HEADER TRANSFERASE 31-DEC-15 5HBJ TITLE CDK8-CYCC IN COMPLEX WITH 8-[2-AMINO-3-CHLORO-5-(1-METHYL-1H-INDAZOL- TITLE 2 5-YL)-PYRIDIN-4-YL]-2,8-DIAZA-SPIRO[4.5]DECAN-1-ONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 3-362; COMPND 5 SYNONYM: CELL DIVISION PROTEIN KINASE 8,MEDIATOR COMPLEX SUBUNIT COMPND 6 CDK8,MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT CDK8,PROTEIN COMPND 7 KINASE K35; COMPND 8 EC: 2.7.11.22,2.7.11.23; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: CYCLIN-C; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: SRB11 HOMOLOG,HSRB11; COMPND 14 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: CDK8; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: CCNC; SOURCE 14 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 15 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CDK8 KINASE / CYCLIN C, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.MUSIL,J.BLAGG,A.MALLINGER REVDAT 2 24-FEB-16 5HBJ 1 JRNL REVDAT 1 03-FEB-16 5HBJ 0 JRNL AUTH A.MALLINGER,K.SCHIEMANN,C.RINK,F.STIEBER,M.CALDERINI, JRNL AUTH 2 S.CRUMPLER,M.STUBBS,O.ADENIJI-POPOOLA,O.POESCHKE,M.BUSCH, JRNL AUTH 3 P.CZODROWSKI,D.MUSIL,D.SCHWARZ,M.J.ORTIZ-RUIZ,R.SCHNEIDER, JRNL AUTH 4 C.THAI,M.VALENTI,A.DE HAVEN BRANDON,R.BURKE,P.WORKMAN, JRNL AUTH 5 T.DALE,D.WIENKE,P.A.CLARKE,C.ESDAR,F.I.RAYNAUD,S.A.ECCLES, JRNL AUTH 6 F.ROHDICH,J.BLAGG JRNL TITL DISCOVERY OF POTENT, SELECTIVE, AND ORALLY BIOAVAILABLE JRNL TITL 2 SMALL-MOLECULE MODULATORS OF THE MEDIATOR COMPLEX-ASSOCIATED JRNL TITL 3 KINASES CDK8 AND CDK19. JRNL REF J.MED.CHEM. V. 59 1078 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 26796641 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01685 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 16992 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) : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.400 REMARK 3 FREE R VALUE TEST SET COUNT : 601 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1218 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.4450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5045 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.02000 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): 0.474 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.383 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 46.457 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.866 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4906 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3346 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6674 ; 1.079 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7993 ; 1.388 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 604 ; 5.293 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 210 ;34.188 ;23.