HEADER TRANSCRIPTION 18-MAR-21 7NXK TITLE CRYSTAL STRUCTURE OF HUMAN CDK12/CYCLIN K IN COMPLEX WITH THE TITLE 2 INHIBITOR BSJ-01-175 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 12; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: CDC2-RELATED KINASE,ARGININE/SERINE-RICH,CRKRS,CELL DIVISION COMPND 5 CYCLE 2-RELATED PROTEIN KINASE 7,CDC2-RELATED PROTEIN KINASE 7,CELL COMPND 6 DIVISION PROTEIN KINASE 12,HCDK12; COMPND 7 EC: 2.7.11.22,2.7.11.23; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CYCLIN-K; COMPND 11 CHAIN: B, D; COMPND 12 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: CDK12, CRK7, CRKRS, KIAA0904; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CCNK, CPR4; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CDK12, CYCLIN K, CCNK, BSJ-01-175, KINASE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.ANAND,S.DUST,I.H.KALTHEUNER,M.GEYER REVDAT 2 31-JAN-24 7NXK 1 REMARK FORMUL REVDAT 1 12-MAY-21 7NXK 0 JRNL AUTH B.JIANG,J.JIANG,I.H.KALTHEUNER,A.B.INIGUEZ,K.ANAND, JRNL AUTH 2 F.M.FERGUSON,S.B.FICARRO,B.K.A.SEONG,A.K.GREIFENBERG,S.DUST, JRNL AUTH 3 N.P.KWIATKOWSKI,J.A.MARTO,K.STEGMAIER,T.ZHANG,M.GEYER, JRNL AUTH 4 N.S.GRAY JRNL TITL STRUCTURE-ACTIVITY RELATIONSHIP STUDY OF THZ531 DERIVATIVES JRNL TITL 2 ENABLES THE DISCOVERY OF BSJ-01-175 AS A DUAL CDK12/13 JRNL TITL 3 COVALENT INHIBITOR WITH EFFICACY IN EWING SARCOMA. JRNL REF EUR.J.MED.CHEM. V. 221 13481 2021 JRNL REFN ISSN 0223-5234 JRNL PMID 33945934 JRNL DOI 10.1016/J.EJMECH.2021.113481 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.950 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 25397 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.210 REMARK 3 FREE R VALUE TEST SET COUNT : 1069 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 49.0000 - 6.0000 0.97 3039 134 0.1816 0.2221 REMARK 3 2 6.0000 - 4.7600 0.98 3087 135 0.2141 0.2688 REMARK 3 3 4.7600 - 4.1600 0.98 3051 134 0.1888 0.2163 REMARK 3 4 4.1600 - 3.7800 0.98 3117 137 0.2059 0.2574 REMARK 3 5 3.7800 - 3.5100 0.96 2997 131 0.2460 0.3001 REMARK 3 6 3.5100 - 3.3000 0.95 2984 132 0.2729 0.3148 REMARK 3 7 3.3000 - 3.1400 0.96 3002 132 0.3367 0.3608 REMARK 3 8 3.1400 - 3.0000 0.96 3051 134 0.3843 0.4402 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.560 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 9210 REMARK 3 ANGLE : 0.566 12508 REMARK 3 CHIRALITY : 0.092 1376 REMARK 3 PLANARITY : 0.003 1585 REMARK 3 DIHEDRAL : 12.906 3314 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 7NXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292114745. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25438 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 49.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.350 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 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) : 3.14 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: 4NST REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.0, 30% PEGMIXTURE REMARK 280 (MEDIUM WEIGHT PEGS), 0.3 M NDSB, 0.2 M MGCL2., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 713 REMARK 465 GLN A 714 REMARK 465 ALA A 799 REMARK 465 LEU A 800 REMARK 465 ASP A 801 REMARK 465 PHE A 802 REMARK 465 GLU A 1041 REMARK 465 LEU A 1042 REMARK 465 TRP A 1043 REMARK 465 SER A 1044 REMARK 465 LYS A 1045 REMARK 465 LYS A 1046 REMARK 465 ARG A 1047 REMARK 465 ARG A 1048 REMARK 465 ARG A 1049 REMARK 465 GLN A 1050 REMARK 465 ARG A 1051 REMARK 465 GLN A 1052 REMARK 465 SER A 1053 REMARK 465 GLY A 1054 REMARK 465 VAL A 1055 REMARK 465 VAL A 1056 REMARK 465 VAL A 1057 REMARK 465 GLU A 1058 REMARK 465 GLU A 1059 REMARK 465 PRO A 1060 REMARK 465 PRO A 1061 REMARK 465 PRO A 1062 REMARK 465 SER A 1063 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 GLU B 3 REMARK 465 ASN B 4 REMARK 465 LYS B 5 REMARK 465 GLU B 6 REMARK 465 ASN B 7 REMARK 465 SER B 8 REMARK 465 SER B 9 REMARK 465 PRO B 10 REMARK 465 SER B 11 REMARK 465 VAL B 12 REMARK 465 THR B 13 REMARK 465 SER B 14 REMARK 465 ALA B 15 REMARK 465 ASN B 16 REMARK 465 LEU B 17 REMARK 465 ASP B 18 REMARK 465 HIS B 19 REMARK 465 PRO B 266 REMARK 465 HIS B 267 REMARK 465 GLY C 713 REMARK 465 GLN C 714 REMARK 465 THR C 715 REMARK 465 GLU C 716 REMARK 465 GLN C 797 REMARK 465 ASP C 798 REMARK 465 ALA C 799 REMARK 465 LEU C 800 REMARK 465 ASP C 801 REMARK 465 PHE C 802 REMARK 465 LYS C 803 REMARK 465 LYS C 804 REMARK 465 ASP C 805 REMARK 465 LYS C 806 REMARK 465 GLU C 1041 REMARK 465 LEU C 1042 REMARK 465 TRP C 1043 REMARK 465 SER C 1044 REMARK 465 LYS C 1045 REMARK 465 LYS C 1046 REMARK 465 ARG C 1047 REMARK 465 ARG C 1048 REMARK 465 ARG C 1049 REMARK 465 GLN C 1050 REMARK 465 ARG C 1051 REMARK 465 GLN C 1052 REMARK 465 SER C 1053 REMARK 465 GLY C 1054 REMARK 465 VAL C 1055 REMARK 465 VAL C 1056 REMARK 465 VAL C 1057 REMARK 465 GLU C 1058 REMARK 465 GLU C 1059 REMARK 465 PRO C 1060 REMARK 465 PRO C 1061 REMARK 465 PRO C 1062 REMARK 465 SER C 1063 REMARK 465 GLY D 0 REMARK 465 MET D 1 REMARK 465 LYS D 2 REMARK 465 GLU D 3 REMARK 465 ASN D 4 REMARK 465 LYS D 5 REMARK 465 GLU D 6 REMARK 465 ASN D 7 REMARK 465 SER D 8 REMARK 465 SER D 9 REMARK 465 PRO D 10 REMARK 465 SER D 11 REMARK 465 VAL D 12 REMARK 465 THR D 13 