PDB Short entry for 3GVU HEADER TRANSFERASE 31-MAR-09 3GVU TITLE THE CRYSTAL STRUCTURE OF HUMAN ABL2 IN COMPLEX WITH GLEEVEC COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE ABL2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEIN KINASE; COMPND 5 SYNONYM: ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 2, ABELSON- COMPND 6 RELATED GENE PROTEIN, TYROSINE KINASE ARG; COMPND 7 EC: 2.7.10.2; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ABL2; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HIGH5 INSECT CELL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS TYROSINE KINASE, ABL, ABELSON MURINE LEUKEMIA VIRAL ONCOGENE, ATP- KEYWDS 2 BINDING, CELL ADHESION, CYTOSKELETON, KINASE, LIPOPROTEIN, KEYWDS 3 MAGNESIUM, MANGANESE, METAL-BINDING, MYRISTATE, NUCLEOTIDE-BINDING, KEYWDS 4 PHOSPHOPROTEIN, SH2 DOMAIN, SH3 DOMAIN, TRANSFERASE, TYROSINE- KEYWDS 5 PROTEIN KINASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 6 SGC EXPDTA X-RAY DIFFRACTION AUTHOR E.UGOCHUKWU,E.SALAH,A.BARR,P.MAHAJAN,B.SHRESTHA,P.SAVITSKY, AUTHOR 2 A.CHAIKUAD,P.FILIPPAKOPOULOS,A.ROOS,A.C.W.PIKE,F.VON DELFT, AUTHOR 3 C.BOUNTRA,C.H.ARROWSMITH,J.WEIGELT,A.EDWARDS,S.KNAPP,STRUCTURAL AUTHOR 4 GENOMICS CONSORTIUM (SGC) REVDAT 4 01-NOV-23 3GVU 1 REMARK SEQADV HETSYN REVDAT 3 01-NOV-17 3GVU 1 REMARK REVDAT 2 13-JUL-11 3GVU 1 VERSN REVDAT 1 21-APR-09 3GVU 0 JRNL AUTH E.SALAH,E.UGOCHUKWU,A.BARR,P.MAHAJAN,B.SHRESTHA,P.SAVITSKY, JRNL AUTH 2 S.KNAPP JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN ABL2 IN COMPLEX WITH GLEEVEC JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0089 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 23225 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1244 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1602 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2167 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.79000 REMARK 3 B22 (A**2) : -1.50000 REMARK 3 B33 (A**2) : -2.29000 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): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.080 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2355 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1571 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3205 ; 1.474 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3770 ; 1.034 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 280 ; 6.819 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;37.158 ;24.314 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 380 ;14.708 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;12.788 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 334 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2598 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 471 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1377 ; 4.535 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 554 ; 1.836 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2220 ; 5.869 ; 7.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 978 ; 7.789 ; 9.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 981 ; 8.238 ;11.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 269 A 367 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6308 4.1759 11.5276 REMARK 3 T TENSOR REMARK 3 T11: 0.0100 T22: 0.0280 REMARK 3 T33: 0.0338 T12: -0.0102 REMARK 3 T13: 0.0173 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 2.9376 L22: 2.0734 REMARK 3 L33: 5.3233 L12: 0.0999 REMARK 3 L13: -0.8965 L23: 1.0574 REMARK 3 S TENSOR REMARK 3 S11: -0.0402 S12: 0.2513 S13: -0.0040 REMARK 3 S21: 0.0246 S22: 0.0136 S23: 0.0428 REMARK 3 S31: -0.0063 S32: 0.0258 S33: 0.0266 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 368 A 546 REMARK 3 ORIGIN FOR THE GROUP (A): 19.9764 17.5564 34.8369 REMARK 3 T TENSOR REMARK 3 T11: 0.0850 T22: 0.0251 REMARK 3 T33: 0.0157 T12: -0.0105 REMARK 3 T13: -0.0245 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 2.4224 L22: 5.5806 REMARK 3 L33: 4.3277 L12: 1.5066 REMARK 3 L13: 0.3709 L23: 3.0241 REMARK 3 S TENSOR REMARK 3 S11: 0.0462 S12: -0.0123 S13: 0.1278 REMARK 3 S21: 0.4846 S22: 0.0238 S23: -0.0663 REMARK 3 S31: 0.2021 S32: 0.1331 S33: -0.0700 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3GVU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24490 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 43.