HEADER TRANSFERASE 30-OCT-15 5FM2 TITLE CRYSTAL STRUCTURE OF HYPER-PHOSPHORYLATED RET KINASE DOMAIN WITH TITLE 2 (PROXIMAL) JUXTAMEMBRANE SEGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 659-1013; COMPND 5 SYNONYM: CADHERIN FAMILY MEMBER 12, PROTO-ONCOGENE 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: SF21 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR I.PLAZA-MENACHO,K.BARNOUIN,R.BARRY,A.BORG,M.ORME,S.MOUILLERON, AUTHOR 2 R.J.MARTINEZ-TORRES,P.MEIER,N.Q.MCDONALD REVDAT 3 24-APR-19 5FM2 1 SOURCE LINK REVDAT 2 01-MAR-17 5FM2 1 JRNL REVDAT 1 28-DEC-16 5FM2 0 JRNL AUTH I.PLAZA-MENACHO,K.BARNOUIN,R.BARRY,A.BORG,M.ORME,R.CHAUHAN, JRNL AUTH 2 S.MOUILLERON,R.J.MARTINEZ-TORRES,P.MEIER,N.Q.MCDONALD JRNL TITL RET FUNCTIONS AS A DUAL-SPECIFICITY KINASE THAT REQUIRES JRNL TITL 2 ALLOSTERIC INPUTS FROM JUXTAMEMBRANE ELEMENTS. JRNL REF CELL REP V. 17 3319 2016 JRNL REFN ESSN 2211-1247 JRNL PMID 28009299 JRNL DOI 10.1016/J.CELREP.2016.11.061 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 6686 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 315 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 55.1347 - 4.1574 1.00 3292 157 0.2230 0.2321 REMARK 3 2 4.1574 - 3.3000 1.00 3079 158 0.2572 0.2941 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 92.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.002 2151 REMARK 3 ANGLE : 0.647 2937 REMARK 3 CHIRALITY : 0.039 328 REMARK 3 PLANARITY : 0.003 368 REMARK 3 DIHEDRAL : 16.152 1247 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 713:737) REMARK 3 ORIGIN FOR THE GROUP (A): -31.1642 13.4489 0.2081 REMARK 3 T TENSOR REMARK 3 T11: 0.5378 T22: 0.5325 REMARK 3 T33: 0.8739 T12: 0.0843 REMARK 3 T13: -0.0586 T23: 0.0821 REMARK 3 L TENSOR REMARK 3 L11: 2.0160 L22: 3.7570 REMARK 3 L33: 5.8614 L12: 2.6723 REMARK 3 L13: 0.6666 L23: -0.2271 REMARK 3 S TENSOR REMARK 3 S11: 0.5473 S12: -0.4206 S13: 1.0045 REMARK 3 S21: 0.0916 S22: -0.1293 S23: 0.4488 REMARK 3 S31: 0.1327 S32: -0.5395 S33: -0.3833 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 738:890) REMARK 3 ORIGIN FOR THE GROUP (A): -26.3619 17.0911 -11.4126 REMARK 3 T TENSOR REMARK 3 T11: 0.4372 T22: 0.6049 REMARK 3 T33: 0.6780 T12: 0.0159 REMARK 3 T13: -0.1847 T23: -0.0942 REMARK 3 L TENSOR REMARK 3 L11: 2.6255 L22: 3.4028 REMARK 3 L33: 3.9130 L12: 0.4894 REMARK 3 L13: -2.4321 L23: -1.0059 REMARK 3 S TENSOR REMARK 3 S11: -0.1351 S12: 0.2871 S13: -0.2245 REMARK 3 S21: -0.4754 S22: 0.0508 S23: -0.0373 REMARK 3 S31: 0.3957 S32: 0.0777 S33: 0.0787 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 891:911) REMARK 3 ORIGIN FOR THE GROUP (A): -29.8836 35.3942 -7.7665 REMARK 3 T TENSOR REMARK 3 T11: 0.8332 T22: 0.7499 REMARK 3 T33: 0.7643 T12: 0.1697 REMARK 3 T13: 0.0261 T23: 0.0266 REMARK 3 L TENSOR REMARK 3 L11: 3.6989 L22: 2.2254 REMARK 3 L33: 3.5607 L12: -1.3453 REMARK 3 L13: -2.8245 L23: 2.5793 REMARK 3 S TENSOR REMARK 3 S11: 0.2056 S12: 0.3039 S13: 0.7106 REMARK 3 S21: -0.0022 S22: -0.2460 