10 20 30 40 50 60 70 80 5I6U - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/TRANSFERASE INHIBITOR 16-FEB-16 5I6U
TITLE THE CRYSTAL STRUCTURE OF PI3KDELTA WITH COMPOUND 32
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC COMPND 3 SUBUNIT DELTA ISOFORM; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 106-1043; COMPND 6 SYNONYM: PTDINS-3-KINASE SUBUNIT DELTA,PHOSPHATIDYLINOSITOL 4,5- COMPND 7 BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA,P110DELTA; COMPND 8 EC: 2.7.1.153; COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PIK3CD; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108
KEYWDS KINASE, P110, KINASE INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.R.SOMOZA,A.G.VILLASENOR
REVDAT 1 22-FEB-17 5I6U 0
JRNL AUTH J.R.SOMOZA,A.G.VILLASENOR JRNL TITL THE CRYSTAL STRUCTURE OF PI3KDELTA WITH COMPOUND 32 JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 68 352 2012 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 22505256 REMARK 1 DOI 10.1107/S0907444912001308 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.D.ADAMS,P.V.AFONINE,G.BUNKOCZI,V.B.CHEN,I.W.DAVIS, REMARK 1 AUTH 2 N.ECHOLS,J.J.HEADD,L.W.HUNG,G.J.KAPRAL,R.W.GROSSE-KUNSTLEVE, REMARK 1 AUTH 3 A.J.MCCOY,N.W.MORIARTY,R.OEFFNER,R.J.READ,D.C.RICHARDSON, REMARK 1 AUTH 4 J.S.RICHARDSON,T.C.TERWILLIGER,P.H.ZWART REMARK 1 TITL PHENIX: A COMPREHENSIVE PYTHON-BASED SYSTEM FOR REMARK 1 TITL 2 MACROMOLECULAR STRUCTURE SOLUTION. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 66 213 2010 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 20124702 REMARK 1 DOI 10.1107/S0907444909052925
REMARK 2 REMARK 2 RESOLUTION. 2.84 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.341 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 24139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.281 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 29.6640 - 6.8229 0.99 1702 154 0.1998 0.2620 REMARK 3 2 6.8229 - 5.4264 0.99 1637 148 0.2380 0.2660 REMARK 3 3 5.4264 - 4.7436 0.99 1632 147 0.1840 0.2793 REMARK 3 4 4.7436 - 4.3113 0.99 1605 144 0.1815 0.2779 REMARK 3 5 4.3113 - 4.0031 0.99 1629 148 0.1883 0.2805 REMARK 3 6 4.0031 - 3.7676 0.99 1619 145 0.1951 0.3286 REMARK 3 7 3.7676 - 3.5792 0.99 1593 144 0.2159 0.3328 REMARK 3 8 3.5792 - 3.4236 0.99 1599 144 0.2179 0.3590 REMARK 3 9 3.4236 - 3.2920 0.99 1639 148 0.2329 0.3230 REMARK 3 10 3.2920 - 3.1786 0.99 1588 144 0.2340 0.3451 REMARK 3 11 3.1786 - 3.0793 0.99 1586 143 0.2374 0.3765 REMARK 3 12 3.0793 - 2.9913 0.95 1552 141 0.2578 0.3800 REMARK 3 13 2.9913 - 2.9127 0.92 1461 131 0.2973 0.3948 