PDB Short entry for 2IVU HEADER TRANSFERASE 16-JUN-06 2IVU TITLE CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN TITLE 2 COMPLEXED WITH THE INHIBITOR ZD6474 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET COMPND 3 PRECURSOR; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: TYROSINE KINASE DOMAIN, RESIDUES 705-1013; COMPND 6 SYNONYM: RET RECEPTOR, C-RET; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: PTR AT 905 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_TAXID: 7108; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBACPAK-HIS3 KEYWDS NUCLEOTIDE-BINDING, HIRSCHSPRUNG DISEASE, PHOSPHORYLATION, DISEASE KEYWDS 2 MUTATION, PHOSPHOTRANSFERASE, TYROSINE-PROTEIN KINASE, CHROMOSOMAL KEYWDS 3 TRANSLOCATION, POLYMORPHISM, GDNF RECEPTOR, TRANSMEMBRANE, PROTO- KEYWDS 4 ONCOGENE, TYROSINE KINASE, RET, KINASE, MEMBRANE, ATP-BINDING, KEYWDS 5 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.P.KNOWLES,J.MURRAY-RUST,N.Q.MCDONALD REVDAT 9 08-MAY-19 2IVU 1 REMARK LINK REVDAT 8 30-JAN-19 2IVU 1 REMARK REVDAT 7 28-FEB-18 2IVU 1 JRNL REVDAT 6 25-OCT-17 2IVU 1 COMPND REMARK HETNAM HETSYN REVDAT 6 2 1 ATOM REVDAT 5 28-JUN-17 2IVU 1 REMARK REVDAT 4 24-FEB-09 2IVU 1 VERSN REVDAT 3 01-NOV-06 2IVU 1 JRNL REVDAT 2 16-AUG-06 2IVU 1 HETNAM FORMUL REVDAT 1 10-AUG-06 2IVU 0 JRNL AUTH P.P.KNOWLES,J.MURRAY-RUST,S.KJAER,R.P.SCOTT,S.HANRAHAN, JRNL AUTH 2 M.SANTORO,C.F.IBANEZ,N.Q.MCDONALD JRNL TITL STRUCTURE AND CHEMICAL INHIBITION OF THE RET TYROSINE KINASE JRNL TITL 2 DOMAIN. JRNL REF J. BIOL. CHEM. V. 281 33577 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16928683 JRNL DOI 10.1074/JBC.M605604200 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) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12835 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 670 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) : 964 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.3870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2189 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : -0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.384 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.267 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.189 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.373 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2274 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3078 ; 1.614 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 5.924 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;36.199 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 375 ;15.589 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.204 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 346 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1653 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 999 ; 0.193 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1558 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 101 ; 0.154 ; 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): 49 ; 0.202 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.072 ; 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): 1484 ; 0.915 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2283 ; 1.537 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 952 ; 2.279 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 795 ; 3.368 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2IVU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1290029134. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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 : 13506 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 15.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 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: IN-HOUSE PART-REFINED STRUCTURE OF RET KINASE REMARK 200 DOMAIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN 3 MG/ML IN 20 MM TRIS-HCL PH REMARK 280 8.0, 100MM NACL, 1MM DTT, 1MM EDTA, 1MM SODIUM VANADATE REMARK 280 RESERVOIR 2.2 M SODIUM FORMATE, 0.1M SODIUM ACETATE PH 4.5 REMARK 280 VAPOUR DIFFUSION, SITTING DROP, 289 K, VAPOR DIFFUSION, SITTING REMARK 280 DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.70450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.71000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.70450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.71000 