HEADER TRANSFERASE 17-FEB-10 2X6K TITLE THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN TITLE 2 COMPLEX WITH PI-103 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOTIDYLINOSITOL 3 KINASE 59F; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HELICAL DOMAIN, KINASE DOMAIN, RESIDUES 258-949; COMPND 5 SYNONYM: GH13170P, VPS34; COMPND 6 EC: 2.7.1.137, 2.7.1.153, 2.7.1.154; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41 RIPL KEYWDS PI103, PI-103, AUTOPHAGY, TRANSFERASE, PI3K CLASS III, KEYWDS 2 PHOSPHOINOSITIDE 3-KINASE CLASS III EXPDTA X-RAY DIFFRACTION AUTHOR S.MILLER,B.TAVSHANJIAN,A.OLEKSY,O.PERISIC,B.T.HOUSEMAN,K.M.SHOKAT, AUTHOR 2 R.L.WILLIAMS REVDAT 4 20-DEC-23 2X6K 1 REMARK REVDAT 3 24-JAN-18 2X6K 1 SOURCE REVDAT 2 13-JUL-11 2X6K 1 VERSN REVDAT 1 07-APR-10 2X6K 0 JRNL AUTH S.MILLER,B.TAVSHANJIAN,A.OLEKSY,O.PERISIC,B.T.HOUSEMAN, JRNL AUTH 2 K.M.SHOKAT,R.L.WILLIAMS JRNL TITL SHAPING DEVELOPMENT OF AUTOPHAGY INHIBITORS WITH THE JRNL TITL 2 STRUCTURE OF THE LIPID KINASE VPS34. JRNL REF SCIENCE V. 327 1638 2010 JRNL REFN ISSN 0036-8075 JRNL PMID 20339072 JRNL DOI 10.1126/SCIENCE.1184429 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 25729 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1340 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) : 3.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1890 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8995 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 0 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) : 75.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.19000 REMARK 3 B22 (A**2) : 2.13000 REMARK 3 B33 (A**2) : -5.32000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.626 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.536 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 76.068 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 9286 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 12581 ; 1.660 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 2415 ;25.182 ; 7.733 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 432 ;38.739 ;23.796 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1662 ;23.104 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 54 ;16.918 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1393 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6942 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 5224 ; 0.280 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 6406 ; 0.323 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 262 ; 0.232 ; 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): 69 ; 0.720 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.468 ; 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): 5511 ; 0.894 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8941 ; 1.448 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3775 ; 0.953 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3640 ; 1.720 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 6 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 329 A 565 6 REMARK 3 1 B 329 B 565 6 REMARK 3 2 A 606 A 619 6 REMARK 3 2 B 606 B 619 6 REMARK 3 3 A 631 A 634 6 REMARK 3 3 B 631 B 634 6 REMARK 3 4 A 706 A 769 6 REMARK 3 4 B 706 B 769 6 REMARK 3 5 A 786 A 804 6 REMARK 3 5 B 786 B 804 6 REMARK 3 6 A 833 A 949 6 REMARK 3 6 B 833 B 949 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 2788 ; 0.67 ; 5.