REMARK 3 14 2.9127 - 2.8420 0.79 1298 118 0.2889 0.4155 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.765 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.77 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 : 0.014 6766 REMARK 3 ANGLE : 1.727 9126 REMARK 3 CHIRALITY : 0.063 1004 REMARK 3 PLANARITY : 0.008 1152 REMARK 3 DIHEDRAL : 17.373 2512 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5I6U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218292.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24148 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.840 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 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: EPMR REMARK 200 STARTING MODEL: 4XE0 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION PROTOCOL CAN BE FOUND REMARK 280 IN SOMOZA ET AL. (2015). JBC 290, PP. 8439-8446., VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293.0K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 71.41800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.46300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.41800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.46300 REMARK 290 SMTRY3 4 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 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 GLY A 106 REMARK 465 ASP A 107 REMARK 465 ARG A 108 REMARK 465 SER A 174 REMARK 465 ALA A 175 REMARK 465 ARG A 176 REMARK 465 GLY A 177 REMARK 465 TRP A 178 REMARK 465 ARG A 179 REMARK 465 ALA A 180 REMARK 465 GLY A 181 REMARK 465 LEU A 182 REMARK 465 LEU A 183 REMARK 465 ARG A 184 REMARK 465 VAL A 185 REMARK 465 SER A 186 REMARK 465 PRO A 231 REMARK 465 LEU A 232 REMARK 465 VAL A 233 REMARK 465 GLU A 234 REMARK 465 PRO A 292 REMARK 465 ALA A 293 REMARK 465 PRO A 294 REMARK 465 GLN A 295 REMARK 465 VAL A 296 REMARK 465 GLN A 297 REMARK 465 LYS A 298 REMARK 465 PRO A 299 REMARK 465 ARG A 300 REMARK 465 ALA A 301 REMARK 465 LYS A 302 REMARK 465 PRO A 303 REMARK 465 PRO A 304 REMARK 465 PRO A 305 REMARK 465 ILE A 306 REMARK 465 PRO A 307 REMARK 465 ALA A 308 REMARK 465 LYS A 309 REMARK 465 LYS A 310 REMARK 465 PRO A 311 REMARK 465 SER A 312 REMARK 465 SER A 313 REMARK 465 VAL A 314 REMARK 465 SER A 315 REMARK 465 VAL A 333 REMARK 465 ASN A 334 REMARK 465 ALA A 335 REMARK 465 ASP A 336 REMARK 465 GLU A 337 REMARK 465 ARG A 338 REMARK 465 GLU A 399 REMARK 465 LYS A 400 REMARK 465 ALA A 401 REMARK 465 LYS A 402 REMARK 465 LYS A 403 REMARK 465 ALA A 404 REMARK 465 ARG A 405 REMARK 465 SER A 406 REMARK 465 THR A 407 REMARK 465 LYS A 408 REMARK 465 LYS A 409 REMARK 465 