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : 0.44500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1FPU.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.1M CITRATE, PH 5.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 43.90500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.90500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 44.23000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.72000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.23000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.72000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.90500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.23000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.72000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.90500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.23000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.72000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 1.000000 0.000000 0.000000 0.00000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 249 LIES ON A SPECIAL POSITION. 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 MET A 255 REMARK 465 GLY A 256 REMARK 465 HIS A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 HIS A 262 REMARK 465 SER A 263 REMARK 465 SER A 264 REMARK 465 GLY A 265 REMARK 465 VAL A 266 REMARK 465 ASP A 267 REMARK 465 LEU A 268 REMARK 465 LEU A 433 REMARK 465 MET A 434 REMARK 465 THR A 435 REMARK 465 HIS A 442 REMARK 465 ALA A 443 REMARK 465 GLY A 444 REMARK 465 ALA A 445 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 321 CG CD OE1 OE2 REMARK 470 ASP A 322 CG OD1 OD2 REMARK 470 ASN A 377 CG OD1 ND2 REMARK 470 GLU A 379 CG CD OE1 OE2 REMARK 470 LYS A 402 CE NZ REMARK 470 ARG A 432 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 446 CG CD CE NZ REMARK 470 ASP A 545 CG OD1 OD2 REMARK 470 SER A 546 OG 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 O HOH A 54 O HOH A 239 2.08 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 MET A 278 CB - CG - SD ANGL. DEV. = 18.8 DEGREES 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 SER A 277 -107.25 -89.92 REMARK 500 SER A 277 138.79 -174.83 REMARK 500 MET A 278 -24.10 -157.48 REMARK 500 MET A 278 -166.80 76.47 REMARK 500 LYS A 280 33.26 -83.64 REMARK 500 LYS A 291 -66.69 -109.40 REMARK 500 ARG A 408 -8.66 84.44 REMARK 500 ASP A 409 46.19 -152.70 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 GLN A 276 SER A 277 -145.70 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 STI A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE STI A 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FPU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL REMARK 900 MOLECULE INHIBITOR DBREF 3GVU A 279 546 UNP P42684 ABL2_HUMAN 279 546 SEQADV 3GVU MET A 255 UNP P42684 EXPRESSION TAG SEQADV 3GVU GLY A 256 UNP P42684 EXPRESSION TAG SEQADV 3GVU HIS A 257 UNP P42684 EXPRESSION TAG SEQADV 3GVU HIS A 258 UNP P42684 EXPRESSION TAG SEQADV 3GVU HIS A 259 UNP P42684 EXPRESSION TAG SEQADV 3GVU HIS A 260 UNP P42684 EXPRESSION TAG SEQADV 3GVU HIS A 261 UNP P42684 EXPRESSION TAG SEQADV 3GVU HIS A 262 UNP P42684 EXPRESSION TAG SEQADV 3GVU SER A 263 UNP P42684 EXPRESSION TAG SEQADV 3GVU SER A 264 UNP P42684 EXPRESSION TAG SEQADV 3GVU GLY A 265 UNP P42684 EXPRESSION TAG SEQADV 3GVU VAL A 266 UNP P42684 EXPRESSION TAG SEQADV 3GVU ASP A 267 UNP P42684 EXPRESSION TAG