HEADER CELL CYCLE 21-MAR-19 6R3S TITLE CRYSTAL STRUCTURE OF CDK8-CYCC IN COMPLEX WITH COMPOUND 1 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: 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 KINASE, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR J.BOETTCHER REVDAT 3 15-MAY-24 6R3S 1 REMARK REVDAT 2 22-APR-20 6R3S 1 JRNL REVDAT 1 08-APR-20 6R3S 0 JRNL AUTH M.H.HOFMANN,R.MANI,H.ENGELHARDT,M.A.IMPAGNATIELLO,S.CAROTTA, JRNL AUTH 2 M.KERENYI,S.LORENZO-HERRERO,J.BOTTCHER,D.SCHARN,H.ARNHOF, JRNL AUTH 3 A.ZOEPHEL,R.SCHNITZER,T.GERSTBERGER,M.P.SANDERSON, JRNL AUTH 4 G.RAJGOLIKAR,S.GOSWAMI,S.VASU,P.ETTMAYER,S.GONZALEZ, JRNL AUTH 5 M.PEARSON,D.B.MCCONNELL,N.KRAUT,N.MUTHUSAMY,J.MOLL JRNL TITL SELECTIVE AND POTENT CDK8/19 INHIBITORS ENHANCE NK-CELL JRNL TITL 2 ACTIVITY AND PROMOTE TUMOR SURVEILLANCE. JRNL REF MOL.CANCER THER. V. 19 1018 2020 JRNL REFN ESSN 1538-8514 JRNL PMID 32024684 JRNL DOI 10.1158/1535-7163.MCT-19-0789 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 41621 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1460 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3034 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5081 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : -0.21000 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): 0.225 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.263 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5117 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4818 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6945 ; 1.242 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11047 ; 2.546 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 615 ; 5.440 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;32.658 ;23.696 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 851 ;11.625 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;12.521 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 758 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5712 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1194 ; 0.003 ; 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): 2466 ; 2.366 ; 2.558 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2467 ; 2.366 ; 2.560 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3079 ; 3.642 ; 4.281 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3080 ; 3.643 ; 4.282 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2651 ; 3.031 ; 2.873 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2645 ; 2.983 ; 2.863 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3867 ; 4.545 ; 4.698 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5924 ; 7.370 ;11.849 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5877 ; 7.346 ;11.744 