REMARK 465 SER D 14 REMARK 465 ALA D 15 REMARK 465 ASN D 16 REMARK 465 LEU D 17 REMARK 465 ASP D 18 REMARK 465 HIS D 19 REMARK 465 THR D 20 REMARK 465 LYS D 262 REMARK 465 GLN D 263 REMARK 465 GLN D 264 REMARK 465 MET D 265 REMARK 465 PRO D 266 REMARK 465 HIS D 267 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 726 CG CD CE NZ REMARK 470 ILE A 732 CD1 REMARK 470 GLU A 735 CG CD OE1 OE2 REMARK 470 GLN A 740 CG CD OE1 NE2 REMARK 470 LYS A 756 NZ REMARK 470 ARG A 759 CZ NH1 NH2 REMARK 470 ASP A 761 CB CG OD1 OD2 REMARK 470 ASP A 798 CG OD1 OD2 REMARK 470 LYS A 804 CG CD CE NZ REMARK 470 GLU A 814 CG CD OE1 OE2 REMARK 470 LEU A 828 CG CD1 CD2 REMARK 470 HIS A 830 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 852 CG CD CE NZ REMARK 470 GLU A 887 CG CD OE1 OE2 REMARK 470 GLU A 888 CG CD OE1 OE2 REMARK 470 LYS A 895 CG CD CE NZ REMARK 470 LYS A 932 CG CD CE NZ REMARK 470 LYS A 933 CG CD CE NZ REMARK 470 GLU A 941 CG CD OE1 OE2 REMARK 470 ARG A 950 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 975 CG CD CE NZ REMARK 470 LYS A1021 CD CE NZ REMARK 470 GLU A1024 CB CG CD OE1 OE2 REMARK 470 LYS A1027 CG CD CE NZ REMARK 470 ASP A1032 CG OD1 OD2 REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 LYS B 112 CG CD CE NZ REMARK 470 LYS B 114 CG CD CE NZ REMARK 470 LYS B 118 CG CD CE NZ REMARK 470 ASP B 126 CG OD1 OD2 REMARK 470 GLU B 158 CD OE1 OE2 REMARK 470 LYS B 172 CG CD CE NZ REMARK 470 LYS B 175 CG CD CE NZ REMARK 470 GLU B 224 CG CD OE1 OE2 REMARK 470 MET B 230 CG SD CE REMARK 470 ARG B 232 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 241 CG OD1 OD2 REMARK 470 GLN B 260 CG CD OE1 NE2 REMARK 470 LYS B 262 CG CD CE NZ REMARK 470 GLN B 264 CG CD OE1 NE2 REMARK 470 LYS C 726 CG CD CE NZ REMARK 470 TYR C 738 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS C 756 CG CD CE NZ REMARK 470 ASP C 761 CG OD1 OD2 REMARK 470 LYS C 764 CG CD CE NZ REMARK 470 GLU C 765 CG CD OE1 OE2 REMARK 470 LYS C 796 CG CD CE NZ REMARK 470 GLU C 825 CG CD OE1 OE2 REMARK 470 GLU C 833 CG CD OE1 OE2 REMARK 470 LYS C 837 CE NZ REMARK 470 LYS C 841 CG CD CE NZ REMARK 470 LYS C 852 CG CD CE NZ REMARK 470 GLU C 887 CG CD OE1 OE2 REMARK 470 GLU C 888 CG CD OE1 OE2 REMARK 470 ARG C 890 CG CD NE CZ NH1 NH2 REMARK 470 TYR C 892 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG C 912 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 933 CG CD CE NZ REMARK 470 LYS C 965 CG CD CE NZ REMARK 470 LYS C 975 CG CD CE NZ REMARK 470 ARG C 979 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 984 CG CD OE1 OE2 REMARK 470 ILE C 989 CG1 CG2 CD1 REMARK 470 MET C1000 