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 2788 ; 3.53 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 291 A 422 REMARK 3 RESIDUE RANGE : B 291 B 422 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3739 57.5176 46.0646 REMARK 3 T TENSOR REMARK 3 T11: 0.3735 T22: 0.4907 REMARK 3 T33: 0.2465 T12: 0.0047 REMARK 3 T13: 0.0539 T23: 0.0929 REMARK 3 L TENSOR REMARK 3 L11: 0.4533 L22: 3.1504 REMARK 3 L33: 0.2939 L12: 1.0126 REMARK 3 L13: 0.3569 L23: 0.8881 REMARK 3 S TENSOR REMARK 3 S11: 0.0417 S12: -0.2874 S13: 0.1253 REMARK 3 S21: 0.1426 S22: -0.1750 S23: 0.3924 REMARK 3 S31: 0.0640 S32: -0.1689 S33: 0.1333 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 531 A 586 REMARK 3 RESIDUE RANGE : B 531 B 586 REMARK 3 ORIGIN FOR THE GROUP (A): 25.6202 56.9494 34.8978 REMARK 3 T TENSOR REMARK 3 T11: 0.3084 T22: 0.1725 REMARK 3 T33: 0.2007 T12: -0.0616 REMARK 3 T13: 0.0895 T23: -0.0159 REMARK 3 L TENSOR REMARK 3 L11: 0.9442 L22: 4.2261 REMARK 3 L33: 1.0538 L12: 1.9345 REMARK 3 L13: 0.9075 L23: 1.8631 REMARK 3 S TENSOR REMARK 3 S11: -0.1152 S12: -0.0573 S13: -0.0469 REMARK 3 S21: -0.4510 S22: 0.0505 S23: -0.2002 REMARK 3 S31: -0.1689 S32: 0.0307 S33: 0.0646 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 587 A 748 REMARK 3 RESIDUE RANGE : B 587 B 748 REMARK 3 ORIGIN FOR THE GROUP (A): 33.4380 57.8580 28.0252 REMARK 3 T TENSOR REMARK 3 T11: 0.2089 T22: 0.2184 REMARK 3 T33: 0.2052 T12: 0.0517 REMARK 3 T13: 0.0716 T23: 0.0567 REMARK 3 L TENSOR REMARK 3 L11: 0.6079 L22: 1.3526 REMARK 3 L33: 1.5210 L12: 0.5206 REMARK 3 L13: 0.3839 L23: 1.1121 REMARK 3 S TENSOR REMARK 3 S11: -0.1017 S12: 0.1340 S13: -0.0475 REMARK 3 S21: -0.1675 S22: 0.2810 S23: -0.1648 REMARK 3 S31: -0.0671 S32: 0.3491 S33: -0.1792 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 749 A 948 REMARK 3 RESIDUE RANGE : B 749 B 949 REMARK 3 ORIGIN FOR THE GROUP (A): 33.8388 56.9875 28.9148 REMARK 3 T TENSOR REMARK 3 T11: 0.2774 T22: 0.3753 REMARK 3 T33: 0.1559 T12: -0.0888 REMARK 3 T13: 0.0455 T23: -0.0592 REMARK 3 L TENSOR REMARK 3 L11: 0.3593 L22: 1.1117 REMARK 3 L33: 1.2100 L12: -0.0479 REMARK 3 L13: 0.4762 L23: 0.4290 REMARK 3 S TENSOR REMARK 3 S11: -0.1477 S12: 0.0326 S13: -0.0100 REMARK 3 S21: -0.2153 S22: 0.2576 S23: -0.0379 REMARK 3 S31: -0.0532 S32: 0.2343 S33: -0.1099 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 2X6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1290041727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-09 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) : 0.979400 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27069 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 77.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.560 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.64 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.330 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: PDB ENTRY 2X6H REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLISED IN 0.88M REMARK 280 AMMONIUM SULPHATE, 100MM DI-POTASSIUM HYDROGEN PHOSPHATE AND REMARK 280 100MM DI-SODIUM HYDROGEN PHOSPHATE (TITRATED TO PH 7.5 WITH REMARK 280 ORTHOPHOSPHORIC ACID). PROTEIN WAS SOAKED WITH 0.5MM PI-103 IN REMARK 280 MOTHER LIQUOR. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 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 -1.000000 0.000000 0.000000 55.72000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 122.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 77.84000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 122.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 55.72000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 77.84000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 55.72000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 77.84000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 122.