S23: 0.1993 REMARK 3 S31: -0.4668 S32: -0.2442 S33: 0.1416 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 912:1012) REMARK 3 ORIGIN FOR THE GROUP (A): -14.3415 31.5242 -23.0069 REMARK 3 T TENSOR REMARK 3 T11: 0.7243 T22: 0.8370 REMARK 3 T33: 0.4890 T12: -0.0628 REMARK 3 T13: -0.1691 T23: 0.1049 REMARK 3 L TENSOR REMARK 3 L11: 4.3225 L22: 6.0885 REMARK 3 L33: 2.6235 L12: 1.4548 REMARK 3 L13: -2.6240 L23: 1.3939 REMARK 3 S TENSOR REMARK 3 S11: -0.1649 S12: 0.3025 S13: 0.3821 REMARK 3 S21: -0.9814 S22: 0.0842 S23: -0.0271 REMARK 3 S31: -0.8097 S32: 0.0378 S33: 0.1087 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 5FM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1290065399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6686 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.27500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.27500 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 72.27500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 72.27500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 72.27500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 72.27500 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: 3470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.6 KCAL/MOL 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 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 CYS A 659 REMARK 465 TYR A 660 REMARK 465 HIS A 661 REMARK 465 LYS A 662 REMARK 465 PHE A 663 REMARK 465 ALA A 664 REMARK 465 HIS A 665 REMARK 465 LYS A 666 REMARK 465 PRO A 667 REMARK 465 PRO A 668 REMARK 465 ILE A 669 REMARK 465 SER A 670 REMARK 465 SER A 671 REMARK 465 ALA A 672 REMARK 465 GLU A 673 REMARK 465 MET A 674 REMARK 465 THR A 675 REMARK 465 PHE A 676 REMARK 465 ARG A 677 REMARK 465 ARG A 678 REMARK 465 PRO A 679 REMARK 465 ALA A 680 REMARK 465 GLN A 681 REMARK 465 ALA A 682 REMARK 465 PHE A 683 REMARK 465 PRO A 684 REMARK 465 VAL A 685 REMARK 465 SER A 686 REMARK 465 TYR A 687 REMARK 465 SER A 688 REMARK 465 SER A 689 REMARK 465 SER A 690 REMARK 465 GLY A 691 REMARK 465 ALA A 692 REMARK 465 ARG A 693 REMARK 465 ARG A 694 REMARK 465 PRO A 695 REMARK 465 SER A 696 REMARK 465 LEU A 697 REMARK 465 ASP A 698 REMARK 465 SER A 699 REMARK 465 MET A 700 REMARK 465 GLU A 701 REMARK 465 ASN A 702 REMARK 465 GLN A 703 REMARK 465 VAL A 704 REMARK 465 SER A 705 REMARK 465 VAL A 706 REMARK 465 ASP A 707 REMARK 465 ALA A 708 REMARK 465 PHE A 709 REMARK 465 ARG A 820 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 ARG A 1012 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 LYS A 710 CG CD CE NZ REMARK 470 GLU A 713 CG CD OE1 OE2 REMARK 470 LYS A 716 CG CD CE NZ REMARK 470 LYS A 722 CG CD CE NZ REMARK 470 LYS A 728 CG CD CE NZ REMARK 470 GLU A 734 CG CD OE1 OE2 REMARK 470 PHE A 744 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 747 CG CD CE NZ REMARK 470 ARG A 749 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 762 CG CD OE1 OE2 REMARK 470 LYS A 789 CD CE NZ REMARK 470 