CG SD CE REMARK 470 LYS C1021 CG CD CE NZ REMARK 470 VAL C1023 CG1 CG2 REMARK 470 GLU C1024 CG CD OE1 OE2 REMARK 470 LYS C1027 CG CD CE NZ REMARK 470 MET C1028 CG SD CE REMARK 470 TRP C1036 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP C1036 CZ3 CH2 REMARK 470 ASP C1038 CG OD1 OD2 REMARK 470 LYS D 21 CG CD CE NZ REMARK 470 LYS D 29 CG CD CE NZ REMARK 470 LYS D 112 CG CD CE NZ REMARK 470 LYS D 114 CG CD CE NZ REMARK 470 LYS D 118 CG CD CE NZ REMARK 470 LYS D 152 CG CD CE NZ REMARK 470 LYS D 169 CG CD CE NZ REMARK 470 GLN D 260 CG CD OE1 NE2 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 LYS A 965 CE REMARK 480 LYS C 790 CE NZ REMARK 480 LYS D 228 CG 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 717 45.13 -87.99 REMARK 500 ALA A 876 -72.72 -95.46 REMARK 500 PHE A 878 48.24 -106.22 REMARK 500 ASN A 894 -82.12 -72.64 REMARK 500 VAL A 896 -48.96 -137.63 REMARK 500 ARG A 912 44.44 -96.02 REMARK 500 LYS A 932 13.19 58.99 REMARK 500 TRP A 960 85.10 -159.15 REMARK 500 LEU A1001 53.67 -114.48 REMARK 500 LYS A1027 35.29 -89.58 REMARK 500 ASP A1038 16.31 -61.13 REMARK 500 CYS A1039 -128.19 -156.39 REMARK 500 THR B 226 -158.98 -111.76 REMARK 500 LYS B 228 77.42 -116.30 REMARK 500 GLU C 765 -62.61 68.56 REMARK 500 ASP C 819 -169.93 -112.76 REMARK 500 SER C 832 -160.05 -118.16 REMARK 500 ARG C 858 -5.29 84.90 REMARK 500 ASP C 859 41.98 -146.83 REMARK 500 SER C 863 2.85 -68.83 REMARK 500 GLU C 887 -20.36 75.05 REMARK 500 GLU C 888 65.61 -114.65 REMARK 500 ARG C 912 50.69 -102.47 REMARK 500 PRO C 915 -4.31 -58.49 REMARK 500 TRP C 960 77.30 -162.40 REMARK 500 PRO C1031 -169.50 -70.27 REMARK 500 ASP C1032 62.01 -109.72 REMARK 500 ASP C1038 -8.35 65.11 REMARK 500 CYS C1039 50.17 -99.29 REMARK 500 SER D 227 43.44 -104.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D 316 DISTANCE = 6.37 ANGSTROMS DBREF 7NXK A 714 1063 UNP Q9NYV4 CDK12_HUMAN 714 1063 DBREF 7NXK B 1 267 UNP O75909 CCNK_HUMAN 1 267 DBREF 7NXK C 714 1063 UNP Q9NYV4 CDK12_HUMAN 714 1063 DBREF 7NXK D 1 267 UNP O75909 CCNK_HUMAN 1 267 SEQADV 7NXK GLY A 713 UNP Q9NYV4 EXPRESSION TAG SEQADV 7NXK GLY B 0 UNP O75909 EXPRESSION TAG SEQADV 7NXK GLY C 713 UNP Q9NYV4 EXPRESSION TAG SEQADV 7NXK GLY D 0 UNP O75909 EXPRESSION TAG SEQRES 1 A 351 GLY GLN THR GLU SER ASP TRP GLY LYS ARG CYS VAL ASP SEQRES 2 A 351 LYS PHE ASP ILE ILE GLY ILE ILE GLY GLU GLY THR TYR SEQRES 3 A 351 GLY GLN VAL TYR LYS ALA LYS ASP LYS ASP THR GLY GLU SEQRES 4 A 351 LEU VAL ALA LEU LYS LYS VAL ARG LEU ASP ASN GLU LYS SEQRES 5 A 351 GLU GLY PHE PRO ILE THR ALA ILE ARG GLU ILE LYS ILE SEQRES 6 A 351 LEU ARG GLN LEU ILE HIS