAL LYS TRP MET ALA ILE SEQRES 18 A 314 GLU SER LEU PHE ASP HIS ILE TYR THR THR GLN SER ASP SEQRES 19 A 314 VAL TRP SER PHE GLY VAL LEU LEU TRP GLU ILE VAL THR SEQRES 20 A 314 LEU GLY GLY ASN PRO TYR PRO GLY ILE PRO PRO GLU ARG SEQRES 21 A 314 LEU PHE ASN LEU LEU LYS THR GLY HIS ARG MET GLU ARG SEQRES 22 A 314 PRO ASP ASN CYS SER GLU GLU MET TYR ARG LEU MET LEU SEQRES 23 A 314 GLN CYS TRP LYS GLN GLU PRO ASP LYS ARG PRO VAL PHE SEQRES 24 A 314 ALA ASP ILE SER LYS ASP LEU GLU LYS MET MET VAL LYS SEQRES 25 A 314 ARG ARG SEQRES 1 B 314 GLY PRO LEU SER LEU SER VAL ASP ALA PHE LYS ILE LEU SEQRES 2 B 314 GLU ASP PRO LYS TRP GLU PHE PRO ARG LYS ASN LEU VAL SEQRES 3 B 314 LEU GLY LYS THR LEU GLY GLU GLY GLU PHE GLY LYS VAL SEQRES 4 B 314 VAL LYS ALA THR ALA PHE HIS LEU LYS GLY ARG ALA GLY SEQRES 5 B 314 TYR THR THR VAL ALA VAL LYS MET LEU LYS GLU ASN ALA SEQRES 6 B 314 SER PRO SER GLU LEU ARG ASP LEU LEU SER GLU PHE ASN SEQRES 7 B 314 VAL LEU LYS GLN VAL ASN HIS PRO HIS VAL ILE LYS LEU SEQRES 8 B 314 TYR GLY ALA CYS SER GLN ASP GLY PRO LEU LEU LEU ILE SEQRES 9 B 314 VAL GLU TYR ALA LYS TYR GLY SER LEU ARG GLY PHE LEU SEQRES 10 B 314 ARG GLU SER ARG LYS VAL GLY PRO GLY TYR LEU GLY SER SEQRES 11 B 314 GLY GLY SER ARG ASN SER SER SER LEU ASP HIS PRO ASP SEQRES 12 B 314 GLU ARG ALA LEU THR MET GLY ASP LEU ILE SER PHE ALA SEQRES 13 B 314 TRP GLN ILE SER GLN GLY MET GLN TYR LEU ALA GLU MET SEQRES 14 B 314 LYS LEU VAL HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU SEQRES 15 B 314 VAL ALA GLU GLY ARG LYS MET LYS ILE SER ASP PHE GLY SEQRES 16 B 314 LEU SER ARG ASP VAL TYR GLU GLU ASP SER PTR VAL LYS SEQRES 17 B 314 ARG SER GLN GLY ARG ILE PRO VAL LYS TRP MET ALA ILE SEQRES 18 B 314 GLU SER LEU PHE ASP HIS ILE TYR THR THR GLN SER ASP SEQRES 19 B 314 VAL TRP SER PHE GLY VAL LEU LEU TRP GLU ILE VAL THR SEQRES 20 B 314 LEU GLY GLY ASN PRO TYR PRO GLY ILE PRO PRO GLU ARG SEQRES 21 B 314 LEU PHE ASN LEU LEU LYS THR GLY HIS ARG MET GLU ARG SEQRES 22 B 314 PRO ASP ASN CYS SER GLU GLU MET TYR ARG LEU MET LEU SEQRES 23 B 314 GLN CYS TRP LYS GLN GLU PRO ASP LYS ARG PRO VAL PHE SEQRES 24 B 314 ALA ASP ILE SER LYS ASP LEU GLU LYS MET MET VAL LYS SEQRES 25 B 314 ARG ARG MODRES 2X2M PTR A 905 TYR O-PHOSPHOTYROSINE MODRES 2X2M PTR B 905 TYR O-PHOSPHOTYROSINE HET PTR A 905 16 HET PTR B 905 16 HET FMT A2014 3 HET FMT A2015 3 HET X2M A2016 18 HET FMT B2012 3 HET FMT B2013 3 HET FMT B2014 3 HET X2M B2015 18 HETNAM PTR O-PHOSPHOTYROSINE HETNAM FMT FORMIC ACID HETNAM X2M (3Z)-3-[(3,5-DIMETHYL-1H-PYRROL-2-YL)METHYLIDENE]-1,3- HETNAM 2 X2M DIHYDRO-2H-INDOL-2-ONE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 PTR 2(C9 H12 N O6 P) FORMUL 3 FMT 5(C H2 O2) FORMUL 5 X2M 2(C15 H14 N2 O) FORMUL 10 HOH *45(H2 O) HELIX 1 1 GLY A 700 ASP A 707 1 8 HELIX 2 2 PRO A 720 LYS A 722 5 3 HELIX 3 3 SER A 765 VAL A 782 1 18 HELIX 4 4 SER A 811 GLU A 818 1 8 HELIX 5 5 THR A 847 MET A 868 1 22 HELIX 6 6 ALA A 876 ARG A 878 5 3 HELIX 7 7 PRO A 914 MET A 918 5 5 HELIX 8 8 ALA A 919 HIS A 926 1 8 HELIX 9 9 THR A 929 THR A 946 1 18 HELIX 10 10 PRO A 956 GLU A 