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): 1.4390 70.2300 58.1440 REMARK 3 T TENSOR REMARK 3 T11: 0.3318 T22: 0.2640 REMARK 3 T33: 0.1734 T12: -0.0279 REMARK 3 T13: -0.0183 T23: 0.0456 REMARK 3 L TENSOR REMARK 3 L11: 2.0338 L22: 5.0104 REMARK 3 L33: 1.0412 L12: -3.1804 REMARK 3 L13: -0.4425 L23: 0.6972 REMARK 3 S TENSOR REMARK 3 S11: 0.2545 S12: 0.2263 S13: -0.0202 REMARK 3 S21: -0.3883 S22: -0.2763 S23: 0.0851 REMARK 3 S31: 0.0120 S32: -0.1210 S33: 0.0218 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 100 A 365 REMARK 3 ORIGIN FOR THE GROUP (A): 10.3240 40.4780 57.5120 REMARK 3 T TENSOR REMARK 3 T11: 0.1670 T22: 0.1088 REMARK 3 T33: 0.0050 T12: 0.0087 REMARK 3 T13: -0.0251 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 1.7424 L22: 2.8747 REMARK 3 L33: 1.1549 L12: 0.7467 REMARK 3 L13: -0.0259 L23: -0.0779 REMARK 3 S TENSOR REMARK 3 S11: -0.0146 S12: 0.2132 S13: -0.0257 REMARK 3 S21: -0.1781 S22: 0.0341 S23: 0.0499 REMARK 3 S31: 0.0364 S32: -0.0564 S33: -0.0194 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -3 B 266 REMARK 3 ORIGIN FOR THE GROUP (A): -3.6370 69.9390 87.1220 REMARK 3 T TENSOR REMARK 3 T11: 0.1305 T22: 0.0791 REMARK 3 T33: 0.0816 T12: -0.0345 REMARK 3 T13: 0.0451 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.7962 L22: 1.4744 REMARK 3 L33: 2.5261 L12: -0.4427 REMARK 3 L13: 0.0784 L23: -0.4017 REMARK 3 S TENSOR REMARK 3 S11: 0.0313 S12: -0.0736 S13: 0.0463 REMARK 3 S21: 0.0330 S22: 0.0351 S23: 0.0033 REMARK 3 S31: -0.0924 S32: 0.0568 S33: -0.0665 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 6R3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 2 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) : 0.99988 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 : 43086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 84.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M SODIUM FORMATE, PH REMARK 280 6.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 35.29900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.89250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 84.89250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.29900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.56000 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: 4730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 THR A 31 REMARK 465 TYR A 32 REMARK 465 GLY A 33 REMARK 465 LYS A 119 REMARK 465 PRO A 120 REMARK 465 VAL A 121 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 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 ASP B -3 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 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 CB CG OD1 OD2 REMARK 480 LYS A 0 CG CD CE NZ REMARK 480 LYS A 6 CE NZ REMARK 480 LYS A 26 CE NZ REMARK 480 ARG