ARG SER VAL VAL ASN MET LYS SEQRES 7 A 351 GLU ILE VAL THR ASP LYS GLN ASP ALA LEU ASP PHE LYS SEQRES 8 A 351 LYS ASP LYS GLY ALA PHE TYR LEU VAL PHE GLU TYR MET SEQRES 9 A 351 ASP HIS ASP LEU MET GLY LEU LEU GLU SER GLY LEU VAL SEQRES 10 A 351 HIS PHE SER GLU ASP HIS ILE LYS SER PHE MET LYS GLN SEQRES 11 A 351 LEU MET GLU GLY LEU GLU TYR CYS HIS LYS LYS ASN PHE SEQRES 12 A 351 LEU HIS ARG ASP ILE LYS CYS SER ASN ILE LEU LEU ASN SEQRES 13 A 351 ASN SER GLY GLN ILE LYS LEU ALA ASP PHE GLY LEU ALA SEQRES 14 A 351 ARG LEU TYR ASN SER GLU GLU SER ARG PRO TYR TPO ASN SEQRES 15 A 351 LYS VAL ILE THR LEU TRP TYR ARG PRO PRO GLU LEU LEU SEQRES 16 A 351 LEU GLY GLU GLU ARG TYR THR PRO ALA ILE ASP VAL TRP SEQRES 17 A 351 SER CYS GLY CYS ILE LEU GLY GLU LEU PHE THR LYS LYS SEQRES 18 A 351 PRO ILE PHE GLN ALA ASN LEU GLU LEU ALA GLN LEU GLU SEQRES 19 A 351 LEU ILE SER ARG LEU CYS GLY SER PRO CYS PRO ALA VAL SEQRES 20 A 351 TRP PRO ASP VAL ILE LYS LEU PRO TYR PHE ASN THR MET SEQRES 21 A 351 LYS PRO LYS LYS GLN TYR ARG ARG ARG LEU ARG GLU GLU SEQRES 22 A 351 PHE SER PHE ILE PRO SER ALA ALA LEU ASP LEU LEU ASP SEQRES 23 A 351 HIS MET LEU THR LEU ASP PRO SER LYS ARG CYS THR ALA SEQRES 24 A 351 GLU GLN THR LEU GLN SER ASP PHE LEU LYS ASP VAL GLU SEQRES 25 A 351 LEU SER LYS MET ALA PRO PRO ASP LEU PRO HIS TRP GLN SEQRES 26 A 351 ASP CYS HIS GLU LEU TRP SER LYS LYS ARG ARG ARG GLN SEQRES 27 A 351 ARG GLN SER GLY VAL VAL VAL GLU GLU PRO PRO PRO SER SEQRES 1 B 268 GLY MET LYS GLU ASN LYS GLU ASN SER SER PRO SER VAL SEQRES 2 B 268 THR SER ALA ASN LEU ASP HIS THR LYS PRO CYS TRP TYR SEQRES 3 B 268 TRP ASP LYS LYS ASP LEU ALA HIS THR PRO SER GLN LEU SEQRES 4 B 268 GLU GLY LEU ASP PRO ALA THR GLU ALA ARG TYR ARG ARG SEQRES 5 B 268 GLU GLY ALA ARG PHE ILE PHE ASP VAL GLY THR ARG LEU SEQRES 6 B 268 GLY LEU HIS TYR ASP THR LEU ALA THR GLY ILE ILE TYR SEQRES 7 B 268 PHE HIS ARG PHE TYR MET PHE HIS SER PHE LYS GLN PHE SEQRES 8 B 268 PRO ARG TYR VAL THR GLY ALA CYS CYS LEU PHE LEU ALA SEQRES 9 B 268 GLY LYS VAL GLU GLU THR PRO LYS LYS CYS LYS ASP ILE SEQRES 10 B 268 ILE LYS THR ALA ARG SER LEU LEU ASN ASP VAL GLN PHE SEQRES 11 B 268 GLY GLN PHE GLY ASP ASP PRO LYS GLU GLU VAL MET VAL SEQRES 12 B 268 LEU GLU ARG ILE LEU LEU GLN THR ILE LYS PHE ASP LEU SEQRES 13 B 268 GLN VAL GLU HIS PRO TYR GLN PHE LEU LEU LYS TYR ALA SEQRES 14 B 268 LYS GLN LEU LYS GLY ASP LYS ASN LYS ILE GLN LYS LEU SEQRES 15 B 268 VAL GLN MET ALA TRP THR PHE VAL ASN ASP SER LEU CYS SEQRES 16 B 268 THR THR LEU SER LEU GLN TRP GLU PRO GLU ILE ILE ALA SEQRES 17 B 268 VAL ALA VAL MET TYR LEU ALA GLY ARG LEU CYS LYS PHE SEQRES 