958 5 3 HELIX 11 11 ARG A 959 THR A 966 1 8 HELIX 12 12 SER A 977 TRP A 988 1 12 HELIX 13 13 GLU A 991 ARG A 995 5 5 HELIX 14 14 VAL A 997 ARG A 1013 1 17 HELIX 15 15 GLY B 700 ASP B 707 1 8 HELIX 16 16 PRO B 720 LYS B 722 5 3 HELIX 17 17 SER B 765 LYS B 780 1 16 HELIX 18 18 SER B 811 GLU B 818 1 8 HELIX 19 19 THR B 847 MET B 868 1 22 HELIX 20 20 ALA B 876 ARG B 878 5 3 HELIX 21 21 PRO B 914 MET B 918 5 5 HELIX 22 22 ALA B 919 HIS B 926 1 8 HELIX 23 23 THR B 929 THR B 946 1 18 HELIX 24 24 PRO B 956 GLU B 958 5 3 HELIX 25 25 ARG B 959 THR B 966 1 8 HELIX 26 26 SER B 977 TRP B 988 1 12 HELIX 27 27 GLU B 991 ARG B 995 5 5 HELIX 28 28 VAL B 997 LYS B 1011 1 15 SHEET 1 AA 5 LEU A 724 GLY A 731 0 SHEET 2 AA 5 LYS A 737 LEU A 746 -1 O VAL A 738 N LEU A 730 SHEET 3 AA 5 ARG A 749 MET A 759 -1 O ARG A 749 N LEU A 746 SHEET 4 AA 5 LEU A 801 GLU A 805 -1 O LEU A 802 N LYS A 758 SHEET 5 AA 5 LEU A 790 CYS A 794 -1 N TYR A 791 O ILE A 803 SHEET 1 AB 2 LEU A 870 VAL A 871 0 SHEET 2 AB 2 ARG A 897 ASP A 898 -1 O ARG A 897 N VAL A 871 SHEET 1 AC 2 ILE A 880 ALA A 883 0 SHEET 2 AC 2 LYS A 887 ILE A 890 -1 O LYS A 887 N ALA A 883 SHEET 1 AD 2 PTR A 905 VAL A 906 0 SHEET 2 AD 2 ILE A 927 TYR A 928 -1 O TYR A 928 N PTR A 905 SHEET 1 BA 5 LEU B 724 GLY B 731 0 SHEET 2 BA 5 VAL B 738 PHE B 744 -1 O VAL B 738 N LEU B 730 SHEET 3 BA 5 TYR B 752 MET B 759 -1 O THR B 753 N ALA B 743 SHEET 4 BA 5 LEU B 801 VAL B 804 -1 O LEU B 802 N LYS B 758 SHEET 5 BA 5 LEU B 790 CYS B 794 -1 N TYR B 791 O ILE B 803 SHEET 1 BB 2 LEU B 870 VAL B 871 0 SHEET 2 BB 2 ARG B 897 ASP B 898 -1 O ARG B 897 N VAL B 871 SHEET 1 BC 2 ILE B 880 ALA B 883 0 SHEET 2 BC 2 LYS B 887 ILE B 890 -1 O LYS B 887 N ALA B 883 SHEET 1 BD 2 PTR B 905 VAL B 906 0 SHEET 2 BD 2 ILE B 927 TYR B 928 -1 O TYR B 928 N PTR B 905 LINK C SER A 904 N PTR A 905 1555 1555 1.32 LINK C PTR A 905 N VAL A 906 1555 1555 1.32 LINK C SER B 904 N PTR B 905 1555 1555 1.33 LINK C PTR B 905 N VAL B 906 1555 1555 1.32 SITE 1 AC1 7 GLN A 910 LEU A 923 HIS A 926 GLY B 700 SITE 2 AC1 7 PRO B 701 LEU B 702 SER B 703 SITE 1 AC2 6 ARG A 873 LEU A 895 LYS A 907 GLY A 911 SITE 2 AC2 6 ARG A 912 ILE A 913 SITE 1 AC3 7 GLY A 700 LEU A 702 SER A 703 GLN B 910 SITE 2 AC3 7 LEU B 923 HIS B 926 HOH B3014 SITE 1 AC4 6 ARG B 873 LEU B 895 LYS B 907 GLY B 911 SITE 2 AC4 6 ARG B 912 ILE B 913 SITE 1 AC5 6 ARG B 721 CYS B 794 ASP B 797 GLY B 798 SITE 2 AC5 6 PRO B 799 LEU B 801 SITE 1 AC6 11 LEU A 730 ALA A 756 LYS A 758 VAL A 804 SITE 2 AC6 11 GLU A 805 TYR A 806 ALA A 807 LYS A 808 SITE 3 AC6 11 GLY A 810 LEU A 881 SER A 891 SITE 1 AC7 9 LEU B 730 ALA B 756 VAL B 804 GLU B 805 SITE 2 AC7 9 TYR B 806 ALA B 807 GLY B 810 LEU B 881 SITE 3 AC7 9 SER B 891 CRYST1 50.697 50.760 74.588 103.50 99.66 89.92 P 1 2 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 0.019725 -0.000028 0.003449 0.00000 SCALE2 0.000000 0.019701 0.004797 0.00000 SCALE3 0.000000 0.000000 0.013997 0.00000 MTRIX1 1 -0.001420 -1.000000 -0.002510 -8.12835 1 MTRIX2 1 -1.000000 0.001420 -0.000650 -8.14759 1 MTRIX3 1 0.000650 0.002510 -1.000000 33.33179 1