SEQADV 3GVU LEU A 268 UNP P42684 EXPRESSION TAG SEQADV 3GVU GLY A 269 UNP P42684 EXPRESSION TAG SEQADV 3GVU THR A 270 UNP P42684 EXPRESSION TAG SEQADV 3GVU GLU A 271 UNP P42684 EXPRESSION TAG SEQADV 3GVU ASN A 272 UNP P42684 EXPRESSION TAG SEQADV 3GVU LEU A 273 UNP P42684 EXPRESSION TAG SEQADV 3GVU TYR A 274 UNP P42684 EXPRESSION TAG SEQADV 3GVU PHE A 275 UNP P42684 EXPRESSION TAG SEQADV 3GVU GLN A 276 UNP P42684 EXPRESSION TAG SEQADV 3GVU SER A 277 UNP P42684 EXPRESSION TAG SEQADV 3GVU MET A 278 UNP P42684 EXPRESSION TAG SEQRES 1 A 292 MET GLY HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP SEQRES 2 A 292 LEU GLY THR GLU ASN LEU TYR PHE GLN SER MET ASP LYS SEQRES 3 A 292 TRP GLU MET GLU ARG THR ASP ILE THR MET LYS HIS LYS SEQRES 4 A 292 LEU GLY GLY GLY GLN TYR GLY GLU VAL TYR VAL GLY VAL SEQRES 5 A 292 TRP LYS LYS TYR SER LEU THR VAL ALA VAL LYS THR LEU SEQRES 6 A 292 LYS GLU ASP THR MET GLU VAL GLU GLU PHE LEU LYS GLU SEQRES 7 A 292 ALA ALA VAL MET LYS GLU ILE LYS HIS PRO ASN LEU VAL SEQRES 8 A 292 GLN LEU LEU GLY VAL CYS THR LEU GLU PRO PRO PHE TYR SEQRES 9 A 292 ILE VAL THR GLU TYR MET PRO TYR GLY ASN LEU LEU ASP SEQRES 10 A 292 TYR LEU ARG GLU CYS ASN ARG GLU GLU VAL THR ALA VAL SEQRES 11 A 292 VAL LEU LEU TYR MET ALA THR GLN ILE SER SER ALA MET SEQRES 12 A 292 GLU TYR LEU GLU LYS LYS ASN PHE ILE HIS ARG ASP LEU SEQRES 13 A 292 ALA ALA ARG ASN CYS LEU VAL GLY GLU ASN HIS VAL VAL SEQRES 14 A 292 LYS VAL ALA ASP PHE GLY LEU SER ARG LEU MET THR GLY SEQRES 15 A 292 ASP THR TYR THR ALA HIS ALA GLY ALA LYS PHE PRO ILE SEQRES 16 A 292 LYS TRP THR ALA PRO GLU SER LEU ALA TYR ASN THR PHE SEQRES 17 A 292 SER ILE LYS SER ASP VAL TRP ALA PHE GLY VAL LEU LEU SEQRES 18 A 292 TRP GLU ILE ALA THR TYR GLY MET SER PRO TYR PRO GLY SEQRES 19 A 292 ILE ASP LEU SER GLN VAL TYR ASP LEU LEU GLU LYS GLY SEQRES 20 A 292 TYR ARG MET GLU GLN PRO GLU GLY CYS PRO PRO LYS VAL SEQRES 21 A 292 TYR GLU LEU MET ARG ALA CYS TRP LYS TRP SER PRO ALA SEQRES 22 A 292 ASP ARG PRO SER PHE ALA GLU THR HIS GLN ALA PHE GLU SEQRES 23 A 292 THR MET PHE HIS ASP SER HET STI A1001 37 HET STI A1002 37 HETNAM STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4- HETNAM 2 STI PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE HETSYN STI STI-571; IMATINIB FORMUL 2 STI 2(C29 H31 N7 O) FORMUL 4 HOH *149(H2 O) HELIX 1 1 GLY A 269 PHE A 275 1 7 HELIX 2 2 GLU A 284 THR A 286 5 3 HELIX 3 3 GLY A 295 GLN A 298 5 4 HELIX 4 4 LYS A 309 SER A 311 5 3 HELIX 5 5 GLU A 325 LYS A 337 1 13 HELIX 6 6 ASN A 368 CYS A 376 1 9 HELIX 7 7 THR A 382 LYS A 403 1 22 HELIX 8 8 ALA A 411 ARG A 413 5 3 HELIX 9 9 GLU A 419 HIS A 421 5 3 HELIX 10 10 PRO A 448 THR A 452 5 5 HELIX 11 11 ALA A 453 ASN A 460 1 8 HELIX 12 12 SER A 463 THR A 480 1 18 HELIX 13 13 ASP A 490 SER A 492 5 3 HELIX 14 14 GLN A 493 GLY A 501 1 9 HELIX 15 15 PRO A 511 TRP A 522 1 12 HELIX 16 16 SER A 525 ARG A 529 5 5 HELIX 17 17 SER A 531 SER A 546 1 16 SHEET 1 A 5 ILE A 288 LYS A 293 0 SHEET 2 A 5 VAL A 302 TRP A 307 -1 O VAL A 304 N LYS A 291 SHEET 3 A 5 LEU A 312 LEU A 319 -1 O LEU A 312 N TRP A 307 SHEET 4 A 5 PHE A 357 GLU A 362 -1 O THR A 361 N ALA A 315 SHEET 5 A 5 LEU A 347 CYS A 351 -1 N LEU A 348 O VAL A 360 SHEET 1 B 2 CYS A 415 VAL A 417 0 SHEET 2 B 2 VAL A 423 VAL A 425 -1 O LYS A 424 N LEU A 416 CISPEP 1 PRO A 355 PRO A 356 0 1.87 SITE 1 AC1 16 HOH A 73 VAL A 302 ALA A 315 LYS A 317 SITE 2 AC1 16 GLU A 332 MET A 336 VAL A 345 ILE A 359 SITE 3 AC1 16 THR A 361 TYR A 363 MET A 364 ILE A 406 SITE 4 AC1 16 HIS A 407 ALA A 426 ASP A 427 PHE A 428 SITE 1 AC2 11 HOH A 30 HOH A 53 ALA A 383 VAL A 384 SITE 2 AC2 11 LEU A 387 TYR A 388 GLU A 508 GLY A 509 SITE 3 AC2 11 PRO A 511 VAL A 514 HOH A 549 CRYST1 88.460 99.440 87.810 90.00 90.00 90.00 C 2 2 21 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 0.011305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011388 0.00000