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 <I/SIGMA(I)> 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 <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: 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
(ATOM LINES ARE NOT SHOWN.)
END