18 B 268 GLU ILE GLN GLU TRP THR SER LYS PRO MET TYR ARG ARG SEQRES 19 B 268 TRP TRP GLU GLN PHE VAL GLN ASP VAL PRO VAL ASP VAL SEQRES 20 B 268 LEU GLU ASP ILE CYS HIS GLN ILE LEU ASP LEU TYR SER SEQRES 21 B 268 GLN GLY LYS GLN GLN MET PRO HIS SEQRES 1 C 351 GLY GLN THR GLU SER ASP TRP GLY LYS ARG CYS VAL ASP SEQRES 2 C 351 LYS PHE ASP ILE ILE GLY ILE ILE GLY GLU GLY THR TYR SEQRES 3 C 351 GLY GLN VAL TYR LYS ALA LYS ASP LYS ASP THR GLY GLU SEQRES 4 C 351 LEU VAL ALA LEU LYS LYS VAL ARG LEU ASP ASN GLU LYS SEQRES 5 C 351 GLU GLY PHE PRO ILE THR ALA ILE ARG GLU ILE LYS ILE SEQRES 6 C 351 LEU ARG GLN LEU ILE HIS ARG SER VAL VAL ASN MET LYS SEQRES 7 C 351 GLU ILE VAL THR ASP LYS GLN ASP ALA LEU ASP PHE LYS SEQRES 8 C 351 LYS ASP LYS GLY ALA PHE TYR LEU VAL PHE GLU TYR MET SEQRES 9 C 351 ASP HIS ASP LEU MET GLY LEU LEU GLU SER GLY LEU VAL SEQRES 10 C 351 HIS PHE SER GLU ASP HIS ILE LYS SER PHE MET LYS GLN SEQRES 11 C 351 LEU MET GLU GLY LEU GLU TYR CYS HIS LYS LYS ASN PHE SEQRES 12 C 351 LEU HIS ARG ASP ILE LYS CYS SER ASN ILE LEU LEU ASN SEQRES 13 C 351 ASN SER GLY GLN ILE LYS LEU ALA ASP PHE GLY LEU ALA SEQRES 14 C 351 ARG LEU TYR ASN SER GLU GLU SER ARG PRO TYR TPO ASN SEQRES 15 C 351 LYS VAL ILE THR LEU TRP TYR ARG PRO PRO GLU LEU LEU SEQRES 16 C 351 LEU GLY GLU GLU ARG TYR THR PRO ALA ILE ASP VAL TRP SEQRES 17 C 351 SER CYS GLY CYS ILE LEU GLY GLU LEU PHE THR LYS LYS SEQRES 18 C 351 PRO ILE PHE GLN ALA ASN LEU GLU LEU ALA GLN LEU GLU SEQRES 19 C 351 LEU ILE SER ARG LEU CYS GLY SER PRO CYS PRO ALA VAL SEQRES 20 C 351 TRP PRO ASP VAL ILE LYS LEU PRO TYR PHE ASN THR MET SEQRES 21 C 351 LYS PRO LYS LYS GLN TYR ARG ARG ARG LEU ARG GLU GLU SEQRES 22 C 351 PHE SER PHE ILE PRO SER ALA ALA LEU ASP LEU LEU ASP SEQRES 23 C 351 HIS MET LEU THR LEU ASP PRO SER LYS ARG CYS THR ALA SEQRES 24 C 351 GLU GLN THR LEU GLN SER ASP PHE LEU LYS ASP VAL GLU SEQRES 25 C 351 LEU SER LYS MET ALA PRO PRO ASP LEU PRO HIS TRP GLN SEQRES 26 C 351 ASP CYS HIS GLU LEU TRP SER LYS LYS ARG ARG ARG GLN SEQRES 27 C 351 ARG GLN SER GLY VAL VAL VAL GLU GLU PRO PRO PRO SER SEQRES 1 D 268 GLY MET LYS GLU ASN LYS GLU ASN SER SER PRO SER VAL SEQRES 2 D 268 THR SER ALA ASN LEU ASP HIS THR LYS PRO CYS TRP TYR SEQRES 3 D 268 TRP ASP LYS LYS ASP LEU ALA HIS THR PRO SER GLN LEU SEQRES 4 D 268 GLU GLY LEU ASP PRO ALA THR GLU ALA ARG TYR ARG ARG SEQRES 5 D 268 GLU GLY ALA ARG PHE ILE PHE ASP VAL GLY THR ARG LEU SEQRES 6 D 268 GLY LEU HIS TYR ASP THR LEU ALA THR GLY ILE ILE TYR SEQRES 7 D 268 PHE HIS ARG PHE TYR MET PHE HIS SER PHE LYS GLN PHE SEQRES 8 D 268 PRO ARG TYR VAL THR GLY ALA CYS CYS LEU PHE