HEADER CELL CYCLE 12-DEC-19 6TPA TITLE CDK8/CYCLINC IN COMPLEX WITH DRUG ETP-50775 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL DIVISION PROTEIN KINASE 8,MEDIATOR COMPLEX SUBUNIT COMPND 5 CDK8,MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT CDK8,PROTEIN COMPND 6 KINASE K35; COMPND 7 EC: 2.7.11.22,2.7.11.23; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CYCLIN-C; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: SRB11 HOMOLOG,HSRB11; COMPND 13 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: INSECT CELL EXPRESSION VECTOR PTIE1; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 266783; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CCNC; SOURCE 13 EXPRESSION_SYSTEM: INSECT CELL EXPRESSION VECTOR PTIE1; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 266783 KEYWDS CELL DIVISION KINASE INHIBITOR, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR I.G.MUNOZ,J.PASTOR,S.MARTINEZ REVDAT 2 24-JAN-24 6TPA 1 REMARK REVDAT 1 18-NOV-20 6TPA 0 JRNL AUTH S.MARTINEZ-GONZALEZ,A.B.GARCIA,M.I.ALBARRAN,A.CEBRIA, JRNL AUTH 2 A.AMEZQUITA-ALVES,F.J.GARCIA-CAMPOS,J.MARTINEZ-GAGO, JRNL AUTH 3 J.MARTINEZ-TORRECUADRADA,I.MUNOZ,C.BLANCO-APARICIO,J.PASTOR JRNL TITL PYRIDO[2,3-B][1,5]BENZOXAZEPIN-5(6H)-ONE DERIVATIVES AS CDK8 JRNL TITL 2 INHIBITORS. JRNL REF EUR.J.MED.CHEM. V. 201 12443 2020 JRNL REFN ISSN 0223-5234 JRNL PMID 32599324 JRNL DOI 10.1016/J.EJMECH.2020.112443 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 94.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 24925 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1241 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 10.0000 - 5.8234 0.98 2757 147 0.2409 0.2524 REMARK 3 2 5.8234 - 4.6222 1.00 2646 170 0.2120 0.2345 REMARK 3 3 4.6222 - 4.0379 0.99 2627 142 0.1905 0.2583 REMARK 3 4 4.0379 - 3.6687 1.00 2636 131 0.1979 0.2307 REMARK 3 5 3.6687 - 3.4058 1.00 2626 122 0.2187 0.3062 REMARK 3 6 3.4058 - 3.2050 1.00 2639 121 0.2371 0.2512 REMARK 3 7 3.2050 - 3.0444 0.99 2599 124 0.2442 0.2974 REMARK 3 8 3.0444 - 2.9119 1.00 2594 128 0.2814 0.3186 REMARK 3 9 2.9119 - 2.8000 0.99 2560 156 0.3251 0.3877 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.72 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6TPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292105471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-17 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9282 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24925 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 94.564 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 5CEI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 200MM NAFORMATE, 3% REMARK 280 BUTANEDIOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 35.99250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 94.56350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.16950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 