A 29 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 39 CG CD CE NZ REMARK 480 ARG A 40 CZ NH1 NH2 REMARK 480 LYS A 44 CG CD CE NZ REMARK 480 LYS A 47 CD CE NZ REMARK 480 GLU A 55 CG CD OE1 OE2 REMARK 480 LYS A 74 CD CE NZ REMARK 480 LYS A 83 CD CE NZ REMARK 480 LYS A 109 CE NZ REMARK 480 ARG A 112 CZ NH1 NH2 REMARK 480 SER A 114 OG REMARK 480 LYS A 115 CG CD CE NZ REMARK 480 ASN A 117 CG OD1 ND2 REMARK 480 LYS A 118 CG CD CE NZ REMARK 480 GLN A 122 CG CD OE1 NE2 REMARK 480 ARG A 209 CD NE CZ NH1 NH2 REMARK 480 ARG A 237 CZ NH1 NH2 REMARK 480 GLN A 238 CG CD OE1 NE2 REMARK 480 SER A 244 OG REMARK 480 ASN A 245 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 281 CE NZ REMARK 480 LYS A 295 CD CE NZ REMARK 480 LYS A 299 CG CD CE NZ REMARK 480 LYS A 301 CD CE NZ REMARK 480 LYS A 303 CD CE NZ REMARK 480 GLN A 350 CG CD OE1 NE2 REMARK 480 GLU A 357 CD OE1 OE2 REMARK 480 LYS B -1 CG CD CE NZ REMARK 480 LYS B 18 CE NZ REMARK 480 LYS B 23 CG CD CE NZ REMARK 480 LYS B 30 CD CE NZ REMARK 480 LYS B 56 CD CE NZ REMARK 480 LYS B 117 CD CE NZ REMARK 480 LYS B 126 CD CE NZ REMARK 480 ARG B 131 CD NE CZ NH1 NH2 REMARK 480 ARG B 157 CZ NH1 NH2 REMARK 480 LYS B 211 CD CE NZ REMARK 480 ARG B 214 CZ NH1 NH2 REMARK 480 GLN B 215 CG CD OE1 NE2 REMARK 480 SER B 221 OG REMARK 480 GLU B 225 CG CD OE1 OE2 REMARK 480 LYS B 226 CD CE NZ REMARK 480 LYS B 259 CG CD CE NZ 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 B 237 CA - CB - CG ANGL. DEV. = 14.1 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 ARG A 29 92.93 -163.02 REMARK 500 ASP A 151 42.89 -161.72 REMARK 500 TRP A 267 80.51 -151.61 REMARK 500 HIS A 300 30.57 -93.86 REMARK 500 LEU A 316 48.82 -93.15 REMARK 500 PHE B 128 108.05 -53.51 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 JRE A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 304 DBREF 6R3S A 1 403 UNP P49336 CDK8_HUMAN 1 403 DBREF 6R3S B 1 283 UNP P24863 CCNC_HUMAN 1 283 SEQADV 6R3S ASP A -2 UNP P49336 EXPRESSION TAG SEQADV 6R3S ASP A -1 UNP P49336 EXPRESSION TAG SEQADV 6R3S LYS A 0 UNP P49336 EXPRESSION TAG SEQADV 6R3S ASP B -3 UNP P24863 EXPRESSION TAG SEQADV 6R3S ASP B -2 UNP P24863 EXPRESSION TAG SEQADV 6R3S LYS B -1 UNP P24863 EXPRESSION TAG SEQADV 6R3S ALA B 0 UNP P24863 EXPRESSION TAG SEQRES 1 A 406 ASP ASP LYS MET ASP TYR ASP PHE LYS VAL LYS LEU SER SEQRES 2 A 406 SER GLU ARG GLU ARG VAL GLU ASP LEU PHE GLU TYR GLU SEQRES 3 A 406 GLY CYS LYS VAL GLY ARG GLY THR TYR GLY HIS VAL TYR SEQRES 4 A 406 LYS ALA LYS ARG LYS ASP GLY LYS ASP ASP LYS ASP TYR SEQRES 5 A 406 ALA LEU LYS GLN ILE GLU GLY THR GLY ILE SER MET SER SEQRES 6 A 406 ALA CYS ARG GLU ILE ALA LEU LEU ARG GLU LEU LYS HIS SEQRES 7 A 406 PRO ASN VAL ILE SER LEU GLN LYS VAL PHE LEU SER HIS SEQRES 8 A 406 ALA ASP