LYS A 410 REMARK 465 SER A 411 REMARK 465 LYS A 412 REMARK 465 LYS A 413 REMARK 465 ALA A 414 REMARK 465 PRO A 446 REMARK 465 ASP A 447 REMARK 465 GLU A 448 REMARK 465 LYS A 449 REMARK 465 GLY A 450 REMARK 465 GLU A 451 REMARK 465 PRO A 480 REMARK 465 HIS A 481 REMARK 465 GLY A 495 REMARK 465 ARG A 496 REMARK 465 HIS A 497 REMARK 465 GLY A 498 REMARK 465 GLU A 499 REMARK 465 ARG A 500 REMARK 465 GLY A 501 REMARK 465 ARG A 502 REMARK 465 ILE A 503 REMARK 465 THR A 504 REMARK 465 GLU A 505 REMARK 465 GLU A 506 REMARK 465 GLU A 507 REMARK 465 GLN A 508 REMARK 465 LEU A 509 REMARK 465 GLN A 510 REMARK 465 ARG A 518 REMARK 465 GLY A 519 REMARK 465 SER A 520 REMARK 465 GLY A 521 REMARK 465 ALA A 846 REMARK 465 THR A 847 REMARK 465 LYS A 920 REMARK 465 THR A 921 REMARK 465 LYS A 922 REMARK 465 PHE A 923 REMARK 465 GLY A 924 REMARK 465 ILE A 925 REMARK 465 ASN A 926 REMARK 465 ARG A 927 REMARK 465 GLU A 928 REMARK 465 TRP A 1027 REMARK 465 LYS A 1028 REMARK 465 THR A 1029 REMARK 465 LYS A 1030 REMARK 465 VAL A 1031 REMARK 465 ASN A 1032 REMARK 465 TRP A 1033 REMARK 465 LEU A 1034 REMARK 465 ALA A 1035 REMARK 465 HIS A 1036 REMARK 465 ASN A 1037 REMARK 465 VAL A 1038 REMARK 465 SER A 1039 REMARK 465 LYS A 1040 REMARK 465 ASP A 1041 REMARK 465 ASN A 1042 REMARK 465 ARG A 1043 REMARK 465 GLN A 1044
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 LEU A 452 CG CD1 CD2
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 NH1 ARG A 957 OD1 ASN A 1020 2.12 REMARK 500 OD1 ASP A 383 ND1 HIS A 558 2.13 REMARK 500 OG1 THR A 604 OE1 GLU A 607 2.16 REMARK 500 OH TYR A 887 NH2 ARG A 929 2.17 REMARK 500 NH1 ARG A 517 OE1 GLU A 544 2.18 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 LEU A 190 CA - CB - CG ANGL. DEV. = 16.0 DEGREES REMARK 500 LEU A 266 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 LEU A 488 CA - CB - CG ANGL. DEV. = -16.2 DEGREES REMARK 500 LEU A 488 CB - CG - CD2 ANGL. DEV. = -12.4 DEGREES REMARK 500 LEU A 515 CA - CB - CG ANGL. DEV. = 15.3 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 ILE A 113 -70.14 -48.85 REMARK 500 ASN A 114 -37.06 -38.24 REMARK 500 PHE A 128 -73.61 -75.97 REMARK 500 ASP A 129 -70.28 -27.90 REMARK 500 SER A 130 -1.07 -34.43 REMARK 500 ARG A 132 46.50 37.99 REMARK 500 LEU A 157 136.98 -31.77 REMARK 500 LYS A 195 -155.16 -108.20 REMARK 500 ALA A 225 2.12 -61.78 REMARK 500 ASN A 253 -39.79 -21.84 REMARK 500 PRO A 255 -178.00 -61.88 REMARK 500 SER A 264 -56.00 165.03 REMARK 500 SER A 268 -8.89 -49.20 REMARK 500 GLN A 289 29.21 -72.32 REMARK 500 LEU A 319 107.69 -55.82 REMARK 500 ILE A 328 -89.43 -130.74 