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 77.84000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.72000 REMARK 290 SMTRY2 7 0.000000 1.000000 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 122.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.9 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLY 455 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, GLY 455 TO ALA 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 254 REMARK 465 SER A 255 REMARK 465 HIS A 256 REMARK 465 MET A 257 REMARK 465 ASP A 258 REMARK 465 SER A 259 REMARK 465 GLU A 260 REMARK 465 ILE A 261 REMARK 465 GLN A 262 REMARK 465 MET A 263 REMARK 465 GLU A 264 REMARK 465 ASN A 265 REMARK 465 LEU A 266 REMARK 465 VAL A 267 REMARK 465 GLU A 268 REMARK 465 ARG A 269 REMARK 465 LYS A 270 REMARK 465 HIS A 271 REMARK 465 HIS A 272 REMARK 465 ARG A 273 REMARK 465 LEU A 274 REMARK 465 ALA A 275 REMARK 465 ARG A 276 REMARK 465 SER A 277 REMARK 465 GLU A 278 REMARK 465 ARG A 279 REMARK 465 SER A 280 REMARK 465 GLY A 281 REMARK 465 ILE A 282 REMARK 465 SER A 283 REMARK 465 ASP A 284 REMARK 465 ARG A 285 REMARK 465 ASP A 286 REMARK 465 ALA A 287 REMARK 465 LYS A 288 REMARK 465 PRO A 289 REMARK 465 THR A 290 REMARK 465 GLU A 423 REMARK 465 ARG A 424 REMARK 465 ASP A 425 REMARK 465 VAL A 426 REMARK 465 VAL A 427 REMARK 465 ARG A 428 REMARK 465 SER A 429 REMARK 465 ILE A 430 REMARK 465 LEU A 431 REMARK 465 ASP A 432 REMARK 465 ASP A 433 REMARK 465 ASN A 434 REMARK 465 GLY A 435 REMARK 465 SER A 436 REMARK 465 LEU A 437 REMARK 465 LEU A 438 REMARK 465 ASP A 439 REMARK 465 GLN A 440 REMARK 465 SER A 441 REMARK 465 SER A 442 REMARK 465 LEU A 443 REMARK 465 SER A 444 REMARK 465 ASP A 445 REMARK 465 LEU A 446 REMARK 465 SER A 447 REMARK 465 ALA A 448 REMARK 465 THR A 449 REMARK 465 SER A 450 REMARK 465 SER A 451 REMARK 465 GLY A 452 REMARK 465 LEU A 453 REMARK 465 HIS A 454 REMARK 465 ALA A 455 REMARK 465 SER A 456 REMARK 465 VAL A 457 REMARK 465 ILE A 458 REMARK 465 PRO A 459 REMARK 465 ALA A 460 REMARK 465 ASN A 461 REMARK 465 GLN A 462 REMARK 465 ARG A 463 REMARK 465 ALA A 464 REMARK 465 ALA A 465 REMARK 465 SER A 466 REMARK 465 VAL A 467 REMARK 465 LEU A 468 REMARK 465 ALA A 469 REMARK 465 ALA A 470 REMARK 465 ILE A 471 REMARK 465 LYS A 472 REMARK 465 SER A 473 REMARK 465 ASP A 474 REMARK 465 LYS A 475 REMARK 465 SER A 476 REMARK 465 VAL A 477 REMARK 465 SER A 478 REMARK 465 PRO A 479 REMARK 465 GLY A 480 REMARK 465 SER A 481 REMARK 465 ALA A 482 REMARK 465 GLY A 483 REMARK 465 GLY A 484 REMARK 465 SER A 485 REMARK 465 GLY A 486 REMARK 465 SER A 487 REMARK 465 GLY A 488 REMARK 465 GLY A 489 REMARK 465 GLN A 490 REMARK 465 GLY A 491 REMARK 465 SER A 492 REMARK 465 VAL A 493 REMARK 465 ALA A 494 REMARK 465 LEU A 495 REMARK 465 PRO A 496 REMARK 465 ASN A 497 REMARK 465 PRO A 498 REMARK 465 SER A 499 REMARK 465 ALA A 500 REMARK 465 PRO A 501 REMARK 465 ALA A 502 REMARK 465 THR A 503 REMARK 465 PRO A 504 REMARK 465 GLY A 505 REMARK 465 SER A 506 REMARK 465 SER A 507 REMARK 465 SER A 508 REMARK 465 LEU A 509 REMARK 465 PRO A 510 REMARK 465 CYS A 511 REMARK 465 ASP A 512 REMARK 465 SER A 513 REMARK 465 ASN A 514 REMARK 465 SER A 515 REMARK 465 ASN A 516 REMARK 465 ALA A 517 REMARK 465 LEU A 518 REMARK 465 MET A 519 REMARK 465 LEU A 520 REMARK 465 ALA A 521 REMARK 465 GLU A 522 REMARK 465 GLY A 523 REMARK 465 ILE A 524 REMARK 465 SER A 525 REMARK 465 PHE A 526 REMARK 