GLN A 796 CG CD OE1 NE2 REMARK 470 ASP A 797 CG OD1 OD2 REMARK 470 LYS A 808 CG CD CE NZ REMARK 470 GLU A 867 CG CD OE1 OE2 REMARK 470 LYS A 869 CG CD CE NZ REMARK 470 ASP A 874 CG OD1 OD2 REMARK 470 LYS A 887 CG CD CE NZ REMARK 470 ASP A 892 CG OD1 OD2 REMARK 470 VAL A 899 CG1 CG2 REMARK 470 TYR A 900 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 901 CG CD OE1 OE2 REMARK 470 GLU A 902 CG CD OE1 OE2 REMARK 470 SER A 904 OG REMARK 470 VAL A 906 CG1 CG2 REMARK 470 LYS A 907 CE NZ REMARK 470 ARG A 908 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 910 CG CD OE1 NE2 REMARK 470 ASP A 925 CG OD1 OD2 REMARK 470 ARG A 959 NE CZ NH1 NH2 REMARK 470 LEU A 963 CG CD1 CD2 REMARK 470 LYS A 965 CG CD CE NZ REMARK 470 GLU A 971 CG CD 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 LYS A 989 CD CE NZ REMARK 470 GLU A 991 CG CD OE1 OE2 REMARK 470 LYS A 994 CG CD CE NZ REMARK 470 LYS A1003 CG CD CE NZ REMARK 470 LYS A1007 CG CD CE NZ REMARK 470 VAL A1010 CG1 CG2 REMARK 470 LYS A1011 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 ARG A 873 -65.75 62.59 REMARK 500 ASP A 892 81.32 58.64 REMARK 500 GLU A 902 51.41 -106.42 REMARK 500 ARG A 969 -165.60 -120.13 REMARK 500 ASN A 975 51.84 -99.66 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 PTR A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SEP A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PTR A 928 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PP1 A 2012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for Ligand PTR A 905 bound to SER A REMARK 800 904 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FM3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE JM-KD DBREF 5FM2 A 659 1013 UNP P07949 RET_HUMAN 659 1013 SEQRES 1 A 355 CYS TYR HIS LYS PHE ALA HIS LYS PRO PRO ILE SER SER SEQRES 2 A 355 ALA GLU MET THR PHE ARG ARG PRO ALA GLN ALA PHE PRO SEQRES 3 A 355 VAL SER TYR SER SER SER GLY ALA ARG ARG PRO SER LEU SEQRES 4 A 355 ASP SER MET GLU ASN GLN VAL SER VAL ASP ALA PHE LYS SEQRES 5 A 355 ILE LEU GLU ASP PRO LYS TRP GLU PHE PRO ARG LYS ASN SEQRES 6 A 355 LEU VAL LEU GLY LYS THR LEU GLY GLU GLY GLU PHE GLY SEQRES 7 A 355 LYS VAL VAL LYS ALA THR ALA PHE HIS LEU LYS GLY ARG SEQRES 8 A 355 ALA GLY TYR THR THR VAL ALA VAL LYS MET LEU LYS GLU SEQRES 9 A 355 ASN ALA SER PRO SER GLU LEU ARG ASP LEU LEU SER GLU SEQRES 10 A 355 PHE ASN VAL LEU LYS GLN VAL ASN HIS PRO HIS VAL ILE SEQRES 11 A 355 LYS LEU TYR GLY ALA CYS SER GLN ASP GLY PRO LEU LEU SEQRES 12 A 355 LEU ILE VAL GLU TYR ALA LYS PTR GLY SER LEU ARG GLY SEQRES 13 A 355 PHE LEU ARG GLU SER ARG LYS VAL GLY PRO GLY TYR LEU SEQRES 14 A 355 GLY SER GLY GLY SER ARG ASN SER SER SER LEU ASP HIS SEQRES 15 A 355 PRO ASP GLU ARG ALA LEU THR MET GLY ASP LEU ILE SER SEQRES 16 A 355 PHE ALA TRP GLN ILE SER GLN GLY MET GLN TYR LEU ALA SEQRES 17 A 355 GLU MET LYS LEU VAL HIS ARG ASP LEU ALA ALA ARG ASN SEQRES 18 A 355 ILE LEU VAL ALA GLU GLY ARG LYS MET LYS ILE SER ASP SEQRES 19 A 355 PHE GLY