HEADER TRANSFERASE 15-JAN-10 2X2U TITLE FIRST TWO CADHERIN-LIKE DOMAINS FROM HUMAN RET COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CADHERIN-LIKE DOMAINS 1 AND 2, RESIDUES 29-270; COMPND 5 SYNONYM: C-RET, RET, CADHERIN FAMILY MEMBER 12; COMPND 6 EC: 2.7.10.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: ASN 151 IS GLYCOSYLATED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: LEC8; SOURCE 9 EXPRESSION_SYSTEM_ORGAN: OVARY; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PCDNA3 KEYWDS HIRSCHSPRUNG DISEASE, EXTRACELLULAR DOMAIN, DISEASE MUTATION, KEYWDS 2 TRANSFERASE, GLYCOPROTEIN, TRANSMEMBRANE, KINASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KJAER,S.HANRAHAN,A.G.PURKISS-TREW,N.TOTTY,N.Q.MCDONALD REVDAT 7 23-OCT-24 2X2U 1 HETSYN REVDAT 6 29-JUL-20 2X2U 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 15-MAY-19 2X2U 1 REMARK LINK REVDAT 4 07-MAR-18 2X2U 1 JRNL REVDAT 3 06-JUL-11 2X2U 1 JRNL REMARK DBREF SEQADV REVDAT 2 26-MAY-10 2X2U 1 JRNL REVDAT 1 19-MAY-10 2X2U 0 JRNL AUTH S.KJAER,S.HANRAHAN,N.TOTTY,N.Q.MCDONALD JRNL TITL MAMMAL-RESTRICTED ELEMENTS PREDISPOSE HUMAN RET TO FOLDING JRNL TITL 2 IMPAIRMENT BY HSCR MUTATIONS. JRNL REF NAT. STRUCT. MOL. BIOL. V. 17 726 2010 JRNL REFN ESSN 1545-9985 JRNL PMID 20473317 JRNL DOI 10.1038/NSMB.1808 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 27156 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1447 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1961 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1921 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 216 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.129 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.129 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2064 ; 0.032 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2818 ; 2.587 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 235 ; 7.840 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;31.862 ;22.020 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 301 ;15.522 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.868 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 298 ; 0.198 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1570 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 870 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1337 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 214 ; 0.196 ; 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): 43 ; 0.166 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.206 ; 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): 1232 ; 1.773 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1929 ; 2.751 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 970 ; 3.887 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 888 ; 5.362 ; 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. RESIDUES 129-135 ARE DISORDERED REMARK 4 REMARK 4 2X2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1290041451. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.946, 1.514 REMARK 200 MONOCHROMATOR : SI (311) AND SI (111) CRYSTALS REMARK 200 OPTICS : TOROIDAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33291 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 55.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 0.86000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M (NH4)2SO4, 50 MM TRIS PH 7.5, 4% REMARK 280 (V/V) 1\,4 BUTANEDIOL AT 15 DEG C., TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -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 55.23750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.03700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.03700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.85625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.03700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.03700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.61875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.03700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.03700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 