465 GLY A 527 REMARK 465 SER A 528 REMARK 465 VAL A 529 REMARK 465 PRO A 530 REMARK 465 LYS A 949 REMARK 465 GLY B 254 REMARK 465 SER B 255 REMARK 465 HIS B 256 REMARK 465 MET B 257 REMARK 465 ASP B 258 REMARK 465 SER B 259 REMARK 465 GLU B 260 REMARK 465 ILE B 261 REMARK 465 GLN B 262 REMARK 465 MET B 263 REMARK 465 GLU B 264 REMARK 465 ASN B 265 REMARK 465 LEU B 266 REMARK 465 VAL B 267 REMARK 465 GLU B 268 REMARK 465 ARG B 269 REMARK 465 LYS B 270 REMARK 465 HIS B 271 REMARK 465 HIS B 272 REMARK 465 ARG B 273 REMARK 465 LEU B 274 REMARK 465 ALA B 275 REMARK 465 ARG B 276 REMARK 465 SER B 277 REMARK 465 GLU B 278 REMARK 465 ARG B 279 REMARK 465 SER B 280 REMARK 465 GLY B 281 REMARK 465 ILE B 282 REMARK 465 SER B 283 REMARK 465 ASP B 284 REMARK 465 ARG B 285 REMARK 465 ASP B 286 REMARK 465 ALA B 287 REMARK 465 LYS B 288 REMARK 465 PRO B 289 REMARK 465 THR B 290 REMARK 465 ARG B 424 REMARK 465 ASP B 425 REMARK 465 VAL B 426 REMARK 465 VAL B 427 REMARK 465 ARG B 428 REMARK 465 SER B 429 REMARK 465 ILE B 430 REMARK 465 LEU B 431 REMARK 465 ASP B 432 REMARK 465 ASP B 433 REMARK 465 ASN B 434 REMARK 465 GLY B 435 REMARK 465 SER B 436 REMARK 465 LEU B 437 REMARK 465 LEU B 438 REMARK 465 ASP B 439 REMARK 465 GLN B 440 REMARK 465 SER B 441 REMARK 465 SER B 442 REMARK 465 LEU B 443 REMARK 465 SER B 444 REMARK 465 ASP B 445 REMARK 465 LEU B 446 REMARK 465 SER B 447 REMARK 465 ALA B 448 REMARK 465 THR B 449 REMARK 465 SER B 450 REMARK 465 SER B 451 REMARK 465 GLY B 452 REMARK 465 LEU B 453 REMARK 465 HIS B 454 REMARK 465 ALA B 455 REMARK 465 SER B 456 REMARK 465 VAL B 457 REMARK 465 ILE B 458 REMARK 465 PRO B 459 REMARK 465 ALA B 460 REMARK 465 ASN B 461 REMARK 465 GLN B 462 REMARK 465 ARG B 463 REMARK 465 ALA B 464 REMARK 465 ALA B 465 REMARK 465 SER B 466 REMARK 465 VAL B 467 REMARK 465 LEU B 468 REMARK 465 ALA B 469 REMARK 465 ALA B 470 REMARK 465 ILE B 471 REMARK 465 LYS B 472 REMARK 465 SER B 473 REMARK 465 ASP B 474 REMARK 465 LYS B 475 REMARK 465 SER B 476 REMARK 465 VAL B 477 REMARK 465 SER B 478 REMARK 465 PRO B 479 REMARK 465 GLY B 480 REMARK 465 SER B 481 REMARK 465 ALA B 482 REMARK 465 GLY B 483 REMARK 465 GLY B 484 REMARK 465 SER B 485 REMARK 465 GLY B 486 REMARK 465 SER B 487 REMARK 465 GLY B 488 REMARK 465 GLY B 489 REMARK 465 GLN B 490 REMARK 465 GLY B 491 REMARK 465 SER B 492 REMARK 465 VAL B 493 REMARK 465 ALA B 494 REMARK 465 LEU B 495 REMARK 465 PRO B 496 REMARK 465 ASN B 497 REMARK 465 PRO B 498 REMARK 465 SER B 499 REMARK 465 ALA B 500 REMARK 465 PRO B 501 REMARK 465 ALA B 502 REMARK 465 THR B 503 REMARK 465 PRO B 504 REMARK 465 GLY B 505 REMARK 465 SER B 506 REMARK 465 SER B 507 REMARK 465 SER B 508 REMARK 465 LEU B 509 REMARK 465 PRO B 510 REMARK 465 CYS B 511 REMARK 465 ASP B 512 REMARK 465 SER B 513 REMARK 465 ASN B 514 REMARK 465 SER B 515 REMARK 465 ASN B 516 REMARK 465 ALA B 517 REMARK 465 LEU B 518 REMARK 465 MET B 519 REMARK 465 LEU B 520 REMARK 465 ALA B 521 REMARK 465 GLU B 522 REMARK 465 GLY B 523 REMARK 465 ILE B 524 REMARK 465 SER B 525 REMARK 465 PHE B 526 REMARK 465 GLY B 527 REMARK 465 SER B 528 REMARK 465 VAL B 529 REMARK 465 PRO B 530 REMARK 465 SER B 564 REMARK 465 VAL B 565 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 B 408 CG CD OE1 OE2 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 GLN B 315 NH2 ARG B 322 1.94 REMARK 500 NH1 ARG B 806 O ASP B 823 1.96 REMARK 500 O TYR A 794 OG1 THR A 798 1.96 REMARK 500 NH2 ARG A 669 O1 SO4 A 1950 2.03 REMARK 500 NE2 GLN B 705 O PHE B 824 2.06 REMARK 500 OG SER A 842 OE1 GLU A 844 2.09 REMARK 500 NZ LYS