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 744 ;13.170 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;14.199 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 729 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5481 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1040 ; 0.001 ; 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): 3045 ; 1.020 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1208 ; 0.113 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4848 ; 1.923 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1861 ; 2.491 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1826 ; 4.062 ; 6.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 5HBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999970 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18594 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 88.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.493 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION : PH 6.90, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 35.37450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.21700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.88700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.21700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.37450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.88700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 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 ASN A 117 REMARK 465 LYS A 118 REMARK 465 LYS A 119 REMARK 465 PRO A 120 REMARK 465 ALA A 177 REMARK 465 ARG A 178 REMARK 465 LYS A 185 REMARK 465 PRO A 186 REMARK 465 LEU A 187 REMARK 465 ALA A 188 REMARK 465 ASP A 189 REMARK 465 LEU A 190 REMARK 465 ASP A 191 REMARK 465 PRO A 192 REMARK 465 VAL A 193 REMARK 465 VAL A 194 REMARK 465 GLU A 239 REMARK 465 ASP A 240 REMARK 465 ILE A 241 REMARK 465 LYS A 242 REMARK 465 THR A 243 REMARK 465 GLU A 362 REMARK 465 ASP B -5 REMARK 465 ASP B -4 REMARK 465 ASP B -3 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A -1 CG OD1 OD2 REMARK 480 LYS A 0 CG CD CE NZ REMARK 480 LYS A 6 CD CE NZ REMARK 480 LYS A 8 CD CE NZ REMARK 480 GLU A 12 CD OE1 OE2 REMARK 480 GLU A 23 CB CG CD OE1 OE2 REMARK 480 LYS A 39 CG CD CE NZ REMARK 480 ARG A 40 CG CD NE CZ NH1 NH2 REMARK 480 ASP A 42 CB CG OD1 OD2 REMARK 480 LYS A 44 CB CG CD CE NZ REMARK 480 ASP A 46 CG OD1 OD2 REMARK 480 LYS A 47 CG CD CE NZ REMARK 480 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 74 CG CD CE NZ REMARK 480 LYS A 83 CG CD CE NZ REMARK 480 LYS A 92 CE NZ REMARK 480 LYS A 109 CD CE NZ REMARK 480 ARG A 112 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 115 CB CG CD CE NZ REMARK 480 VAL A 121 CB CG1 CG2 REMARK 480 GLN A 122 CG CD OE1 NE2 REMARK 480 LEU A 123 CB CG CD1 CD2 REMARK 480 ARG A 125 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 153 NZ REMARK 480 PHE A 176 CB CG CD1 CD2 CE1 CE2 CZ REMARK 480 LEU A 179 CB CG CD1 CD2 REMARK 480 SER A 182 CB OG REMARK 480 LEU A 184 CB CG CD1 CD2 REMARK 480 VAL A 195 CG1 CG2 REMARK 