94.56350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.99250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.16950 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: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 ALA A 116 REMARK 465 ASN A 117 REMARK 465 LYS A 118 REMARK 465 PHE A 180 REMARK 465 ASN A 181 REMARK 465 SER A 182 REMARK 465 PRO A 183 REMARK 465 LEU A 184 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 VAL A 195 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 SER A 244 REMARK 465 THR A 360 REMARK 465 GLU A 361 REMARK 465 GLU A 362 REMARK 465 GLU A 363 REMARK 465 PRO A 364 REMARK 465 ASP A 365 REMARK 465 ASP A 366 REMARK 465 LYS A 367 REMARK 465 GLY A 368 REMARK 465 ASP A 369 REMARK 465 LYS A 370 REMARK 465 LYS A 371 REMARK 465 ASN A 372 REMARK 465 GLN A 373 REMARK 465 GLN A 374 REMARK 465 GLN A 375 REMARK 465 GLN A 376 REMARK 465 GLN A 377 REMARK 465 GLY A 378 REMARK 465 ASN A 379 REMARK 465 ASN A 380 REMARK 465 HIS A 381 REMARK 465 THR A 382 REMARK 465 ASN A 383 REMARK 465 GLY A 384 REMARK 465 THR A 385 REMARK 465 GLY A 386 REMARK 465 HIS A 387 REMARK 465 PRO A 388 REMARK 465 GLY A 389 REMARK 465 ASN A 390 REMARK 465 GLN A 391 REMARK 465 ASP A 392 REMARK 465 SER A 393 REMARK 465 SER A 394 REMARK 465 HIS A 395 REMARK 465 THR A 396 REMARK 465 GLN A 397 REMARK 465 GLY A 398 REMARK 465 PRO A 399 REMARK 465 PRO A 400 REMARK 465 LEU A 401 REMARK 465 LYS A 402 REMARK 465 LYS A 403 REMARK 465 PRO B 264 REMARK 465 ASN B 265 REMARK 465 SER B 266 REMARK 465 GLU B 267 REMARK 465 GLY B 268 REMARK 465 GLU B 269 REMARK 465 GLN B 270 REMARK 465 GLY B 271 REMARK 465 PRO B 272 REMARK 465 ASN B 273 REMARK 465 GLY B 274 REMARK 465 SER B 275 REMARK 465 GLN B 276 REMARK 465 ASN B 277 REMARK 465 SER B 278 REMARK 465 SER B 279 REMARK 465 TYR B 280 REMARK 465 SER B 281 REMARK 465 GLN B 282 REMARK 465 SER B 283 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 LYS A 0 CG CD CE NZ REMARK 470 LYS A 6 NZ REMARK 470 LYS A 8 CD CE NZ REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 VAL A 27 CB CG1 CG2 REMARK 470 ARG A 29 CB CG CD NE CZ NH1 NH2 REMARK 470 THR A 31 CB OG1 CG2 REMARK 470 LYS A 39 CG CD CE NZ REMARK 470 ARG A 40 NE CZ NH1 NH2 REMARK 470 ASP A 42 CG OD1 OD2 REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 ASP A 46 CG OD1 OD2 REMARK 470 LYS A 47 CD CE NZ REMARK 470 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 LYS A 109 CE NZ REMARK 470 SER A 114 OG REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 GLN A 122 CG CD OE1 NE2 REMARK 470 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 179 CB CG CD1 CD2 REMARK 470 ARG A 209 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 237 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 238 CG CD OE1 NE2 REMARK 470 ASP A 264 CG OD1 OD2 REMARK 470 LYS A 271 CD CE NZ REMARK 470 LYS A 281 CE NZ REMARK 