B 681 O3 SO4 B 1951 2.11 REMARK 500 OE2 GLU B 723 NE2 HIS B 874 2.12 REMARK 500 O TRP B 319 CE2 PHE B 323 2.14 REMARK 500 O TYR B 777 N ILE B 779 2.18 REMARK 500 O ASN A 645 O ASN A 648 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 391 OD1 ASN A 724 6555 1.87 REMARK 500 ND2 ASN B 600 OE2 GLU B 782 8565 2.11 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 GLY A 590 C GLY A 590 O 0.125 REMARK 500 SER B 311 CB SER B 311 OG 0.131 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 LYS A 818 N - CA - C ANGL. DEV. = -18.2 DEGREES REMARK 500 LEU B 710 CA - CB - CG ANGL. DEV. = -16.6 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 312 -77.98 -131.03 REMARK 500 ILE A 420 -71.08 -103.90 REMARK 500 GLU A 563 -4.68 53.20 REMARK 500 SER A 564 55.84 -96.68 REMARK 500 LYS A 567 -117.31 54.56 REMARK 500 ASN A 591 -103.81 -147.32 REMARK 500 GLU A 638 108.49 -56.26 REMARK 500 LYS A 664 146.23 2.53 REMARK 500 ALA A 689 26.27 41.10 REMARK 500 HIS A 690 17.37 48.06 REMARK 500 HIS A 691 121.69 -39.54 REMARK 500 ASN A 724 7.75 86.21 REMARK 500 PRO A 731 71.98 -115.54 REMARK 500 SER A 738 124.28 -33.44 REMARK 500 SER A 739 150.65 -48.27 REMARK 500 LYS A 740 -6.57 81.92 REMARK 500 ASP A 823 70.33 48.24 REMARK 500 PRO A 836 -167.96 -68.16 REMARK 500 GLN A 909 34.99 79.54 REMARK 500 SER B 311 63.71 62.08 REMARK 500 LEU B 325 51.90 -93.29 REMARK 500 GLU B 408 173.85 -43.94 REMARK 500 PHE B 592 -49.26 -26.88 REMARK 500 ASP B 640 17.94 91.08 REMARK 500 THR B 663 -62.37 -90.31 REMARK 500 ALA B 689 21.41 49.57 REMARK 500 LYS B 740 7.40 83.84 REMARK 500 ASP B 805 2.23 80.66 REMARK 500 HIS B 874 54.87 -94.56 REMARK 500 THR B 889 12.32 102.28 REMARK 500 TYR B 946 -61.45 -21.45 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 ASN A 589 GLY A 590 -147.70 REMARK 500 LYS A 664 ILE A 665 149.53 REMARK 500 ALA A 680 LYS A 681 149.52 REMARK 500 MET A 835 PRO A 836 148.08 REMARK 500 PRO A 836 PRO A 837 30.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 590 -16.27 REMARK 500 ASN A 591 -13.36 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 SO4 A 1949 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE X6K A 1951 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE X6K B 1950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1951 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X6H RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 REMARK 900 RELATED ID: 2X6F RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 REMARK 900 IN COMPLEX WITH 3-METHYLADENINE REMARK 900 RELATED ID: 2X6J RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 REMARK 900 IN COMPLEX WITH PIK-93 REMARK 900 RELATED ID: 2X6I RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 REMARK 900 IN COMPLEX WITH PIK-90 DBREF 2X6K A 254 257 PDB 2X6K 2X6K 254 257 DBREF 2X6K A 258 949 UNP Q9W1M7 Q9W1M7_DROME 258 949 DBREF 2X6K B 254 257 PDB 2X6K 2X6K 254 257 DBREF 2X6K B 258 949 UNP Q9W1M7 Q9W1M7_DROME 258 949 SEQADV 2X6K ALA A 455 UNP Q9W1M7 GLY 455 ENGINEERED MUTATION SEQADV 2X6K ALA B 455 UNP Q9W1M7 GLY 455 ENGINEERED MUTATION SEQRES 1 A 696 GLY SER HIS MET ASP SER GLU ILE GLN MET GLU ASN LEU SEQRES 2 A 696 VAL GLU ARG LYS HIS HIS ARG LEU ALA ARG SER GLU ARG SEQRES 3 A 696 SER GLY ILE SER ASP ARG ASP ALA LYS PRO THR ALA SER SEQRES 4 A 696 ILE ARG ASP GLN LEU HIS THR ILE VAL TYR ARG TYR PRO SEQRES 5 A 696 PRO THR TYR VAL LEU SER SER GLU GLU GLN ASP LEU VAL SEQRES 6 A 696 TRP LYS PHE ARG PHE TYR LEU SER SER HIS LYS LYS ALA SEQRES 7 A 696 LEU THR LYS PHE LEU LYS CYS ILE ASN TRP LYS LEU GLU SEQRES 8 A 696 ASP GLU VAL