HEADER TRANSFERASE 21-JUL-07 2Z60 TITLE CRYSTAL STRUCTURE OF THE T315I MUTANT OF ABL KINASE BOUND WITH PPY-A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 228-511; COMPND 5 SYNONYM: P150, C-ABL, ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG COMPND 6 1, ABL KINASE; COMPND 7 EC: 2.7.10.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ABL, KINASE, MUTANT, T315I, ALTERNATIVE SPLICING, ATP-BINDING, CELL KEYWDS 2 ADHESION, CHROMOSOMAL REARRANGEMENT, CYTOPLASM, CYTOSKELETON, KEYWDS 3 LIPOPROTEIN, MAGNESIUM, MANGANESE, METAL-BINDING, MYRISTATE, KEYWDS 4 NUCLEOTIDE-BINDING, NUCLEUS, PHOSPHORYLATION, PROTO-ONCOGENE, SH2 KEYWDS 5 DOMAIN, SH3 DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.ZHOU,D.DALGARNO,X.ZHU REVDAT 4 01-NOV-23 2Z60 1 REMARK REVDAT 3 10-NOV-21 2Z60 1 REMARK SEQADV REVDAT 2 24-FEB-09 2Z60 1 VERSN REVDAT 1 18-SEP-07 2Z60 0 JRNL AUTH T.ZHOU,L.PARILLON,F.LI,Y.WANG,J.KEATS,S.LAMORE,Q.XU, JRNL AUTH 2 W.SHAKESPEARE,D.DALGARNO,X.ZHU JRNL TITL CRYSTAL STRUCTURE OF THE T315I MUTANT OF ABL KINASE JRNL REF CHEM.BIOL.DRUG DES. V. 70 171 2007 JRNL REFN ISSN 1747-0277 JRNL PMID 17718712 JRNL DOI 10.1111/J.1747-0285.2007.00556.X REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 25260 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2280 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z60 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25260 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : 0.37000 REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2GQG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4K, 0.1M TRIS, 0.2M SODIUM REMARK 280 ACETATE, PH 8.5, EVAPORATION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.64000 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASP A 276 REMARK 465 THR A 277 REMARK 465 MET A 278 REMARK 465 LYS A 512 REMARK 465 ARG A 513 REMARK 465 GLY A 514 REMARK 465 THR A 515 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 245 -77.15 -109.11 REMARK 500 ASP A 363 43.62 -151.37 REMARK 500 ASP A 381 81.83 59.64 REMARK 500 PRO A 402 96.21 -62.25 REMARK 500 ASP A 455 18.34 80.84 REMARK 500 GLU A 509 49.09 -85.11 REMARK 500 LEU A 510 -43.22 -134.60 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 P3Y A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QOH RELATED DB: PDB DBREF 2Z60 A 229 515 UNP P00520 ABL1_MOUSE 229 515 SEQADV 2Z60 GLY A 228 UNP P00520 EXPRESSION TAG SEQADV 2Z60 ILE A 315 UNP P00520 THR 315 ENGINEERED MUTATION SEQRES 1 A 288 GLY SER PRO ASN TYR ASP LYS TRP GLU MET GLU ARG THR SEQRES 2 A 288 ASP ILE THR MET LYS HIS LYS LEU GLY GLY GLY GLN TYR SEQRES 3 A 288 GLY GLU VAL TYR GLU GLY VAL TRP LYS LYS TYR SER LEU SEQRES 4 A 288 THR VAL ALA VAL LYS THR LEU LYS GLU ASP THR MET GLU SEQRES 5 A 288 VAL GLU GLU PHE LEU LYS GLU ALA ALA VAL MET LYS GLU SEQRES 6 A 288 ILE LYS HIS PRO