ARG LYS VAL TRP LEU LEU PHE ASP TYR ALA GLU SEQRES 9 A 406 HIS ASP LEU TRP HIS ILE ILE LYS PHE HIS ARG ALA SER SEQRES 10 A 406 LYS ALA ASN LYS LYS PRO VAL GLN LEU PRO ARG GLY MET SEQRES 11 A 406 VAL LYS SER LEU LEU TYR GLN ILE LEU ASP GLY ILE HIS SEQRES 12 A 406 TYR LEU HIS ALA ASN TRP VAL LEU HIS ARG ASP LEU LYS SEQRES 13 A 406 PRO ALA ASN ILE LEU VAL MET GLY GLU GLY PRO GLU ARG SEQRES 14 A 406 GLY ARG VAL LYS ILE ALA ASP MET GLY PHE ALA ARG LEU SEQRES 15 A 406 PHE ASN SER PRO LEU LYS PRO LEU ALA ASP LEU ASP PRO SEQRES 16 A 406 VAL VAL VAL THR PHE TRP TYR ARG ALA PRO GLU LEU LEU SEQRES 17 A 406 LEU GLY ALA ARG HIS TYR THR LYS ALA ILE ASP ILE TRP SEQRES 18 A 406 ALA ILE GLY CYS ILE PHE ALA GLU LEU LEU THR SER GLU SEQRES 19 A 406 PRO ILE PHE HIS CYS ARG GLN GLU ASP ILE LYS THR SER SEQRES 20 A 406 ASN PRO TYR HIS HIS ASP GLN LEU ASP ARG ILE PHE ASN SEQRES 21 A 406 VAL MET GLY PHE PRO ALA ASP LYS ASP TRP GLU ASP ILE SEQRES 22 A 406 LYS LYS MET PRO GLU HIS SER THR LEU MET LYS ASP PHE SEQRES 23 A 406 ARG ARG ASN THR TYR THR ASN CYS SER LEU ILE LYS TYR SEQRES 24 A 406 MET GLU LYS HIS LYS VAL LYS PRO ASP SER LYS ALA PHE SEQRES 25 A 406 HIS LEU LEU GLN LYS LEU LEU THR MET ASP PRO ILE LYS SEQRES 26 A 406 ARG ILE THR SER GLU GLN ALA MET GLN ASP PRO TYR PHE SEQRES 27 A 406 LEU GLU ASP PRO LEU PRO THR SER ASP VAL PHE ALA GLY SEQRES 28 A 406 CYS GLN ILE PRO TYR PRO LYS ARG GLU PHE LEU THR GLU SEQRES 29 A 406 GLU GLU PRO ASP ASP LYS GLY ASP LYS LYS ASN GLN GLN SEQRES 30 A 406 GLN GLN GLN GLY ASN ASN HIS THR ASN GLY THR GLY HIS SEQRES 31 A 406 PRO GLY ASN GLN ASP SER SER HIS THR GLN GLY PRO PRO SEQRES 32 A 406 LEU LYS LYS SEQRES 1 B 287 ASP ASP LYS ALA MET ALA GLY ASN PHE TRP GLN SER SER SEQRES 2 B 287 HIS TYR LEU GLN TRP ILE LEU ASP LYS GLN ASP LEU LEU SEQRES 3 B 287 LYS GLU ARG GLN LYS ASP LEU LYS PHE LEU SER GLU GLU SEQRES 4 B 287 GLU TYR TRP LYS LEU GLN ILE PHE PHE THR ASN VAL ILE SEQRES 5 B 287 GLN ALA LEU GLY GLU HIS LEU LYS LEU ARG GLN GLN VAL SEQRES 6 B 287 ILE ALA THR ALA THR VAL TYR PHE LYS ARG PHE TYR ALA SEQRES 7 B 287 ARG TYR SER LEU LYS SER ILE ASP PRO VAL LEU MET ALA SEQRES 8 B 287 PRO THR CYS VAL PHE LEU ALA SER LYS VAL GLU GLU PHE SEQRES 9 B 287 GLY VAL VAL SER ASN THR ARG LEU ILE ALA ALA ALA THR SEQRES 10 B 287 SER VAL LEU LYS THR ARG PHE SER TYR ALA PHE PRO LYS SEQRES 11 B 287 GLU PHE PRO TYR ARG MET ASN HIS ILE LEU GLU CYS GLU SEQRES 12 B 287 PHE TYR LEU LEU GLU LEU MET ASP CYS CYS LEU ILE VAL SEQRES 13 B 287 TYR HIS PRO TYR ARG PRO LEU LEU GLN TYR VAL GLN ASP SEQRES 14 B 287 MET GLY GLN GLU ASP MET LEU LEU PRO LEU ALA TRP ARG SEQRES 15 B 287 ILE VAL ASN ASP THR TYR ARG THR ASP LEU CYS LEU LEU SEQRES 16 B 287 TYR PRO PRO PHE MET ILE ALA LEU ALA CYS LEU HIS VAL SEQRES 17 B 287 ALA CYS VAL VAL GLN