480 THR A 196 OG1 CG2 REMARK 480 ARG A 209 CD NE CZ NH1 NH2 REMARK 480 GLU A 231 CG CD OE1 OE2 REMARK 480 ARG A 237 CG CD NE CZ NH1 NH2 REMARK 480 GLN A 238 CG CD OE1 NE2 REMARK 480 SER A 244 OG REMARK 480 ASN A 257 CG OD1 ND2 REMARK 480 LYS A 265 CG CD CE NZ REMARK 480 LYS A 271 CG CD CE NZ REMARK 480 LYS A 272 CD CE NZ REMARK 480 LYS A 281 CE NZ REMARK 480 ARG A 284 NE CZ NH1 NH2 REMARK 480 ASN A 290 CB CG OD1 ND2 REMARK 480 LYS A 295 CE NZ REMARK 480 LYS A 299 CG CD CE NZ REMARK 480 LYS A 301 CG CD CE NZ REMARK 480 LYS A 303 CG CD CE NZ REMARK 480 LEU A 340 CG CD1 CD2 REMARK 480 GLN A 350 CG CD OE1 NE2 REMARK 480 GLU A 357 CG CD OE1 OE2 REMARK 480 GLU A 361 CG CD OE1 OE2 REMARK 480 ASP B -2 N CA CB CG OD1 OD2 REMARK 480 LYS B -1 CG CD CE NZ REMARK 480 LYS B 18 CE NZ REMARK 480 GLN B 19 CB CG CD OE1 NE2 REMARK 480 LEU B 22 CG CD1 CD2 REMARK 480 LYS B 23 CG CD CE NZ REMARK 480 GLU B 24 CG CD OE1 OE2 REMARK 480 LYS B 27 CG CD CE NZ REMARK 480 LYS B 30 CG CD CE NZ REMARK 480 LYS B 56 CG CD CE NZ REMARK 480 ARG B 58 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 79 CD CE NZ REMARK 480 LYS B 96 NZ REMARK 480 GLU B 99 CG CD OE1 OE2 REMARK 480 PHE B 100 CG CD1 CD2 CE1 CE2 CZ REMARK 480 VAL B 102 CG1 CG2 REMARK 480 LYS B 117 CG CD CE NZ REMARK 480 LYS B 126 CG CD CE NZ REMARK 480 GLU B 127 CG CD OE1 OE2 REMARK 480 ARG B 131 CG CD NE CZ NH1 NH2 REMARK 480 LEU B 145 CD1 CD2 REMARK 480 ARG B 157 CD NE CZ NH1 NH2 REMARK 480 GLU B 169 CD OE1 OE2 REMARK 480 ASP B 170 CG OD1 OD2 REMARK 480 MET B 171 CG SD CE REMARK 480 GLN B 210 CG CD OE1 NE2 REMARK 480 LYS B 211 CG CD CE NZ REMARK 480 ARG B 214 CG CD NE CZ NH1 NH2 REMARK 480 GLU B 225 CG CD OE1 OE2 REMARK 480 LYS B 226 CG CD CE NZ REMARK 480 LYS B 236 CG CD CE NZ REMARK 480 LYS B 256 CE NZ REMARK 480 LYS B 259 CG CD CE NZ REMARK 480 LYS B 261 CG CD CE NZ 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 41 -70.81 -74.02 REMARK 500 SER A 114 -170.92 59.38 REMARK 500 ASP A 151 41.61 -163.20 REMARK 500 ASP A 173 89.31 71.07 REMARK 500 MET A 174 61.90 -114.96 REMARK 500 LEU A 316 52.78 -95.06 REMARK 500 GLN B 13 -52.64 -142.25 REMARK 500 LYS B 56 74.37 59.10 REMARK 500 ALA B 213 24.44 -142.38 REMARK 500 LEU B 237 -47.79 -26.76 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 5Y8 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 301 DBREF 5HBJ A 1 362 UNP P49336 CDK8_HUMAN 1 362 DBREF 5HBJ B 1 264 UNP P24863 CCNC_HUMAN 1 264 SEQADV 5HBJ ASP A -1 UNP P49336 EXPRESSION TAG SEQADV 5HBJ LYS A 0 UNP P49336 EXPRESSION TAG SEQADV 5HBJ ASP B -5 UNP P24863 EXPRESSION TAG SEQADV 5HBJ ASP B -4 UNP P24863 EXPRESSION TAG SEQADV 5HBJ ASP B -3 UNP P24863 EXPRESSION TAG SEQADV 5HBJ ASP B -2 UNP P24863 EXPRESSION TAG SEQADV 5HBJ LYS B -1 UNP P24863 EXPRESSION TAG SEQADV 5HBJ ALA B 0 UNP P24863 EXPRESSION TAG SEQRES 1 A 364 ASP LYS MET ASP TYR ASP PHE LYS VAL LYS LEU SER SER SEQRES 2 A 364 GLU ARG GLU ARG VAL