470 ARG A 284 NE CZ NH1 NH2 REMARK 470 ASN A 286 OD1 ND2 REMARK 470 ASN A 290 CG OD1 ND2 REMARK 470 LYS A 299 CG CD CE NZ REMARK 470 LYS A 301 CG CD CE NZ REMARK 470 LYS A 303 CG CD CE NZ REMARK 470 GLN A 350 CG CD OE1 NE2 REMARK 470 LYS A 355 NZ REMARK 470 GLU A 357 CG CD OE1 OE2 REMARK 470 GLN B 19 CG CD OE1 NE2 REMARK 470 ASP B 20 CG OD1 OD2 REMARK 470 LEU B 22 CG CD1 CD2 REMARK 470 LYS B 23 CG CD CE NZ REMARK 470 GLN B 26 CG CD OE1 NE2 REMARK 470 LYS B 27 CG CD CE NZ REMARK 470 LYS B 30 CG CD CE NZ REMARK 470 GLU B 35 CG CD OE1 OE2 REMARK 470 LYS B 56 CG CD CE NZ REMARK 470 ARG B 58 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 59 CG CD OE1 NE2 REMARK 470 LYS B 79 NZ REMARK 470 PHE B 100 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 117 CD CE NZ REMARK 470 ARG B 119 NE CZ NH1 NH2 REMARK 470 GLU B 127 CG CD OE1 OE2 REMARK 470 ASN B 133 CG OD1 ND2 REMARK 470 LEU B 145 CG CD1 CD2 REMARK 470 ARG B 157 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 170 CG OD1 OD2 REMARK 470 MET B 171 CG SD CE REMARK 470 GLN B 210 CG CD OE1 NE2 REMARK 470 LYS B 211 CG CD CE NZ REMARK 470 ARG B 214 CG CD NE CZ NH1 NH2 REMARK 470 SER B 221 OG REMARK 470 VAL B 222 CG1 CG2 REMARK 470 ASP B 223 CG OD1 OD2 REMARK 470 GLU B 225 CG CD OE1 OE2 REMARK 470 LYS B 236 CE NZ REMARK 470 LYS B 256 NZ REMARK 470 LYS B 259 NZ REMARK 470 LYS B 261 CG CD CE NZ 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 71 O HOH A 601 1.93 REMARK 500 OE1 GLU A 165 NH1 ARG A 168 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 ARG A 13 CA - CB - CG ANGL. DEV. = 17.3 DEGREES REMARK 500 LEU B 237 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 THR A 31 -22.79 113.58 REMARK 500 ALA A 89 -72.87 -64.49 REMARK 500 ARG A 91 70.31 -59.19 REMARK 500 ASP A 151 33.76 -170.80 REMARK 500 ARG A 178 -77.19 -43.43 REMARK 500 ARG A 237 -177.02 -64.91 REMARK 500 ALA A 347 -118.76 58.02 REMARK 500 GLN B 13 -0.04 -143.28 REMARK 500 GLU B 99 -2.46 66.45 REMARK 500 GLU B 127 139.38 122.27 REMARK 500 ASP B 223 94.86 -58.54 REMARK 500 ASP B 245 77.54 -116.29 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 NZ8 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NZ5 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NZ5 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NZ5 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NZ5 B 310 DBREF 6TPA A 1 403 UNP P49336 CDK8_HUMAN 1 403 DBREF 6TPA B 1 283 UNP P24863 CCNC_HUMAN 1 283 SEQADV 6TPA SER A -1 UNP P49336 EXPRESSION TAG SEQADV 6TPA LYS A 0 UNP P49336 EXPRESSION TAG SEQADV 6TPA LYS B -1 UNP P24863 EXPRESSION TAG SEQADV 6TPA ALA B 0 UNP P24863 EXPRESSION TAG SEQRES 1 A 405 SER LYS MET ASP TYR ASP PHE LYS VAL LYS LEU SER SER SEQRES 2 A 405 GLU ARG GLU ARG VAL GLU ASP LEU PHE GLU TYR GLU GLY SEQRES 3 A 405 CYS LYS VAL GLY ARG GLY THR TYR GLY HIS VAL TYR LYS SEQRES 4 A 405 ALA LYS ARG LYS ASP GLY LYS ASP ASP LYS ASP