ASN LEU VAL GLN LEU LEU GLY VAL CYS SEQRES 7 A 288 THR ARG GLU PRO PRO PHE TYR ILE ILE ILE GLU PHE MET SEQRES 8 A 288 THR TYR GLY ASN LEU LEU ASP TYR LEU ARG GLU CYS ASN SEQRES 9 A 288 ARG GLN GLU VAL SER ALA VAL VAL LEU LEU TYR MET ALA SEQRES 10 A 288 THR GLN ILE SER SER ALA MET GLU TYR LEU GLU LYS LYS SEQRES 11 A 288 ASN PHE ILE HIS ARG ASP LEU ALA ALA ARG ASN CYS LEU SEQRES 12 A 288 VAL GLY GLU ASN HIS LEU VAL LYS VAL ALA ASP PHE GLY SEQRES 13 A 288 LEU SER ARG LEU MET THR GLY ASP THR TYR THR ALA HIS SEQRES 14 A 288 ALA GLY ALA LYS PHE PRO ILE LYS TRP THR ALA PRO GLU SEQRES 15 A 288 SER LEU ALA TYR ASN LYS PHE SER ILE LYS SER ASP VAL SEQRES 16 A 288 TRP ALA PHE GLY VAL LEU LEU TRP GLU ILE ALA THR TYR SEQRES 17 A 288 GLY MET SER PRO TYR PRO GLY ILE ASP LEU SER GLN VAL SEQRES 18 A 288 TYR GLU LEU LEU GLU LYS ASP TYR ARG MET GLU ARG PRO SEQRES 19 A 288 GLU GLY CYS PRO GLU LYS VAL TYR GLU LEU MET ARG ALA SEQRES 20 A 288 CYS TRP GLN TRP ASN PRO SER ASP ARG PRO SER PHE ALA SEQRES 21 A 288 GLU ILE HIS GLN ALA PHE GLU THR MET PHE GLN GLU SER SEQRES 22 A 288 SER ILE SER ASP GLU VAL GLU LYS GLU LEU GLY LYS ARG SEQRES 23 A 288 GLY THR HET P3Y A 1 28 HETNAM P3Y 5-[3-(2-METHOXYPHENYL)-1H-PYRROLO[2,3-B]PYRIDIN-5-YL]- HETNAM 2 P3Y N,N-DIMETHYLPYRIDINE-3-CARBOXAMIDE FORMUL 2 P3Y C22 H20 N4 O2 FORMUL 3 HOH *168(H2 O) HELIX 1 1 GLU A 238 THR A 240 5 3 HELIX 2 2 GLY A 249 GLN A 252 5 4 HELIX 3 3 LYS A 263 SER A 265 5 3 HELIX 4 4 GLU A 279 ILE A 293 1 15 HELIX 5 5 ASN A 322 CYS A 330 1 9 HELIX 6 6 SER A 336 LYS A 357 1 22 HELIX 7 7 ALA A 365 ARG A 367 5 3 HELIX 8 8 GLU A 373 HIS A 375 5 3 HELIX 9 9 PRO A 402 THR A 406 5 5 HELIX 10 10 ALA A 407 ASN A 414 1 8 HELIX 11 11 SER A 417 THR A 434 1 18 HELIX 12 12 GLN A 447 LYS A 454 1 8 HELIX 13 13 PRO A 465 TRP A 476 1 12 HELIX 14 14 ASN A 479 ARG A 483 5 5 HELIX 15 15 SER A 485 GLU A 509 1 25 SHEET 1 A 5 ILE A 242 LYS A 247 0 SHEET 2 A 5 VAL A 256 TRP A 261 -1 O GLU A 258 N HIS A 246 SHEET 3 A 5 LEU A 266 THR A 272 -1 O LEU A 266 N TRP A 261 SHEET 4 A 5 TYR A 312 GLU A 316 -1 O ILE A 315 N ALA A 269 SHEET 5 A 5 LEU A 301 CYS A 305 -1 N LEU A 302 O ILE A 314 SHEET 1 B 2 PHE A 359 ILE A 360 0 SHEET 2 B 2 ARG A 386 LEU A 387 -1 O ARG A 386 N ILE A 360 SHEET 1 C 2 CYS A 369 VAL A 371 0 SHEET 2 C 2 VAL A 377 VAL A 379 -1 O LYS A 378 N LEU A 370 SHEET 1 D 2 TYR A 393 THR A 394 0 SHEET 2 D 2 LYS A 415 PHE A 416 -1 O PHE A 416 N TYR A 393 CISPEP 1 PRO A 309 PRO A 310 0 0.07 SITE 1 AC1 11 GLY A 249 TYR A 253 ALA A 269 GLU A 316 SITE 2 AC1 11 PHE A 317 MET A 318 THR A 319 GLY A 321 SITE 3 AC1 11 ASN A 322 ARG A 367 LEU A 370 CRYST1 43.035 59.280 66.520 90.00 94.88 90.00 P 1 21 1 2 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 0.023237 0.000000 0.001984 0.00000 SCALE2 0.000000 0.016869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015088 0.00000