82.85625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.03700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.03700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.61875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.23750 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: 8800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -219.2 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 87 TO ARG REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 98 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 199 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 216 TO SER 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 PRO A 129 REMARK 465 THR A 130 REMARK 465 SER A 131 REMARK 465 LEU A 132 REMARK 465 ARG A 133 REMARK 465 GLU A 134 REMARK 465 GLY A 135 REMARK 465 ALA A 247 REMARK 465 GLY A 248 REMARK 465 ALA A 249 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 GLU A 61 CD OE1 OE2 REMARK 470 GLU A 107 CD OE1 OE2 REMARK 470 LYS A 108 NZ REMARK 470 SER A 128 OG REMARK 470 GLU A 136 CG CD OE1 OE2 REMARK 470 GLN A 138 OE1 NE2 REMARK 470 LYS A 161 CD CE NZ REMARK 470 ARG A 215 NE CZ NH1 NH2 REMARK 470 ARG A 226 CZ NH1 NH2 REMARK 470 GLU A 232 CG CD OE1 OE2 REMARK 470 GLN A 233 CG CD OE1 NE2 REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 ARG A 250 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 NH2 ARG A 87 O HOH A 2060 1.94 REMARK 500 O HOH A 2087 O HOH A 2090 2.04 REMARK 500 O HOH A 2079 O HOH A 2208 2.12 REMARK 500 O4 SO4 A 1277 O HOH A 2203 2.19 REMARK 500 O HOH A 2169 O HOH A 2170 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 174 CE1 PHE A 174 CZ 0.127 REMARK 500 GLN A 187 CB GLN A 187 CG -0.170 REMARK 500 GLU A 251 CB GLU A 251 CG -0.151 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 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 189 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 205 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 205 NE - CZ - NH2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 230 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 230 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES 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 LEU A 206 LEU A 207 149.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 SULPHATE (SO4): RESIDUE 8 APPEARS TO HAVE TWO REMARK 600 CONFORMATIONS. REMARK 600 DUMMY ATOMS (UNX): THESE DUMMY ATOMS REPRESENT A TRIS REMARK 600 MOLECULE WHICH IS PRESENT ON A TWO FOLD CRYSTALLOGRAPHIC REMARK 600 AXIS. ATTEMPTS TO REFINE THIS TRIS USING A DICTIONARY FILE REMARK 600 FAILED DUE TO THE FLEXIBILITY OF THE MOLECULE, SO THE REMARK 600 APPROXIMATE POSITIONS OF ATOMS WERE REFINED USING DUMMY REMARK 600 ATOMS. REMARK 600 N-ACETYL-D-GLUCOSAMINE (NAG): TWO NAG RESIDUES ATTACHED TO REMARK 600 ASN 151 WITH A BETA 1-4 LINK BETWEEN THE NAG RESIDUES. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG B 2 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: PROVIDED BY DEPOSITOR REMARK 900 REMARK 900 RELATED ENTRIES 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: 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: 2X2M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN WITH REMARK 900 INHIBITOR REMARK 900 RELATED ID: 2IVS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NON-PHOSPHORYLATED RET TYROSINE KINASE DOMAIN REMARK 900 RELATED ID: 1XPD RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF RET_HUMAN 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 900 RELATED ID: 2X2L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN WITH REMARK 900 INHIBITOR DBREF 2X2U A 29 270 UNP P07949 RET_HUMAN 29 270 SEQADV 2X2U ARG A 87 UNP P07949 CYS 87 