THR GLN ALA LEU TRP MET LEU ALA ASN TRP SEQRES 9 A 696 ALA PRO MET ASP VAL GLU ASP ALA LEU GLU LEU LEU SER SEQRES 10 A 696 PRO THR PHE THR HIS PRO GLN VAL ARG LYS TYR ALA VAL SEQRES 11 A 696 SER ARG LEU ALA GLN ALA PRO ASP GLU ASP LEU LEU LEU SEQRES 12 A 696 TYR LEU LEU GLN LEU VAL GLN ALA LEU LYS TYR GLU ASP SEQRES 13 A 696 PRO ARG HIS ILE VAL HIS LEU HIS GLY CYS ILE PHE PRO SEQRES 14 A 696 GLU ARG ASP VAL VAL ARG SER ILE LEU ASP ASP ASN GLY SEQRES 15 A 696 SER LEU LEU ASP GLN SER SER LEU SER ASP LEU SER ALA SEQRES 16 A 696 THR SER SER GLY LEU HIS ALA SER VAL ILE PRO ALA ASN SEQRES 17 A 696 GLN ARG ALA ALA SER VAL LEU ALA ALA ILE LYS SER ASP SEQRES 18 A 696 LYS SER VAL SER PRO GLY SER ALA GLY GLY SER GLY SER SEQRES 19 A 696 GLY GLY GLN GLY SER VAL ALA LEU PRO ASN PRO SER ALA SEQRES 20 A 696 PRO ALA THR PRO GLY SER SER SER LEU PRO CYS ASP SER SEQRES 21 A 696 ASN SER ASN ALA LEU MET LEU ALA GLU GLY ILE SER PHE SEQRES 22 A 696 GLY SER VAL PRO ALA ASN LEU CYS THR PHE LEU ILE GLN SEQRES 23 A 696 ARG ALA CYS THR ASN ALA THR LEU ALA ASN TYR PHE TYR SEQRES 24 A 696 TRP TYR LEU SER ILE GLU VAL GLU GLU VAL GLU SER VAL SEQRES 25 A 696 ARG LYS GLN ASP GLU ARG ALA HIS ASP MET TYR ALA MET SEQRES 26 A 696 VAL LEU LYS MET PHE LEU LYS VAL LEU GLU ASN GLY ASN SEQRES 27 A 696 PHE ASN LEU ARG GLY ILE PHE TYR ASN LEU ARG LYS GLN SEQRES 28 A 696 ARG ARG PHE ILE ASP GLU LEU VAL LYS LEU VAL LYS LEU SEQRES 29 A 696 VAL ALA LYS GLU PRO GLY ASN ARG ASN LYS LYS THR GLU SEQRES 30 A 696 LYS PHE GLN LYS LEU LEU ALA GLU GLN ASP MET PHE LYS SEQRES 31 A 696 VAL ASN PHE THR ASN PHE GLU PRO ILE PRO PHE PRO LEU SEQRES 32 A 696 ASP PRO GLU ILE TYR ILE THR LYS ILE VAL PRO MET ARG SEQRES 33 A 696 THR SER LEU PHE LYS SER ALA LEU MET PRO ALA LYS LEU SEQRES 34 A 696 THR PHE VAL THR SER ILE ALA HIS HIS GLU TYR ALA ALA SEQRES 35 A 696 ILE PHE LYS HIS GLY ASP ASP LEU ARG GLN ASP GLN LEU SEQRES 36 A 696 ILE LEU GLN MET ILE THR LEU MET ASP LYS LEU LEU ARG SEQRES 37 A 696 ARG GLU ASN LEU ASP LEU LYS LEU THR PRO TYR LYS VAL SEQRES 38 A 696 LEU ALA THR SER SER LYS HIS GLY PHE LEU GLN TYR VAL SEQRES 39 A 696 ASP SER CYS THR VAL ALA GLU VAL LEU ALA ARG GLU GLY SEQRES 40 A 696 ASN ILE HIS ASN PHE PHE ARG LYS HIS HIS PRO CYS ASP SEQRES 41 A 696 ASN GLY PRO TYR GLY ILE SER ALA GLU VAL MET ASP THR SEQRES 42 A 696 TYR ILE LYS SER CYS ALA GLY TYR CYS VAL ILE THR TYR SEQRES 43 A 696 LEU LEU GLY VAL GLY ASP ARG HIS LEU ASP ASN LEU LEU SEQRES 44 A 696 LEU THR THR ASN GLY LYS LEU PHE HIS ILE ASP PHE GLY SEQRES 45 A 696 TYR ILE LEU GLY ARG ASP PRO LYS PRO MET PRO PRO PRO SEQRES 46 A 696 MET LYS LEU SER LYS GLU MET VAL GLU ALA MET GLY GLY SEQRES 47 A 696 ILE SER SER GLU HIS HIS HIS GLU PHE ARG LYS GLN CYS SEQRES 48 A 696 TYR THR ALA TYR LEU HIS LEU ARG ARG HIS ALA ASN VAL SEQRES 49 A 696 MET LEU ASN LEU PHE SER LEU MET VAL ASP ALA THR VAL SEQRES 50 A 696 PRO ASP ILE ALA LEU GLU PRO ASP LYS ALA VAL LYS LYS SEQRES 51 A 696 VAL GLU GLU ASN LEU GLN LEU GLY LEU THR ASP GLU GLU SEQRES 52 A 696 ALA VAL GLN HIS LEU GLN SER LEU LEU ASP VAL SER ILE SEQRES 53 A 696 THR ALA VAL MET PRO ALA LEU VAL GLU GLN ILE HIS ARG SEQRES 54 A 696 PHE THR GLN TYR TRP ARG LYS SEQRES 1 B 696 GLY SER HIS MET ASP SER GLU ILE GLN MET GLU ASN LEU SEQRES 2 B 696 VAL GLU ARG LYS HIS HIS ARG LEU ALA ARG SER GLU ARG SEQRES 3 B 696 SER GLY ILE SER ASP ARG ASP ALA LYS PRO THR ALA SER SEQRES 4 B 696 ILE ARG ASP GLN LEU HIS THR ILE VAL TYR ARG TYR PRO SEQRES 5 B 696 PRO THR TYR VAL LEU SER SER GLU GLU GLN ASP LEU VAL SEQRES 6 B 696 TRP LYS PHE ARG PHE TYR LEU SER SER HIS LYS LYS ALA SEQRES 7 