LEU ALA SEQRES 9 D 268 GLY LYS VAL GLU GLU THR PRO LYS LYS CYS LYS ASP ILE SEQRES 10 D 268 ILE LYS THR ALA ARG SER LEU LEU ASN ASP VAL GLN PHE SEQRES 11 D 268 GLY GLN PHE GLY ASP ASP PRO LYS GLU GLU VAL MET VAL SEQRES 12 D 268 LEU GLU ARG ILE LEU LEU GLN THR ILE LYS PHE ASP LEU SEQRES 13 D 268 GLN VAL GLU HIS PRO TYR GLN PHE LEU LEU LYS TYR ALA SEQRES 14 D 268 LYS GLN LEU LYS GLY ASP LYS ASN LYS ILE GLN LYS LEU SEQRES 15 D 268 VAL GLN MET ALA TRP THR PHE VAL ASN ASP SER LEU CYS SEQRES 16 D 268 THR THR LEU SER LEU GLN TRP GLU PRO GLU ILE ILE ALA SEQRES 17 D 268 VAL ALA VAL MET TYR LEU ALA GLY ARG LEU CYS LYS PHE SEQRES 18 D 268 GLU ILE GLN GLU TRP THR SER LYS PRO MET TYR ARG ARG SEQRES 19 D 268 TRP TRP GLU GLN PHE VAL GLN ASP VAL PRO VAL ASP VAL SEQRES 20 D 268 LEU GLU ASP ILE CYS HIS GLN ILE LEU ASP LEU TYR SER SEQRES 21 D 268 GLN GLY LYS GLN GLN MET PRO HIS MODRES 7NXK TPO A 893 THR MODIFIED RESIDUE MODRES 7NXK TPO C 893 THR MODIFIED RESIDUE HET TPO A 893 11 HET TPO C 893 11 HET UUB A2000 42 HET UUB C2000 44 HETNAM TPO PHOSPHOTHREONINE HETNAM UUB (E)-N-[4-[(1R,3R)-3-[[5-CHLORANYL-4-(1H-INDOL-3-YL) HETNAM 2 UUB PYRIMIDIN-2-YL]AMINO]CYCLOHEXYL]OXYPHENYL]-4- HETNAM 3 UUB (DIMETHYLAMINO)BUT-2-ENAMIDE HETSYN TPO PHOSPHONOTHREONINE HETSYN UUB (~{E})-~{N}-[4-[(1~{R},3~{R})-3-[[5-CHLORANYL-4-(1~{H}- HETSYN 2 UUB INDOL-3-YL)PYRIMIDIN-2-YL]AMINO]CYCLOHEXYL]OXYPHENYL]- HETSYN 3 UUB 4-(DIMETHYLAMINO)BUT-2-ENAMIDE FORMUL 1 TPO 2(C4 H10 N O6 P) FORMUL 5 UUB 2(C30 H33 CL N6 O2) FORMUL 7 HOH *58(H2 O) HELIX 1 AA1 CYS A 723 ASP A 725 5 3 HELIX 2 AA2 PRO A 768 ARG A 779 1 12 HELIX 3 AA3 LEU A 820 SER A 826 1 7 HELIX 4 AA4 SER A 832 LYS A 853 1 22 HELIX 5 AA5 LYS A 861 SER A 863 5 3 HELIX 6 AA6 PRO A 903 LEU A 908 1 6 HELIX 7 AA7 PRO A 915 PHE A 930 1 16 HELIX 8 AA8 LEU A 940 GLY A 953 1 14 HELIX 9 AA9 ASP A 962 LEU A 966 5 5 HELIX 10 AB1 ARG A 981 PHE A 986 1 6 HELIX 11 AB2 PRO A 990 LEU A 1001 1 12 HELIX 12 AB3 THR A 1010 GLN A 1016 1 7 HELIX 13 AB4 LYS B 29 HIS B 33 5 5 HELIX 14 AB5 THR B 34 GLU B 39 1 6 HELIX 15 AB6 ASP B 42 LEU B 64 1 23 HELIX 16 AB7 HIS B 67 TYR B 82 1 16 HELIX 17 AB8 PRO B 91 GLU B 107 1 17 HELIX 18 AB9 LYS B 112 SER B 122 1 11 HELIX 19 AC1 ASN B 125 GLY B 130 1 6 HELIX 20 AC2 ASP B 135 ILE B 151 1 17 HELIX 21 AC3 HIS B 159 GLN B 170 1 12 HELIX 22 AC4 ASP B 174 LEU B 193 1 20 HELIX 23 AC5 CYS B 194 THR B 195 5 2 HELIX 24 AC6 THR B 196 GLN B 200 5 5 HELIX 25 AC7 GLU B 202 CYS B 218 1 17 HELIX 26 AC8 GLU B 221 THR B 226 5 6 HELIX 27 AC9 ARG B 233 PHE B 238 5 6 HELIX 28 AD1 PRO B 243 TYR B 258 1 16 HELIX 29 AD2 SER B 259 LYS B 262 5 4 HELIX 30 AD3 CYS C 