ENGINEERED MUTATION SEQADV 2X2U GLN A 98 UNP P07949 ASN 98 ENGINEERED MUTATION SEQADV 2X2U GLN A 199 UNP P07949 ASN 199 ENGINEERED MUTATION SEQADV 2X2U SER A 216 UNP P07949 CYS 216 ENGINEERED MUTATION SEQADV 2X2U GLU A 271 UNP P07949 EXPRESSION TAG SEQADV 2X2U PHE A 272 UNP P07949 EXPRESSION TAG SEQADV 2X2U GLU A 273 UNP P07949 EXPRESSION TAG SEQADV 2X2U ASN A 274 UNP P07949 EXPRESSION TAG SEQRES 1 A 246 LEU TYR PHE SER ARG ASP ALA TYR TRP GLU LYS LEU TYR SEQRES 2 A 246 VAL ASP GLN ALA ALA GLY THR PRO LEU LEU TYR VAL HIS SEQRES 3 A 246 ALA LEU ARG ASP ALA PRO GLU GLU VAL PRO SER PHE ARG SEQRES 4 A 246 LEU GLY GLN HIS LEU TYR GLY THR TYR ARG THR ARG LEU SEQRES 5 A 246 HIS GLU ASN ASN TRP ILE ARG ILE GLN GLU ASP THR GLY SEQRES 6 A 246 LEU LEU TYR LEU GLN ARG SER LEU ASP HIS SER SER TRP SEQRES 7 A 246 GLU LYS LEU SER VAL ARG ASN ARG GLY PHE PRO LEU LEU SEQRES 8 A 246 THR VAL TYR LEU LYS VAL PHE LEU SER PRO THR SER LEU SEQRES 9 A 246 ARG GLU GLY GLU CYS GLN TRP PRO GLY CYS ALA ARG VAL SEQRES 10 A 246 TYR PHE SER PHE PHE ASN THR SER PHE PRO ALA CYS SER SEQRES 11 A 246 SER LEU LYS PRO ARG GLU LEU CYS PHE PRO GLU THR ARG SEQRES 12 A 246 PRO SER PHE ARG ILE ARG GLU ASN ARG PRO PRO GLY THR SEQRES 13 A 246 PHE HIS GLN PHE ARG LEU LEU PRO VAL GLN PHE LEU CYS SEQRES 14 A 246 PRO GLN ILE SER VAL ALA TYR ARG LEU LEU GLU GLY GLU SEQRES 15 A 246 GLY LEU PRO PHE ARG SER ALA PRO ASP SER LEU GLU VAL SEQRES 16 A 246 SER THR ARG TRP ALA LEU ASP ARG GLU GLN ARG GLU LYS SEQRES 17 A 246 TYR GLU LEU VAL ALA VAL CYS THR VAL HIS ALA GLY ALA SEQRES 18 A 246 ARG GLU GLU VAL VAL MET VAL PRO PHE PRO VAL THR VAL SEQRES 19 A 246 TYR ASP GLU ASP ASP SER ALA PRO GLU PHE GLU ASN MODRES 2X2U ASN A 151 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 11 HET UNX A1283 1 HET UNX A1284 1 HET UNX A1285 1 HET UNX A1286 1 HET UNX A1287 1 HET UNX A1288 1 HET UNX A1289 1 HET UNX A1290 1 HET UNX A1291 1 HET UNX A1292 1 HET UNX A1297 1 HET SO4 A1275 5 HET SO4 A1276 5 HET SO4 A1277 5 HET SO4 A1278 5 HET SO4 A1279 5 HET SO4 A1280 5 HET SO4 A1281 5 HET SO4 A1282 10 HET BU1 A1293 6 HET BU1 A1294 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM UNX UNKNOWN ATOM OR ION HETNAM SO4 SULFATE ION HETNAM BU1 1,4-BUTANEDIOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 UNX 11(X) FORMUL 14 SO4 8(O4 S 2-) FORMUL 22 BU1 2(C4 H10 O2) FORMUL 24 HOH *216(H2 O) HELIX 1 1 THR A 75 ARG A 77 5 3 HELIX 2 2 HIS A 103 ARG A 112 1 10 HELIX 3 3 CYS A 157 SER A 159 5 3 HELIX 4 4 PRO A 162 CYS A 166 1 5 HELIX 5 5 LEU A 191 CYS A 197 1 7 SHEET 1 AA 2 TYR A 30 PHE A 31 0 SHEET 2 AA 2 ALA A 55 LEU A 56 -1 O LEU A 56 N TYR A 30 SHEET 1 AB 4 ALA A 35 TYR A 41 0 SHEET 2 AB 4 CYS A 142 PHE A 150 1 O ARG A 144 N TYR A 36 SHEET 3 AB 4 THR A 120 PHE A 126 -1 O VAL A 121 N PHE A 147 SHEET 4 AB 4 ARG A 67 LEU A 68 -1 O ARG A 67 N PHE A 126 SHEET 1 AC 3 PRO A 49 TYR A 52 0 SHEET 2 AC 3 LEU A 94 LEU A 97 -1 O LEU A 95 N LEU A 50 SHEET 3 AC 3 ILE A 86 ILE A 88 -1 O ARG A 87 N TYR A 96 SHEET 1 AD 2 HIS A 71 TYR A 73 0 SHEET 2 AD 2 ARG A 79 GLU A 82 -1 N LEU A 80 O LEU A 72 SHEET 1 AE 4 PHE A 174 ARG A 177 0 SHEET 2 AE 4 GLU A 252 TYR A 263 1 O PRO A 259 N PHE A 174 SHEET 3 AE 4 LYS A 236 VAL A 245 -1 O TYR A 237 N VAL A 260 SHEET 4 AE 4 VAL A 202 LEU A 207 -1 O ALA A 203 N THR A 244 SHEET 1 AF 3 THR A 184 GLN A 187 0 SHEET 2 AF 3 GLU A 222 THR A 225 -1 O VAL A 223 N PHE A 185 SHEET 3 AF 3 PHE A 214 ARG A 215 -1 O ARG A 215 N SER A 224 SSBOND 1 CYS A 137 CYS A 142 1555 1555 2.05 SSBOND 2 CYS A 157 CYS A 197 1555 1555 2.13 SSBOND 3 CYS A 166 CYS A 243 1555 1555 2.02 LINK ND2 ASN A 151 C1 NAG B 1 1555 1555 1.47 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.46 CISPEP 1 TRP A 139 PRO A 140 0 9.11 CRYST1 86.074 86.074 110.475 90.00 90.00 90.00 P 43 21 2 8 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 0.011618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009052 0.00000