GLN LYS ASP ALA ARG GLN TRP PHE SEQRES 18 B 287 ALA GLU LEU SER VAL ASP MET GLU LYS ILE LEU GLU ILE SEQRES 19 B 287 ILE ARG VAL ILE LEU LYS LEU TYR GLU GLN TRP LYS ASN SEQRES 20 B 287 PHE ASP GLU ARG LYS GLU MET ALA THR ILE LEU SER LYS SEQRES 21 B 287 MET PRO LYS PRO LYS PRO PRO PRO ASN SER GLU GLY GLU SEQRES 22 B 287 GLN GLY PRO ASN GLY SER GLN ASN SER SER TYR SER GLN SEQRES 23 B 287 SER HET JRE A 501 23 HET EDO B 301 4 HET FMT B 302 3 HET FMT B 303 3 HET FMT B 304 3 HETNAM JRE 6-[5-CHLORANYL-4-[(1~{S})-1-OXIDANYLETHYL]PYRIDIN-3- HETNAM 2 JRE YL]-3,4-DIHYDRO-2~{H}-1,8-NAPHTHYRIDINE-1-CARBOXAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 JRE C16 H17 CL N4 O2 FORMUL 4 EDO C2 H6 O2 FORMUL 5 FMT 3(C H2 O2) FORMUL 8 HOH *213(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 ASN A 117 1 14 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 ARG A 178 SER A 182 5 5 HELIX 8 AA8 ALA A 201 LEU A 206 1 6 HELIX 9 AA9 THR A 212 SER A 230 1 19 HELIX 10 AB1 HIS A 248 GLY A 260 1 13 HELIX 11 AB2 ALA A 263 MET A 273 5 11 HELIX 12 AB3 GLU A 275 PHE A 283 1 9 HELIX 13 AB4 ARG A 284 THR A 289 5 6 HELIX 14 AB5 SER A 292 HIS A 300 1 9 HELIX 15 AB6 SER A 306 LEU A 316 1 11 HELIX 16 AB7 ASP A 319 ARG A 323 5 5 HELIX 17 AB8 THR A 325 GLN A 331 1 7 HELIX 18 AB9 ASP A 332 LEU A 336 5 5 HELIX 19 AC1 ASN B 4 GLN B 7 5 4 HELIX 20 AC2 SER B 8 ILE B 15 1 8 HELIX 21 AC3 ASP B 17 GLN B 26 1 10 HELIX 22 AC4 LYS B 27 PHE B 31 5 5 HELIX 23 AC5 SER B 33 LEU B 55 1 23 HELIX 24 AC6 ARG B 58 TYR B 76 1 19 HELIX 25 AC7 ASP B 82 GLU B 98 1 17 HELIX 26 AC8 SER B 104 PHE B 120 1 17 HELIX 27 AC9 ARG B 131 MET B 146 1 16 HELIX 28 AD1 PRO B 155 GLY B 167 1 13 HELIX 29 AD2 GLN B 168 TYR B 184 1 17 HELIX 30 AD3 ASP B 187 TYR B 192 1 6 HELIX 31 AD4 PRO B 193 GLN B 209 1 17 HELIX 32 AD5 ALA B 213 GLU B 219 1 7 HELIX 33 AD6 ASP B 223 PHE B 244 1 22 HELIX 34 AD7 ASP B 245 LYS B 256 1 12 SHEET 1 AA1 3 PHE A 20 GLU A 21 0 SHEET 2 AA1 3 VAL A 35 ARG A 40 -1 O LYS A 39 N GLU A 21 SHEET 3 AA1 3 LYS A 26 GLY A 28 -1 N GLY A 28 O VAL A 35 SHEET 1 AA2 5 PHE A 20 GLU A 21 0 SHEET 2 AA2 5 VAL A 35 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 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 0.65 SITE 1 AC1 15 VAL A 27 GLY A 28 ALA A 50 ILE A 79 SITE 2 AC1 15 PHE A 97 ASP A 98 ALA A 100 ASP A 103 SITE 3 AC1 15 ALA A 155 LEU A 158 ALA A 172 ASP A 173 SITE 4 AC1 15 ARG A 356 HOH A 623 HOH A 684 SITE 1 AC2 4 ARG A 71 LYS A 83 VAL A 84 ASP B 147 SITE 1 AC3 3 ALA B 0 VAL B 152 TYR B 153 SITE 1 AC4 4 GLN B 41 PHE B 69 HOH B 402 HOH B 410 SITE 1 AC5 4 LYS B 27 TYR B 76 SER B 77 SER B 80 CRYST1 70.598 71.120 169.785 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 0.014165 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005890 0.00000