REMARK 500 ARG A 331 70.15 -152.25 REMARK 500 ASN A 351 -74.91 -59.40 REMARK 500 CYS A 355 -150.89 -79.02 REMARK 500 SER A 359 -153.70 -66.97 REMARK 500 CYS A 366 80.67 -33.61 REMARK 500 GLU A 368 97.46 -12.22 REMARK 500 LYS A 372 27.39 12.38 REMARK 500 CYS A 382 8.83 -64.10 REMARK 500 ASP A 383 17.03 -140.00 REMARK 500 MET A 387 -112.83 -80.36 REMARK 500 ALA A 388 117.59 60.99 REMARK 500 TYR A 395 -162.73 -125.82 REMARK 500 VAL A 397 -158.79 -157.31 REMARK 500 ILE A 418 -65.27 -124.18 REMARK 500 ALA A 421 133.72 -171.63 REMARK 500 ASP A 427 143.21 -31.83 REMARK 500 ASP A 430 -26.90 102.24 REMARK 500 LEU A 432 151.06 -46.21 REMARK 500 ASN A 464 19.43 -69.84 REMARK 500 THR A 465 -60.98 0.82 REMARK 500 VAL A 478 7.93 -162.77 REMARK 500 TYR A 484 -167.30 -77.70 REMARK 500 ALA A 487 -166.97 -58.81 REMARK 500 GLU A 493 -61.00 -19.01 REMARK 500 GLU A 513 28.53 -69.93 REMARK 500 LEU A 515 -67.78 -130.81 REMARK 500 GLU A 516 -175.43 -68.99 REMARK 500 GLU A 525 35.95 -93.51 REMARK 500 MET A 534 53.26 -101.82 REMARK 500 PHE A 542 41.55 -153.61 REMARK 500 GLU A 544 40.53 -75.85 REMARK 500 SER A 586 31.23 -69.89 REMARK 500 PHE A 587 55.21 -144.39 REMARK 500 ASP A 589 110.81 -24.99 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. 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 SER A 444 VAL A 445 145.43 REMARK 500 LYS A 490 ILE A 491 143.11 REMARK 500 ILE A 514 LEU A 515 -144.25 REMARK 500 GLU A 516 ARG A 517 147.17 REMARK 500 LEU A 523 TYR A 524 141.81 REMARK 500 GLU A 525 HIS A 526 145.72 REMARK 500 GLU A 537 VAL A 538 149.15 REMARK 500 HIS A 914 PHE A 915 -145.03 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 68R A 1101
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5I4U RELATED DB: PDB
DBREF 5I6U A 106 1044 UNP O35904 PK3CD_MOUSE 106 1043
SEQADV 5I6U GLN A 508 UNP O35904 INSERTION
SEQRES 1 A 939 GLY ASP ARG VAL LYS LYS LEU ILE ASN SER GLN ILE SER SEQRES 2 A 939 LEU LEU ILE GLY LYS GLY LEU HIS GLU PHE ASP SER LEU SEQRES 3 A 939 ARG ASP PRO GLU VAL ASN ASP PHE ARG THR LYS MET ARG SEQRES 4 A 939 GLN PHE CYS GLU GLU ALA ALA ALA HIS ARG GLN GLN LEU SEQRES 5 A 939 GLY TRP VAL GLU TRP LEU GLN TYR SER PHE PRO LEU GLN SEQRES 6 A 939 LEU GLU PRO SER ALA ARG GLY TRP ARG ALA GLY LEU LEU SEQRES 7 A 939 ARG VAL SER ASN ARG ALA LEU LEU VAL ASN VAL LYS PHE SEQRES 8 A 939 GLU GLY SER GLU GLU SER PHE THR PHE GLN VAL SER THR SEQRES 9 A 939 LYS ASP MET PRO LEU ALA LEU MET ALA CYS ALA LEU ARG SEQRES 10 A 939 LYS LYS ALA THR VAL PHE ARG GLN PRO LEU VAL GLU GLN SEQRES 11 A 939 PRO GLU GLU TYR ALA LEU GLN VAL ASN GLY ARG HIS GLU SEQRES 12 A 939 TYR