REMARK 290 SMTRY3 4 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: PQS 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 BIOMT1 2 -1.000000 0.000000 0.000000 -71.40900 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 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 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 LYS A 716 CG CD CE NZ REMARK 470 LYS A 722 CD CE NZ REMARK 470 GLU A 732 CD OE1 OE2 REMARK 470 GLU A 734 CG CD OE1 OE2 REMARK 470 PHE A 735 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 749 CZ NH1 NH2 REMARK 470 GLU A 762 CD OE1 OE2 REMARK 470 ARG A 770 CZ NH1 NH2 REMARK 470 LYS A 789 CE NZ REMARK 470 ASP A 797 CG OD1 OD2 REMARK 470 GLU A 818 CG CD OE1 OE2 REMARK 470 ARG A 820 NE CZ NH1 NH2 REMARK 470 ARG A 844 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 867 CG CD OE1 OE2 REMARK 470 LYS A 869 CD CE NZ REMARK 470 GLU A 884 CG CD OE1 OE2 REMARK 470 ARG A 886 CZ NH1 NH2 REMARK 470 TYR A 900 O CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 901 CG CD OE2 REMARK 470 GLU A 902 CG CD OE1 OE2 REMARK 470 ARG A 912 CD 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 OE1 OE2 REMARK 470 ASN A 975 CG OD1 ND2 REMARK 470 GLU A 978 CG CD OE1 OE2 REMARK 470 GLU A 979 CG CD OE1 OE2 REMARK 470 ARG A 982 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 986 CG CD OE1 NE2 REMARK 470 GLU A 991 CG CD OE1 OE2 REMARK 470 LYS A 994 CD CE NZ REMARK 470 LYS A1007 CD CE NZ REMARK 470 MET A1009 CE REMARK 470 LYS A1011 CE NZ REMARK 470 ARG A1012 CG CD NE CZ NH1 NH2 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 OE2 GLU A 775 O HOH A 2029 2.13 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 710 19.80 -64.33 REMARK 500 ILE A 711 10.43 -149.46 REMARK 500 LYS A 747 54.10 39.98 REMARK 500 GLN A 796 -91.49 -70.23 REMARK 500 ARG A 873 -31.91 76.28 REMARK 500 ASP A 892 72.42 56.91 REMARK 500 GLU A 901 -76.11 -55.13 REMARK 500 ASP A 903 7.97 56.92 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 ZD6 A3015 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A3013 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A3014 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IVS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NON-PHOSPHORYLATED RET TYROSINE KINASE DOMAIN REMARK 900 RELATED ID: 2IVT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 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 999 REMARK 999 SEQUENCE REMARK 999 705-1013 CORRESPOND WITH P07949, 700-704 ARE VECTOR- REMARK 999 DERIVED DBREF 2IVU A 700 704 PDB 2IVU 2IVU 700 704 DBREF 2IVU A 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 MODRES 2IVU PTR A 905 TYR O-PHOSPHOTYROSINE HET PTR A 905 16 HET FMT A3013 3 HET FMT A3014 3 HET ZD6 A3015 30 HETNAM PTR O-PHOSPHOTYROSINE HETNAM FMT FORMIC ACID HETNAM ZD6 VANDETANIB HETSYN PTR PHOSPHONOTYROSINE HETSYN ZD6 ZD6474 FORMUL 1 PTR C9 H12 N O6 P FORMUL 2 FMT 2(C H2 O2) FORMUL 4 ZD6 C22 H24 BR F N4 O2 FORMUL 5 HOH *71(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 LYS A 780 1 16 HELIX 4 4 LEU A 812 GLU A 818 1 7 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 1012 1 16 SHEET 1 AA 5 LEU A 724 GLU A 732 0 SHEET 2 AA 5 LYS A 737 PHE A 744 -1 O VAL A 738 N LEU A 730 SHEET 3 AA 5 TYR A 752 MET A 759 -1 O THR A 753 N ALA A 743 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 3 GLY A 810 SER A 811 0 SHEET 2 AB 3 ILE A 880 ALA A 883 -1 N VAL A 882 O GLY A 810 SHEET 3 AB 3 LYS A 887 ILE A 890 -1 O LYS A 887 N ALA A 883 SHEET 1 AC 2 LEU A 870 VAL A 871 0 SHEET 2 AC 2 ARG A 897 ASP A 898 -1 O ARG A 897 N VAL A 871 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 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 SITE 1 AC1 15 LEU A 730 VAL A 738 ALA A 756 LYS A 758 SITE 2 AC1 15 GLU A 775 LEU A 779 VAL A 804 GLU A 805 SITE 3 AC1 15 TYR A 806 ALA A 807 LYS A 808 GLY A 810 SITE 4 AC1 15 LEU A 881 SER A 891 HOH A2071 SITE 1 AC2 8 GLY A 700 PRO A 701 LEU A 702 SER A 703 SITE 2 AC2 8 GLN A 910 LEU A 923 PHE A 924 HIS A 926 SITE 1 AC3 4 ARG A 873 LYS A 907 GLY A 911 ARG A 912 CRYST1 71.409 71.420 78.834 90.00 101.23 90.00 C 1 2 1 4 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 0.014004 0.000000 0.002780 0.00000 SCALE2 0.000000 0.014002 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012932 0.00000