723 ASP C 725 5 3 HELIX 31 AD4 PRO C 768 ARG C 779 1 12 HELIX 32 AD5 LEU C 820 GLY C 827 1 8 HELIX 33 AD6 SER C 832 LYS C 853 1 22 HELIX 34 AD7 LYS C 861 SER C 863 5 3 HELIX 35 AD8 ASP C 877 ALA C 881 5 5 HELIX 36 AD9 PRO C 903 LEU C 908 1 6 HELIX 37 AE1 PRO C 915 PHE C 930 1 16 HELIX 38 AE2 LEU C 940 GLY C 953 1 14 HELIX 39 AE3 ASP C 962 LEU C 966 5 5 HELIX 40 AE4 ARG C 981 PHE C 986 1 6 HELIX 41 AE5 PRO C 990 LEU C 1001 1 12 HELIX 42 AE6 THR C 1010 LEU C 1015 1 6 HELIX 43 AE7 LYS D 29 HIS D 33 5 5 HELIX 44 AE8 THR D 34 GLU D 39 1 6 HELIX 45 AE9 ASP D 42 LEU D 64 1 23 HELIX 46 AF1 HIS D 67 TYR D 82 1 16 HELIX 47 AF2 PRO D 91 GLU D 107 1 17 HELIX 48 AF3 LYS D 112 SER D 122 1 11 HELIX 49 AF4 ASN D 125 GLY D 130 1 6 HELIX 50 AF5 GLN D 131 GLY D 133 5 3 HELIX 51 AF6 ASP D 135 ILE D 151 1 17 HELIX 52 AF7 HIS D 159 GLN D 170 1 12 HELIX 53 AF8 ASP D 174 LEU D 193 1 20 HELIX 54 AF9 CYS D 194 THR D 195 5 2 HELIX 55 AG1 THR D 196 GLN D 200 5 5 HELIX 56 AG2 GLU D 202 CYS D 218 1 17 HELIX 57 AG3 GLU D 221 THR D 226 5 6 HELIX 58 AG4 ARG D 233 PHE D 238 5 6 HELIX 59 AG5 PRO D 243 SER D 259 1 17 SHEET 1 AA1 5 PHE A 727 GLY A 734 0 SHEET 2 AA1 5 VAL A 741 ASP A 746 -1 O LYS A 743 N ILE A 730 SHEET 3 AA1 5 LEU A 752 VAL A 758 -1 O VAL A 753 N ALA A 744 SHEET 4 AA1 5 PHE A 809 GLU A 814 -1 O PHE A 809 N VAL A 758 SHEET 5 AA1 5 MET A 789 THR A 794 -1 N VAL A 793 O TYR A 810 SHEET 1 AA2 3 HIS A 818 ASP A 819 0 SHEET 2 AA2 3 ILE A 865 LEU A 867 -1 O LEU A 867 N HIS A 818 SHEET 3 AA2 3 ILE A 873 LEU A 875 -1 O LYS A 874 N LEU A 866 SHEET 1 AA3 2 PHE A 855 LEU A 856 0 SHEET 2 AA3 2 ARG A 882 LEU A 883 -1 O ARG A 882 N LEU A 856 SHEET 1 AA4 5 PHE C 727 GLU C 735 0 SHEET 2 AA4 5 GLN C 740 ASP C 746 -1 O LYS C 743 N GLY C 731 SHEET 3 AA4 5 LEU C 752 ARG C 759 -1 O LEU C 755 N TYR C 742 SHEET 4 AA4 5 ALA C 808 GLU C 814 -1 O PHE C 809 N VAL C 758 SHEET 5 AA4 5 MET C 789 THR C 794 -1 N GLU C 791 O VAL C 812 SHEET 1 AA5 2 PHE C 855 LEU C 856 0 SHEET 2 AA5 2 ARG C 882 LEU C 883 -1 O ARG C 882 N LEU C 856 SHEET 1 AA6 2 ILE C 865 LEU C 867 0 SHEET 2 AA6 2 ILE C 873 LEU C 875 -1 O LYS C 874 N LEU C 866 LINK C TYR A 892 N TPO A 893 1555 1555 1.33 LINK C TPO A 893 N ASN A 894 1555 1555 1.33 LINK SG CYS A1039 C35 UUB A2000 1555 1555 1.77 LINK C TYR C 892 N TPO C 893 1555 1555 1.34 LINK C TPO C 893 N ASN C 894 1555 1555 1.32 LINK SG CYS C1039 C35 UUB C2000 1555 1555 1.74 CRYST1 50.210 77.460 91.530 103.61 85.89 102.56 P 1 2 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 0.019916 0.004435 -0.000443 0.00000 SCALE2 0.000000 0.013226 0.003063 0.00000 SCALE3 0.000000 0.000000 0.011244 0.00000