LEU SER ARG ASP VAL TYR GLU GLU ASP SER PTR SEQRES 20 A 355 VAL LYS ARG SEP GLN GLY ARG ILE PRO VAL LYS TRP MET SEQRES 21 A 355 ALA ILE GLU SER LEU PHE ASP HIS ILE PTR THR THR GLN SEQRES 22 A 355 SER ASP VAL TRP SER PHE GLY VAL LEU LEU TRP GLU ILE SEQRES 23 A 355 VAL THR LEU GLY GLY ASN PRO TYR PRO GLY ILE PRO PRO SEQRES 24 A 355 GLU ARG LEU PHE ASN LEU LEU LYS THR GLY HIS ARG MET SEQRES 25 A 355 GLU ARG PRO ASP ASN CYS SER GLU GLU MET TYR ARG LEU SEQRES 26 A 355 MET LEU GLN CYS TRP LYS GLN GLU PRO ASP LYS ARG PRO SEQRES 27 A 355 VAL PHE ALA ASP ILE SER LYS ASP LEU GLU LYS MET MET SEQRES 28 A 355 VAL LYS ARG ARG MODRES 5FM2 PTR A 809 TYR O-PHOSPHOTYROSINE MODRES 5FM2 PTR A 905 TYR O-PHOSPHOTYROSINE MODRES 5FM2 SEP A 909 SER PHOSPHOSERINE MODRES 5FM2 PTR A 928 TYR O-PHOSPHOTYROSINE HET PTR A 809 16 HET PTR A 905 16 HET SEP A 909 10 HET PTR A 928 16 HET PP1 A2012 21 HETNAM PTR O-PHOSPHOTYROSINE HETNAM SEP PHOSPHOSERINE HETNAM PP1 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4- HETNAM 2 PP1 YLAMINE HETSYN PTR PHOSPHONOTYROSINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 PTR 3(C9 H12 N O6 P) FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 PP1 C16 H19 N5 FORMUL 3 HOH *3(H2 O) HELIX 1 1 PRO A 720 LYS A 722 5 3 HELIX 2 2 LEU A 746 ARG A 749 5 4 HELIX 3 3 SER A 765 VAL A 782 1 18 HELIX 4 4 SER A 811 SER A 819 1 9 HELIX 5 5 THR A 847 MET A 868 1 22 HELIX 6 6 PRO A 914 MET A 918 5 5 HELIX 7 7 ALA A 919 HIS A 926 1 8 HELIX 8 8 THR A 929 THR A 946 1 18 HELIX 9 9 PRO A 956 GLU A 958 5 3 HELIX 10 10 ARG A 959 THR A 966 1 8 HELIX 11 11 SER A 977 TRP A 988 1 12 HELIX 12 12 GLU A 991 ARG A 995 5 5 HELIX 13 13 VAL A 997 LYS A 1011 1 15 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 VAL A 804 -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 LINK C LYS A 808 N PTR A 809 1555 1555 1.33 LINK C PTR A 809 N GLY A 810 1555 1555 1.33 LINK C SER A 904 N PTR A 905 1555 1555 1.33 LINK C PTR A 905 N VAL A 906 1555 1555 1.33 LINK C ARG A 908 N SEP A 909 1555 1555 1.33 LINK C SEP A 909 N GLN A 910 1555 1555 1.33 LINK C ILE A 927 N PTR A 928 1555 1555 1.33 LINK C PTR A 928 N THR A 929 1555 1555 1.33 SITE 1 AC1 7 ALA A 807 LYS A 808 GLY A 810 VAL A 882 SITE 2 AC1 7 ALA A 883 GLU A 884 GLY A 885 SITE 1 AC2 8 ARG A 873 GLY A 894 LEU A 895 ARG A 897 SITE 2 AC2 8 LYS A 907 ARG A 908 GLN A 910 PTR A 928 SITE 1 AC3 10 ARG A 873 ARG A 897 SEP A 909 GLY A 911 SITE 2 AC3 10 MET A 918 SER A 922 HIS A 926 ILE A 927 SITE 3 AC3 10 THR A 929 SER A 932 SITE 1 AC4 11 LEU A 730 PHE A 735 VAL A 738 ALA A 756 SITE 2 AC4 11 LYS A 758 GLU A 775 VAL A 804 GLU A 805 SITE 3 AC4 11 ALA A 807 LEU A 881 SER A 891 SITE 1 AC5 7 PRO A 720 ASN A 723 HIS A 745 ASP A 903 SITE 2 AC5 7 SER A 904 VAL A 906 LYS A 907 CRYST1 98.430 98.430 144.550 90.00 90.00 120.00 P 63 2 2 12 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 0.010160 0.005866 0.000000 0.00000 SCALE2 0.000000 0.011731 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006918 0.00000