LEU TYR GLY ASN TYR PRO LEU CYS HIS PHE GLN TYR SEQRES 13 A 939 ILE CYS SER CYS LEU HIS SER GLY LEU THR PRO HIS LEU SEQRES 14 A 939 THR MET VAL HIS SER SER SER ILE LEU ALA MET ARG ASP SEQRES 15 A 939 GLU GLN SER ASN PRO ALA PRO GLN VAL GLN LYS PRO ARG SEQRES 16 A 939 ALA LYS PRO PRO PRO ILE PRO ALA LYS LYS PRO SER SER SEQRES 17 A 939 VAL SER LEU TRP SER LEU GLU GLN PRO PHE SER ILE GLU SEQRES 18 A 939 LEU ILE GLU GLY ARG LYS VAL ASN ALA ASP GLU ARG MET SEQRES 19 A 939 LYS LEU VAL VAL GLN ALA GLY LEU PHE HIS GLY ASN GLU SEQRES 20 A 939 MET LEU CYS LYS THR VAL SER SER SER GLU VAL ASN VAL SEQRES 21 A 939 CYS SER GLU PRO VAL TRP LYS GLN ARG LEU GLU PHE ASP SEQRES 22 A 939 ILE SER VAL CYS ASP LEU PRO ARG MET ALA ARG LEU CYS SEQRES 23 A 939 PHE ALA LEU TYR ALA VAL VAL GLU LYS ALA LYS LYS ALA SEQRES 24 A 939 ARG SER THR LYS LYS LYS SER LYS LYS ALA ASP CYS PRO SEQRES 25 A 939 ILE ALA TRP ALA ASN LEU MET LEU PHE ASP TYR LYS ASP SEQRES 26 A 939 GLN LEU LYS THR GLY GLU ARG CYS LEU TYR MET TRP PRO SEQRES 27 A 939 SER VAL PRO ASP GLU LYS GLY GLU LEU LEU ASN PRO ALA SEQRES 28 A 939 GLY THR VAL ARG GLY ASN PRO ASN THR GLU SER ALA ALA SEQRES 29 A 939 ALA LEU VAL ILE TYR LEU PRO GLU VAL ALA PRO HIS PRO SEQRES 30 A 939 VAL TYR PHE PRO ALA LEU GLU LYS ILE LEU GLU LEU GLY SEQRES 31 A 939 ARG HIS GLY GLU ARG GLY ARG ILE THR GLU GLU GLU GLN SEQRES 32 A 939 LEU GLN LEU ARG GLU ILE LEU GLU ARG ARG GLY SER GLY SEQRES 33 A 939 GLU LEU TYR GLU HIS GLU LYS ASP LEU VAL TRP LYS MET SEQRES 34 A 939 ARG HIS GLU VAL GLN GLU HIS PHE PRO GLU ALA LEU ALA SEQRES 35 A 939 ARG LEU LEU LEU VAL THR LYS TRP ASN LYS HIS GLU ASP SEQRES 36 A 939 VAL ALA GLN MET LEU TYR LEU LEU CYS SER TRP PRO GLU SEQRES 37 A 939 LEU PRO VAL LEU SER ALA LEU GLU LEU LEU ASP PHE SER SEQRES 38 A 939 PHE PRO ASP CYS TYR VAL GLY SER PHE ALA ILE LYS SER SEQRES 39 A 939 LEU ARG LYS LEU THR ASP ASP GLU LEU PHE GLN TYR LEU SEQRES 40 A 939 LEU GLN LEU VAL GLN VAL LEU LYS TYR GLU SER TYR LEU SEQRES 41 A 939 ASP CYS GLU LEU THR LYS PHE LEU LEU GLY ARG ALA LEU SEQRES 42 A 939 ALA ASN ARG LYS ILE GLY HIS PHE LEU PHE TRP HIS LEU SEQRES 43 A 939 ARG SER GLU MET HIS VAL PRO SER VAL ALA LEU ARG PHE SEQRES 44 A 939 GLY LEU ILE MET GLU ALA TYR CYS ARG GLY SER THR HIS SEQRES 45 A 939 HIS MET LYS VAL LEU MET LYS GLN GLY GLU ALA LEU SER SEQRES 46 A 939 LYS LEU LYS ALA LEU ASN ASP PHE VAL LYS VAL SER SER SEQRES 47 A 939 GLN LYS THR THR LYS PRO GLN THR LYS GLU MET MET HIS SEQRES 48 A 939 MET CYS MET ARG GLN GLU THR TYR MET GLU ALA LEU SER SEQRES 49 A 939 HIS LEU GLN SER PRO LEU ASP PRO SER THR LEU LEU GLU SEQRES 50 A 939 GLU VAL CYS