B 696 LEU THR LYS PHE LEU LYS CYS ILE ASN TRP LYS LEU GLU SEQRES 8 B 696 ASP GLU VAL THR GLN ALA LEU TRP MET LEU ALA ASN TRP SEQRES 9 B 696 ALA PRO MET ASP VAL GLU ASP ALA LEU GLU LEU LEU SER SEQRES 10 B 696 PRO THR PHE THR HIS PRO GLN VAL ARG LYS TYR ALA VAL SEQRES 11 B 696 SER ARG LEU ALA GLN ALA PRO ASP GLU ASP LEU LEU LEU SEQRES 12 B 696 TYR LEU LEU GLN LEU VAL GLN ALA LEU LYS TYR GLU ASP SEQRES 13 B 696 PRO ARG HIS ILE VAL HIS LEU HIS GLY CYS ILE PHE PRO SEQRES 14 B 696 GLU ARG ASP VAL VAL ARG SER ILE LEU ASP ASP ASN GLY SEQRES 15 B 696 SER LEU LEU ASP GLN SER SER LEU SER ASP LEU SER ALA SEQRES 16 B 696 THR SER SER GLY LEU HIS ALA SER VAL ILE PRO ALA ASN SEQRES 17 B 696 GLN ARG ALA ALA SER VAL LEU ALA ALA ILE LYS SER ASP SEQRES 18 B 696 LYS SER VAL SER PRO GLY SER ALA GLY GLY SER GLY SER SEQRES 19 B 696 GLY GLY GLN GLY SER VAL ALA LEU PRO ASN PRO SER ALA SEQRES 20 B 696 PRO ALA THR PRO GLY SER SER SER LEU PRO CYS ASP SER SEQRES 21 B 696 ASN SER ASN ALA LEU MET LEU ALA GLU GLY ILE SER PHE SEQRES 22 B 696 GLY SER VAL PRO ALA ASN LEU CYS THR PHE LEU ILE GLN SEQRES 23 B 696 ARG ALA CYS THR ASN ALA THR LEU ALA ASN TYR PHE TYR SEQRES 24 B 696 TRP TYR LEU SER ILE GLU VAL GLU GLU VAL GLU SER VAL SEQRES 25 B 696 ARG LYS GLN ASP GLU ARG ALA HIS ASP MET TYR ALA MET SEQRES 26 B 696 VAL LEU LYS MET PHE LEU LYS VAL LEU GLU ASN GLY ASN SEQRES 27 B 696 PHE ASN LEU ARG GLY ILE PHE TYR ASN LEU ARG LYS GLN SEQRES 28 B 696 ARG ARG PHE ILE ASP GLU LEU VAL LYS LEU VAL LYS LEU SEQRES 29 B 696 VAL ALA LYS GLU PRO GLY ASN ARG ASN LYS LYS THR GLU SEQRES 30 B 696 LYS PHE GLN LYS LEU LEU ALA GLU GLN ASP MET PHE LYS SEQRES 31 B 696 VAL ASN PHE THR ASN PHE GLU PRO ILE PRO PHE PRO LEU SEQRES 32 B 696 ASP PRO GLU ILE TYR ILE THR LYS ILE VAL PRO MET ARG SEQRES 33 B 696 THR SER LEU PHE LYS SER ALA LEU MET PRO ALA LYS LEU SEQRES 34 B 696 THR PHE VAL THR SER ILE ALA HIS HIS GLU TYR ALA ALA SEQRES 35 B 696 ILE PHE LYS HIS GLY ASP ASP LEU ARG GLN ASP GLN LEU SEQRES 36 B 696 ILE LEU GLN MET ILE THR LEU MET ASP LYS LEU LEU ARG SEQRES 37 B 696 ARG GLU ASN LEU ASP LEU LYS LEU THR PRO TYR LYS VAL SEQRES 38 B 696 LEU ALA THR SER SER LYS HIS GLY PHE LEU GLN TYR VAL SEQRES 39 B 696 ASP SER CYS THR VAL ALA GLU VAL LEU ALA ARG GLU GLY SEQRES 40 B 696 ASN ILE HIS ASN PHE PHE ARG LYS HIS HIS PRO CYS ASP SEQRES 41 B 696 ASN GLY PRO TYR GLY ILE SER ALA GLU VAL MET ASP THR SEQRES 42 B 696 TYR ILE LYS SER CYS ALA GLY TYR CYS VAL ILE THR TYR SEQRES 43 B 696 LEU LEU GLY VAL GLY ASP ARG HIS LEU ASP ASN LEU LEU SEQRES 44 B 696 LEU THR THR ASN GLY LYS LEU PHE HIS ILE ASP PHE GLY SEQRES 45 B 696 TYR ILE LEU GLY ARG ASP PRO LYS PRO MET PRO PRO PRO SEQRES 46 B 696 MET LYS LEU SER LYS GLU MET VAL GLU ALA MET GLY GLY SEQRES 47 B 696 ILE SER SER GLU HIS HIS HIS GLU PHE ARG LYS GLN CYS SEQRES 48 B 696 TYR THR ALA TYR LEU HIS LEU ARG ARG HIS ALA ASN VAL SEQRES 49 B 696 MET LEU ASN LEU PHE SER LEU MET VAL ASP ALA THR VAL SEQRES 50 B 696 PRO ASP ILE ALA LEU GLU PRO ASP LYS ALA VAL LYS LYS SEQRES 51 B 696 VAL GLU GLU ASN LEU GLN LEU GLY LEU THR ASP GLU GLU SEQRES 52 B 696 ALA VAL GLN HIS LEU GLN SER LEU LEU ASP VAL SER ILE SEQRES 53 B 696 THR ALA VAL MET PRO ALA LEU VAL GLU GLN ILE HIS ARG SEQRES 54 B 696 PHE THR GLN TYR TRP ARG LYS HET SO4 A1949 5 HET SO4 A1950 5 HET X6K A1951 26 HET X6K B1950 26 HET SO4 B1951 5 HETNAM SO4 SULFATE ION HETNAM X6K 3-(4-MORPHOLIN-4-YLPYRIDO[3',2':4,5]FURO[3,2- HETNAM 2 X6K D]PYRIMIDIN-2-YL)PHENOL HETSYN X6K PI-103 FORMUL 3 SO4 3(O4 S 2-) FORMUL 5 X6K 2(C19 H16 N4 O3) HELIX 1 1 ILE A 293 TYR A 304 1 12 HELIX 2 2 GLU A 313 