TYR ALA SEQRES 5 A 405 LEU LYS GLN ILE GLU GLY THR GLY ILE SER MET SER ALA SEQRES 6 A 405 CYS ARG GLU ILE ALA LEU LEU ARG GLU LEU LYS HIS PRO SEQRES 7 A 405 ASN VAL ILE SER LEU GLN LYS VAL PHE LEU SER HIS ALA SEQRES 8 A 405 ASP ARG LYS VAL TRP LEU LEU PHE ASP TYR ALA GLU HIS SEQRES 9 A 405 ASP LEU TRP HIS ILE ILE LYS PHE HIS ARG ALA SER LYS SEQRES 10 A 405 ALA ASN LYS LYS PRO VAL GLN LEU PRO ARG GLY MET VAL SEQRES 11 A 405 LYS SER LEU LEU TYR GLN ILE LEU ASP GLY ILE HIS TYR SEQRES 12 A 405 LEU HIS ALA ASN TRP VAL LEU HIS ARG ASP LEU LYS PRO SEQRES 13 A 405 ALA ASN ILE LEU VAL MET GLY GLU GLY PRO GLU ARG GLY SEQRES 14 A 405 ARG VAL LYS ILE ALA ASP MET GLY PHE ALA ARG LEU PHE SEQRES 15 A 405 ASN SER PRO LEU LYS PRO LEU ALA ASP LEU ASP PRO VAL SEQRES 16 A 405 VAL VAL THR PHE TRP TYR ARG ALA PRO GLU LEU LEU LEU SEQRES 17 A 405 GLY ALA ARG HIS TYR THR LYS ALA ILE ASP ILE TRP ALA SEQRES 18 A 405 ILE GLY CYS ILE PHE ALA GLU LEU LEU THR SER GLU PRO SEQRES 19 A 405 ILE PHE HIS CYS ARG GLN GLU ASP ILE LYS THR SER ASN SEQRES 20 A 405 PRO TYR HIS HIS ASP GLN LEU ASP ARG ILE PHE ASN VAL SEQRES 21 A 405 MET GLY PHE PRO ALA ASP LYS ASP TRP GLU ASP ILE LYS SEQRES 22 A 405 LYS MET PRO GLU HIS SER THR LEU MET LYS ASP PHE ARG SEQRES 23 A 405 ARG ASN THR TYR THR ASN CYS SER LEU ILE LYS TYR MET SEQRES 24 A 405 GLU LYS HIS LYS VAL LYS PRO ASP SER LYS ALA PHE HIS SEQRES 25 A 405 LEU LEU GLN LYS LEU LEU THR MET ASP PRO ILE LYS ARG SEQRES 26 A 405 ILE THR SER GLU GLN ALA MET GLN ASP PRO TYR PHE LEU SEQRES 27 A 405 GLU ASP PRO LEU PRO THR SER ASP VAL PHE ALA GLY CYS SEQRES 28 A 405 GLN ILE PRO TYR PRO LYS ARG GLU PHE LEU THR GLU GLU SEQRES 29 A 405 GLU PRO ASP ASP LYS GLY ASP LYS LYS ASN GLN GLN GLN SEQRES 30 A 405 GLN GLN GLY ASN ASN HIS THR ASN GLY THR GLY HIS PRO SEQRES 31 A 405 GLY ASN GLN ASP SER SER HIS THR GLN GLY PRO PRO LEU SEQRES 32 A 405 LYS LYS SEQRES 1 B 285 LYS ALA MET ALA GLY ASN PHE TRP GLN SER SER HIS TYR SEQRES 2 B 285 LEU GLN TRP ILE LEU ASP LYS GLN ASP LEU LEU LYS GLU SEQRES 3 B 285 ARG GLN LYS ASP LEU LYS PHE LEU SER GLU GLU GLU TYR SEQRES 4 B 285 TRP LYS LEU GLN ILE PHE PHE THR ASN VAL ILE GLN ALA SEQRES 5 B 285 LEU GLY GLU HIS LEU LYS LEU ARG GLN GLN VAL ILE ALA SEQRES 6 B 285 THR ALA THR VAL TYR PHE LYS ARG PHE TYR ALA ARG TYR SEQRES 7 B 285 SER LEU LYS SER ILE ASP PRO VAL LEU MET ALA PRO THR SEQRES 8 B 285 CYS VAL PHE LEU ALA SER LYS VAL GLU GLU PHE GLY VAL SEQRES 9 B 285 VAL SER ASN THR ARG LEU ILE ALA ALA ALA THR SER VAL SEQRES 10 B 285 LEU LYS THR ARG PHE SER TYR ALA PHE PRO LYS GLU PHE SEQRES 11 B 285 PRO TYR ARG MET ASN HIS ILE LEU GLU CYS GLU PHE TYR SEQRES 12 B 285 LEU LEU GLU LEU MET ASP CYS CYS LEU ILE VAL TYR HIS SEQRES 13 B 285 PRO TYR ARG PRO LEU LEU GLN TYR VAL GLN ASP MET GLY SEQRES 14 B 285 GLN GLU ASP MET LEU LEU PRO LEU ALA TRP ARG ILE VAL SEQRES 15 B 285 ASN ASP THR TYR ARG THR ASP LEU CYS LEU LEU TYR PRO SEQRES 16 B 285 