VAL GLU GLN CYS THR PHE MET ASP SER LYS SEQRES 51 A 939 MET LYS PRO LEU TRP ILE MET TYR SER SER GLU GLU ALA SEQRES 52 A 939 GLY SER ALA GLY ASN VAL GLY ILE ILE PHE LYS ASN GLY SEQRES 53 A 939 ASP ASP LEU ARG GLN ASP MET LEU THR LEU GLN MET ILE SEQRES 54 A 939 GLN LEU MET ASP VAL LEU TRP LYS GLN GLU GLY LEU ASP SEQRES 55 A 939 LEU ARG MET THR PRO TYR GLY CYS LEU PRO THR GLY ASP SEQRES 56 A 939 ARG THR GLY LEU ILE GLU VAL VAL LEU HIS SER ASP THR SEQRES 57 A 939 ILE ALA ASN ILE GLN LEU ASN LYS SER ASN MET ALA ALA SEQRES 58 A 939 THR ALA ALA PHE ASN LYS ASP ALA LEU LEU ASN TRP LEU SEQRES 59 A 939 LYS SER LYS ASN PRO GLY GLU ALA LEU ASP ARG ALA ILE SEQRES 60 A 939 GLU GLU PHE THR LEU SER CYS ALA GLY TYR CYS VAL ALA SEQRES 61 A 939 THR TYR VAL LEU GLY ILE GLY ASP ARG HIS SER ASP ASN SEQRES 62 A 939 ILE MET ILE ARG GLU SER GLY GLN LEU PHE HIS ILE ASP SEQRES 63 A 939 PHE GLY HIS PHE LEU GLY ASN PHE LYS THR LYS PHE GLY SEQRES 64 A 939 ILE ASN ARG GLU ARG VAL PRO PHE ILE LEU THR TYR ASP SEQRES 65 A 939 PHE VAL HIS VAL ILE GLN GLN GLY LYS THR ASN ASN SER SEQRES 66 A 939 GLU LYS PHE GLU ARG PHE ARG GLY TYR CYS GLU ARG ALA SEQRES 67 A 939 TYR THR ILE LEU ARG ARG HIS GLY LEU LEU PHE LEU HIS SEQRES 68 A 939 LEU PHE ALA LEU MET ARG ALA ALA GLY LEU PRO GLU LEU SEQRES 69 A 939 SER CYS SER LYS ASP ILE GLN TYR LEU LYS ASP SER LEU SEQRES 70 A 939 ALA LEU GLY LYS THR GLU GLU GLU ALA LEU LYS HIS PHE SEQRES 71 A 939 ARG VAL LYS PHE ASN GLU ALA LEU ARG GLU SER TRP LYS SEQRES 72 A 939 THR LYS VAL ASN TRP LEU ALA HIS ASN VAL SER LYS ASP SEQRES 73 A 939 ASN ARG GLN
HET 68R A1101 35
HETNAM 68R 2-[(1S)-1-({6-AMINO-5-[(1H-PYRAZOL-4-YL) HETNAM 2 68R ETHYNYL]PYRIMIDIN-4-YL}AMINO)ETHYL]-5-CHLORO-3- HETNAM 3 68R PHENYLQUINAZOLIN-4(3H)-ONE
FORMUL 2 68R C25 H19 CL N8 O
HELIX 1 AA1 VAL A 109 GLY A 122 1 14 HELIX 2 AA2 LEU A 125 SER A 130 1 6 HELIX 3 AA3 ASP A 133 GLN A 155 1 23 HELIX 4 AA4 GLY A 158 PHE A 167 1 10 HELIX 5 AA5 MET A 212 LYS A 223 1 12 HELIX 6 AA6 GLN A 235 GLU A 237 5 3 HELIX 7 AA7 TYR A 261 LEU A 266 1 6 HELIX 8 AA8 SER A 279 GLN A 289 1 11 HELIX 9 AA9 GLU A 527 MET A 534 1 8 HELIX 10 AB1 MET A 534 PHE A 542 1 9 HELIX 11 AB2 ALA A 545 LEU A 551 1 7 HELIX 12 AB3 LYS A 557 CYS A 569 1 13 HELIX 13 AB4 PRO A 575 LEU A 583 1 9 HELIX 14 AB5 ASP A 589 ARG A 601 1 13 HELIX 15 AB6 THR A 604 LEU A 619 1 16 HELIX 16 AB7 CYS A 627 ASN A 640 1 14 HELIX 17 AB8 ASN A 640 SER A 653 1 14 HELIX 18 AB9 VAL A 660 GLY A 674 1 15 HELIX 19 AC1 SER A 675 THR A 706 1 32 HELIX 20 AC2 THR A 707 ARG A 720 1 14 HELIX 21 AC3 GLN A 721 SER A 729 1 9 HELIX 22 AC4 VAL A 746 CYS A 749 5 4 HELIX 23 