PHE A 323 1 11 HELIX 3 3 HIS A 328 LYS A 337 1 10 HELIX 4 4 ASP A 345 TRP A 357 1 13 HELIX 5 5 ASP A 361 SER A 370 1 10 HELIX 6 6 HIS A 375 ALA A 389 1 15 HELIX 7 7 PRO A 390 LEU A 405 1 16 HELIX 8 8 PRO A 410 CYS A 419 1 10 HELIX 9 9 ALA A 531 ASN A 544 1 14 HELIX 10 10 ASN A 544 GLU A 560 1 17 HELIX 11 11 GLN A 568 GLY A 590 1 23 HELIX 12 12 ASN A 591 GLU A 621 1 31 HELIX 13 13 ASN A 624 GLU A 638 1 15 HELIX 14 14 LEU A 703 ASN A 724 1 22 HELIX 15 15 VAL A 752 GLU A 759 1 8 HELIX 16 16 ASN A 761 HIS A 770 1 10 HELIX 17 17 SER A 780 GLY A 802 1 23 HELIX 18 18 SER A 842 ALA A 848 1 7 HELIX 19 19 SER A 854 HIS A 874 1 21 HELIX 20 20 HIS A 874 MET A 885 1 12 HELIX 21 21 VAL A 890 LEU A 895 1 6 HELIX 22 22 GLU A 896 GLN A 909 1 14 HELIX 23 23 THR A 913 MET A 933 1 21 HELIX 24 24 MET A 933 ARG A 948 1 16 HELIX 25 25 ILE B 293 TYR B 304 1 12 HELIX 26 26 SER B 311 PHE B 323 1 13 HELIX 27 27 TYR B 324 SER B 327 5 4 HELIX 28 28 HIS B 328 ASN B 340 1 13 HELIX 29 29 GLU B 344 TRP B 357 1 14 HELIX 30 30 ASP B 361 SER B 370 1 10 HELIX 31 31 HIS B 375 ALA B 389 1 15 HELIX 32 32 PRO B 390 ALA B 404 1 15 HELIX 33 33 LEU B 405 TYR B 407 5 3 HELIX 34 34 ASP B 409 PHE B 421 1 13 HELIX 35 35 ALA B 531 ASN B 544 1 14 HELIX 36 36 ASN B 544 GLU B 560 1 17 HELIX 37 37 GLN B 568 ASN B 589 1 22 HELIX 38 38 ASN B 591 GLU B 621 1 31 HELIX 39 39 ASN B 624 GLU B 638 1 15 HELIX 40 40 ASP B 702 GLU B 723 1 22 HELIX 41 41 VAL B 752 GLU B 759 1 8 HELIX 42 42 ASN B 761 HIS B 770 1 10 HELIX 43 43 SER B 780 GLY B 802 1 23 HELIX 44 44 SER B 842 ALA B 848 1 7 HELIX 45 45 SER B 854 HIS B 874 1 21 HELIX 46 46 HIS B 874 MET B 885 1 12 HELIX 47 47 VAL B 890 GLU B 896 1 7 HELIX 48 48 GLU B 896 GLN B 909 1 14 HELIX 49 49 THR B 913 MET B 933 1 21 HELIX 50 50 MET B 933 ARG B 948 1 16 SHEET 1 AA 2 ILE A 652 PRO A 653 0 SHEET 2 AA 2 TYR A 661 ILE A 662 -1 O ILE A 662 N ILE A 652 SHEET 1 AB 5 ILE A 665 LEU A 672 0 SHEET 2 AB 5 ALA A 680 PHE A 684 -1 O LYS A 681 N SER A 671 SHEET 3 AB 5 TYR A 693 LYS A 698 -1 O TYR A 693 N PHE A 684 SHEET 4 AB 5 GLY A 742 GLN A 745 -1 O GLY A 742 N LYS A 698 SHEET 5 AB 5 VAL A 734 ALA A 736 -1 O LEU A 735 N PHE A 743 SHEET 1 AC 3 CYS A 750 THR A 751 0 SHEET 2 AC 3 LEU A 812 LEU A 813 -1 O LEU A 813 N CYS A 750 SHEET 3 AC 3 LEU A 819 PHE A 820 -1 O PHE A 820 N LEU A 812 SHEET 1 BA 6 ILE B 652 PRO B 653 0 SHEET 2 BA 6 TYR B 661 LEU B 672 -1 O ILE B 662 N ILE B 652 SHEET 3 BA 6 ALA B 680 THR B 686 -1 O LYS B 681 N SER B 671 SHEET 4 BA 6 ALA B 694 LYS B 698 -1 O ALA B 695 N LEU B 682 SHEET 5 BA 6 HIS B 741 GLN B 745 -1 O GLY B 742 N LYS B 698 SHEET 6 BA 6 VAL B 734 SER B 738 -1 O LEU B 735 N PHE B 743 SHEET 1 BB 3 CYS B 750 THR B 751 0 SHEET 2 BB 3 LEU B 811 LEU B 813 -1 O LEU B 813 N CYS B 750 SHEET 3 BB 3 LEU B 819 HIS B 821 -1 O PHE B 820 N LEU B 812 CISPEP 1 GLU B 408 ASP B 409 0 3.34 SITE 1 AC1 4 ASN A 624 ARG A 625 SER A 675 ALA A 676 SITE 1 AC2 2 ARG A 669 LYS A 681 SITE 1 AC3 9 LYS A 674 ILE A 696 LYS A 698 ASP A 706 SITE 2 AC3 9 LEU A 744 VAL A 747 SER A 749 ILE A 822 SITE 3 AC3 9 ASP A 823 SITE 1 AC4 10 LYS B 674 LYS B 698 ASP B 706 TYR B 732 SITE 2 AC4 10 LEU B 744 GLN B 745 TYR B 746 VAL B 747 SITE 3 AC4 10 SER B 749 ILE B 822 SITE 1 AC5 2 ARG B 669 LYS B 681 CRYST1 111.440 155.680 244.000 90.00 90.00 90.00 I 21 21 21 16 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 0.008973 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004098 0.00000 MTRIX1 1 -0.007605 -0.113200 -0.993500 69.65000 1 MTRIX2 1 0.001212 -0.993600 -0.113200 109.40000 1 MTRIX3 1 -1.000000 -0.000343 0.007693 63.20000 1