PRO PHE MET ILE ALA LEU ALA CYS LEU HIS VAL ALA CYS SEQRES 17 B 285 VAL VAL GLN GLN LYS ASP ALA ARG GLN TRP PHE ALA GLU SEQRES 18 B 285 LEU SER VAL ASP MET GLU LYS ILE LEU GLU ILE ILE ARG SEQRES 19 B 285 VAL ILE LEU LYS LEU TYR GLU GLN TRP LYS ASN PHE ASP SEQRES 20 B 285 GLU ARG LYS GLU MET ALA THR ILE LEU SER LYS MET PRO SEQRES 21 B 285 LYS PRO LYS PRO PRO PRO ASN SER GLU GLY GLU GLN GLY SEQRES 22 B 285 PRO ASN GLY SER GLN ASN SER SER TYR SER GLN SER HET NZ8 A 501 37 HET FMT A 502 3 HET FMT A 503 3 HET FMT A 504 3 HET NZ5 A 505 6 HET NZ5 A 506 6 HET NZ5 A 507 6 HET FMT B 301 3 HET FMT B 302 3 HET FMT B 303 3 HET FMT B 304 3 HET FMT B 305 3 HET FMT B 306 3 HET FMT B 307 3 HET FMT B 308 3 HET FMT B 309 3 HET NZ5 B 310 6 HETNAM NZ8 1-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENYL]-3-(5- HETNAM 2 NZ8 OXIDANYLIDENE-6-PYRIDIN-4-YL-PYRIDO[2,3-B][1, HETNAM 3 NZ8 5]BENZOXAZEPIN-9-YL)UREA HETNAM FMT FORMIC ACID HETNAM NZ5 (2~{R})-BUTANE-1,2-DIOL FORMUL 3 NZ8 C25 H15 CL F3 N5 O3 FORMUL 4 FMT 12(C H2 O2) FORMUL 7 NZ5 4(C4 H10 O2) FORMUL 20 HOH *88(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 ARG A 71 1 12 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 LYS B 27 PHE B 31 5 5 HELIX 22 AC4 SER B 33 LEU B 55 1 23 HELIX 23 AC5 ARG B 58 TYR B 76 1 19 HELIX 24 AC6 ASP B 82 GLU B 98 1 17 HELIX 25 AC7 SER B 104 PHE B 120 1 17 HELIX 26 AC8 ARG B 131 ASP B 147 1 17 HELIX 27 AC9 PRO B 155 GLY B 167 1 13 HELIX 28 AD1 GLN B 168 TYR B 184 1 17 HELIX 29 AD2 ASP B 187 TYR B 192 1 6 HELIX 30 AD3 PRO B 193 GLN B 210 1 18 HELIX 31 AD4 ALA B 213 LEU B 220 1 8 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 CYS A 25 ARG A 29 -1 N VAL A 27 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 GLN A 53 -1 O TYR A 49 N ALA A 38 SHEET 4 AA2 5 LYS A 92 ASP A 98 -1 O LEU A 95 N LYS A 52 SHEET 5 AA2 5 LEU A 81 SER A 87 -1 N GLN A 82 O LEU A 96 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 -10.90 SITE 1 AC1 20 TYR A 32 VAL A 35 ALA A 50 LYS A 52 SITE 2 AC1 20 GLU A 66 LEU A 70 LEU A 73 VAL A 78 SITE 3 AC1 20 ILE A 79 PHE A 97 ASP A 98 ALA A 100 SITE 4 AC1 20 LEU A 142 HIS A 149 ILE A 171 ALA A 172 SITE 5 AC1 20 ASP A 173 MET A 174 PHE A 176 ARG A 356 SITE 1 AC2 1 LEU A 73 SITE 1 AC3 2 LEU A 148 ARG A 150 SITE 1 AC4 1 NZ5 A 505 SITE 1 AC5 2 GLN A 82 FMT A 504 SITE 1 AC6 2 PRO A 341 SER A 343 SITE 1 AC7 5 ARG A 125 ALA A 308 TYR A 334 GLU A 337 SITE 2 AC7 5 HOH A 645 SITE 1 AC8 2 LYS B 226 GLU B 229 SITE 1 AC9 2 SER B 9 GLN B 13 SITE 1 AD1 3 ASP B 187 LEU B 191 VAL B 233 SITE 1 AD2 2 ASN B 46 ASP B 182 SITE 1 AD3 1 LEU B 173 SITE 1 AD4 2 ALA B 0 VAL B 152 SITE 1 AD5 2 ILE B 15 HOH B 411 SITE 1 AD6 4 LYS A 307 LEU A 336 GLU A 337 HOH B 410 SITE 1 AD7 1 VAL B 207 SITE 1 AD8 1 ARG B 178 CRYST1 71.985 72.339 189.127 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 0.013892 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005287 0.00000