GLU ASP LEU PHE GLU TYR GLU GLY SEQRES 3 A 364 CYS LYS VAL GLY ARG GLY THR TYR GLY HIS VAL TYR LYS SEQRES 4 A 364 ALA LYS ARG LYS ASP GLY LYS ASP ASP LYS ASP TYR ALA SEQRES 5 A 364 LEU LYS GLN ILE GLU GLY THR GLY ILE SER MET SER ALA SEQRES 6 A 364 CYS ARG GLU ILE ALA LEU LEU ARG GLU LEU LYS HIS PRO SEQRES 7 A 364 ASN VAL ILE SER LEU GLN LYS VAL PHE LEU SER HIS ALA SEQRES 8 A 364 ASP ARG LYS VAL TRP LEU LEU PHE ASP TYR ALA GLU HIS SEQRES 9 A 364 ASP LEU TRP HIS ILE ILE LYS PHE HIS ARG ALA SER LYS SEQRES 10 A 364 ALA ASN LYS LYS PRO VAL GLN LEU PRO ARG GLY MET VAL SEQRES 11 A 364 LYS SER LEU LEU TYR GLN ILE LEU ASP GLY ILE HIS TYR SEQRES 12 A 364 LEU HIS ALA ASN TRP VAL LEU HIS ARG ASP LEU LYS PRO SEQRES 13 A 364 ALA ASN ILE LEU VAL MET GLY GLU GLY PRO GLU ARG GLY SEQRES 14 A 364 ARG VAL LYS ILE ALA ASP MET GLY PHE ALA ARG LEU PHE SEQRES 15 A 364 ASN SER PRO LEU LYS PRO LEU ALA ASP LEU ASP PRO VAL SEQRES 16 A 364 VAL VAL THR PHE TRP TYR ARG ALA PRO GLU LEU LEU LEU SEQRES 17 A 364 GLY ALA ARG HIS TYR THR LYS ALA ILE ASP ILE TRP ALA SEQRES 18 A 364 ILE GLY CYS ILE PHE ALA GLU LEU LEU THR SER GLU PRO SEQRES 19 A 364 ILE PHE HIS CYS ARG GLN GLU ASP ILE LYS THR SER ASN SEQRES 20 A 364 PRO TYR HIS HIS ASP GLN LEU ASP ARG ILE PHE ASN VAL SEQRES 21 A 364 MET GLY PHE PRO ALA ASP LYS ASP TRP GLU ASP ILE LYS SEQRES 22 A 364 LYS MET PRO GLU HIS SER THR LEU MET LYS ASP PHE ARG SEQRES 23 A 364 ARG ASN THR TYR THR ASN CYS SER LEU ILE LYS TYR MET SEQRES 24 A 364 GLU LYS HIS LYS VAL LYS PRO ASP SER LYS ALA PHE HIS SEQRES 25 A 364 LEU LEU GLN LYS LEU LEU THR MET ASP PRO ILE LYS ARG SEQRES 26 A 364 ILE THR SER GLU GLN ALA MET GLN ASP PRO TYR PHE LEU SEQRES 27 A 364 GLU ASP PRO LEU PRO THR SER ASP VAL PHE ALA GLY CYS SEQRES 28 A 364 GLN ILE PRO TYR PRO LYS ARG GLU PHE LEU THR GLU GLU SEQRES 1 B 270 ASP ASP ASP ASP LYS ALA MET ALA GLY ASN PHE TRP GLN SEQRES 2 B 270 SER SER HIS TYR LEU GLN TRP ILE LEU ASP LYS GLN ASP SEQRES 3 B 270 LEU LEU LYS GLU ARG GLN LYS ASP LEU LYS PHE LEU SER SEQRES 4 B 270 GLU GLU GLU TYR TRP LYS LEU GLN ILE PHE PHE THR ASN SEQRES 5 B 270 VAL ILE GLN ALA LEU GLY GLU HIS LEU LYS LEU ARG GLN SEQRES 6 B 270 GLN VAL ILE ALA THR ALA THR VAL TYR PHE LYS ARG PHE SEQRES 7 B 270 TYR ALA ARG TYR SER LEU LYS SER ILE ASP PRO VAL LEU SEQRES 8 B 270 MET ALA PRO THR CYS VAL PHE LEU ALA SER LYS VAL GLU SEQRES 9 B 270 GLU PHE GLY VAL VAL SER ASN THR ARG LEU ILE ALA ALA SEQRES 10 B 270 ALA THR SER VAL LEU LYS THR ARG PHE SER TYR ALA PHE SEQRES 11 B 270 PRO LYS GLU PHE PRO TYR ARG MET ASN HIS ILE LEU GLU SEQRES 12 B 270 CYS GLU PHE TYR LEU LEU GLU LEU MET ASP CYS CYS LEU SEQRES 13 B 270 ILE VAL TYR HIS PRO TYR ARG PRO LEU LEU GLN TYR VAL SEQRES 14 B 270 GLN ASP MET GLY GLN GLU ASP MET LEU LEU PRO LEU ALA SEQRES 15 B 270 TRP ARG ILE VAL ASN ASP THR TYR ARG THR ASP LEU CYS SEQRES 16 B 270 LEU LEU TYR PRO PRO PHE MET ILE ALA LEU ALA CYS LEU SEQRES 17 B 270 HIS VAL ALA CYS