AC5 SER A 765 ASN A 773 5 9 HELIX 24 AC6 LEU A 784 GLN A 803 1 20 HELIX 25 AC7 ILE A 834 LEU A 839 1 6 HELIX 26 AC8 PHE A 850 LYS A 852 5 3 HELIX 27 AC9 ASP A 853 ASN A 863 1 11 HELIX 28 AD1 PRO A 864 GLU A 866 5 3 HELIX 29 AD2 ALA A 867 GLY A 890 1 24 HELIX 30 AD3 HIS A 895 ASP A 897 5 3 HELIX 31 AD4 THR A 935 GLN A 943 1 9 HELIX 32 AD5 ASN A 949 ARG A 969 1 21 HELIX 33 AD6 HIS A 970 ARG A 982 1 13 HELIX 34 AD7 ALA A 983 GLY A 985 5 3 HELIX 35 AD8 ILE A 995 ALA A 1003 1 9 HELIX 36 AD9 THR A 1007 ARG A 1024 1 18
SHEET 1 AA1 2 ALA A 189 LEU A 191 0 SHEET 2 AA1 2 GLN A 206 SER A 208 -1 O VAL A 207 N LEU A 190 SHEET 1 AA2 4 ASN A 193 VAL A 194 0 SHEET 2 AA2 4 HIS A 273 HIS A 278 1 O LEU A 274 N ASN A 193 SHEET 3 AA2 4 TYR A 239 VAL A 243 -1 N ALA A 240 O VAL A 277 SHEET 4 AA2 4 TYR A 249 LEU A 250 -1 O LEU A 250 N LEU A 241 SHEET 1 AA3 4 ARG A 374 SER A 380 0 SHEET 2 AA3 4 PRO A 322 GLY A 330 -1 N PHE A 323 O ILE A 379 SHEET 3 AA3 4 ALA A 470 LEU A 475 -1 O TYR A 474 N GLU A 326 SHEET 4 AA3 4 GLY A 435 TYR A 440 -1 N LEU A 439 O LEU A 471 SHEET 1 AA4 5 VAL A 363 ASN A 364 0 SHEET 2 AA4 5 LYS A 340 PHE A 348 -1 N LEU A 341 O VAL A 363 SHEET 3 AA4 5 ARG A 389 TYR A 395 -1 O ARG A 389 N PHE A 348 SHEET 4 AA4 5 ALA A 419 MET A 424 -1 O LEU A 423 N LEU A 390 SHEET 5 AA4 5 TRP A 442 PRO A 443 -1 O TRP A 442 N TRP A 420 SHEET 1 AA5 2 LEU A 731 SER A 733 0 SHEET 2 AA5 2 ASP A 736 LEU A 741 -1 O LEU A 741 N LEU A 731 SHEET 1 AA6 3 GLU A 743 VAL A 744 0 SHEET 2 AA6 3 LEU A 759 SER A 764 -1 O SER A 764 N GLU A 743 SHEET 3 AA6 3 THR A 750 PHE A 751 -1 N THR A 750 O TRP A 760 SHEET 1 AA7 5 GLU A 743 VAL A 744 0 SHEET 2 AA7 5 LEU A 759 SER A 764 -1 O SER A 764 N GLU A 743 SHEET 3 AA7 5 GLY A 775 ASN A 780 -1 O ILE A 776 N ILE A 761 SHEET 4 AA7 5 THR A 822 GLU A 826 -1 O ILE A 825 N ILE A 777 SHEET 5 AA7 5 CYS A 815 GLY A 819 -1 N LEU A 816 O LEU A 824 SHEET 1 AA8 3 SER A 831 THR A 833 0 SHEET 2 AA8 3 ILE A 899 ARG A 902 -1 O ILE A 901 N ASP A 832 SHEET 3 AA8 3 LEU A 907 HIS A 909 -1 O PHE A 908 N MET A 900
CISPEP 1 SER A 367 GLU A 368 0 4.84 CISPEP 2 THR A 434 GLY A 435 0 -3.02
SITE 1 AC1 18 THR A 750 PHE A 751 MET A 752 PRO A 758 SITE 2 AC1 18 LEU A 759 TRP A 760 ILE A 777 LYS A 779 SITE 3 AC1 18 ASP A 787 ILE A 825 GLU A 826 VAL A 827 SITE 4 AC1 18 VAL A 828 SER A 831 ASP A 832 MET A 900 SITE 5 AC1 18 ILE A 910 ASP A 911
CRYST1 142.836 64.926 117.058 90.00 103.17 90.00 C 1 2 1 4
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 0.007001 0.000000 0.001638 0.00000
SCALE2 0.000000 0.015402 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008774 0.00000