VAL VAL GLN GLN LYS ASP ALA ARG GLN SEQRES 18 B 270 TRP PHE ALA GLU LEU SER VAL ASP MET GLU LYS ILE LEU SEQRES 19 B 270 GLU ILE ILE ARG VAL ILE LEU LYS LEU TYR GLU GLN TRP SEQRES 20 B 270 LYS ASN PHE ASP GLU ARG LYS GLU MET ALA THR ILE LEU SEQRES 21 B 270 SER LYS MET PRO LYS PRO LYS PRO PRO PRO HET 5Y8 A 401 29 HET EDO A 402 4 HET FMT B 301 3 HETNAM 5Y8 8-[2-AZANYL-3-CHLORANYL-5-(1-METHYLINDAZOL-5-YL) HETNAM 2 5Y8 PYRIDIN-4-YL]-2,8-DIAZASPIRO[4.5]DECAN-1-ONE HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 5Y8 C21 H23 CL N6 O FORMUL 4 EDO C2 H6 O2 FORMUL 5 FMT C H2 O2 FORMUL 6 HOH *16(H2 O) HELIX 1 AA1 ASP A 2 ARG A 13 1 12 HELIX 2 AA2 ARG A 15 LEU A 19 1 5 HELIX 3 AA3 SER A 60 LEU A 73 1 14 HELIX 4 AA4 LEU A 104 SER A 114 1 11 HELIX 5 AA5 PRO A 124 ASN A 145 1 22 HELIX 6 AA6 LYS A 153 ALA A 155 5 3 HELIX 7 AA7 ALA A 201 LEU A 206 1 6 HELIX 8 AA8 THR A 212 SER A 230 1 19 HELIX 9 AA9 HIS A 248 GLY A 260 1 13 HELIX 10 AB1 TRP A 267 MET A 273 5 7 HELIX 11 AB2 GLU A 275 PHE A 283 1 9 HELIX 12 AB3 ARG A 284 THR A 289 5 6 HELIX 13 AB4 SER A 292 HIS A 300 1 9 HELIX 14 AB5 SER A 306 LEU A 316 1 11 HELIX 15 AB6 ASP A 319 ARG A 323 5 5 HELIX 16 AB7 THR A 325 GLN A 331 1 7 HELIX 17 AB8 ASP A 332 GLU A 337 5 6 HELIX 18 AB9 ASN B 4 GLN B 7 5 4 HELIX 19 AC1 SER B 8 ILE B 15 1 8 HELIX 20 AC2 ASP B 17 GLN B 26 1 10 HELIX 21 AC3 SER B 33 LYS B 56 1 24 HELIX 22 AC4 ARG B 58 TYR B 76 1 19 HELIX 23 AC5 ASP B 82 GLU B 98 1 17 HELIX 24 AC6 SER B 104 ARG B 119 1 16 HELIX 25 AC7 ARG B 131 MET B 146 1 16 HELIX 26 AC8 PRO B 155 GLY B 167 1 13 HELIX 27 AC9 LEU B 172 THR B 183 1 12 HELIX 28 AD1 TYR B 184 THR B 186 5 3 HELIX 29 AD2 ASP B 187 TYR B 192 1 6 HELIX 30 AD3 PRO B 193 GLN B 209 1 17 HELIX 31 AD4 ALA B 213 GLU B 219 1 7 HELIX 32 AD5 ASP B 223 PHE B 244 1 22 HELIX 33 AD6 ASP B 245 MET B 257 1 13 SHEET 1 AA1 3 PHE A 20 GLU A 21 0 SHEET 2 AA1 3 GLY A 33 ARG A 40 -1 O LYS A 39 N GLU A 21 SHEET 3 AA1 3 LYS A 26 GLY A 30 -1 N GLY A 28 O VAL A 35 SHEET 1 AA2 5 PHE A 20 GLU A 21 0 SHEET 2 AA2 5 GLY A 33 ARG A 40 -1 O LYS A 39 N GLU A 21 SHEET 3 AA2 5 ASP A 48 ILE A 54 -1 O GLN A 53 N HIS A 34 SHEET 4 AA2 5 LYS A 92 ASP A 98 -1 O PHE A 97 N ALA A 50 SHEET 5 AA2 5 LEU A 81 SER A 87 -1 N PHE A 85 O TRP A 94 SHEET 1 AA3 3 HIS A 102 ASP A 103 0 SHEET 2 AA3 3 ILE A 157 VAL A 159 -1 O VAL A 159 N HIS A 102 SHEET 3 AA3 3 VAL A 169 ILE A 171 -1 O LYS A 170 N LEU A 158 CISPEP 1 ASP A 338 PRO A 339 0 -0.63 SITE 1 AC1 13 VAL A 27 TYR A 32 VAL A 35 ALA A 50 SITE 2 AC1 13 LYS A 52 ILE A 79 ASP A 98 ALA A 100 SITE 3 AC1 13 ASP A 103 LEU A 158 ALA A 172 ASP A 173 SITE 4 AC1 13 ARG A 356 SITE 1 AC2 2 PRO A 124 GLY A 126 SITE 1 AC3 1 GLN B 41 CRYST1 70.749 71.774 176.434 90.00 90.00 90.00 P 21 21 21 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 0.014134 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013933 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005668 0.00000