HEADER TRANSFERASE/INHIBITOR 21-SEP-17 6B3E TITLE CRYSTAL STRUCTURE OF HUMAN CDK12/CYCLINK IN COMPLEX WITH AN INHIBITOR 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 INHIBITOR, COMPLEX, KINASE, TRANSFERASE, TRANSFERASE-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.D.FERGUSON REVDAT 5 04-OCT-23 6B3E 1 REMARK REVDAT 4 21-FEB-18 6B3E 1 JRNL REVDAT 3 14-FEB-18 6B3E 1 JRNL REVDAT 2 03-JAN-18 6B3E 1 JRNL REVDAT 1 27-DEC-17 6B3E 0 JRNL AUTH J.W.JOHANNES,C.R.DENZ,N.SU,A.WU,A.C.IMPASTATO,S.MLYNARSKI, JRNL AUTH 2 J.G.VARNES,D.B.PRINCE,J.CIDADO,N.GAO,M.HADDRICK,N.H.JONES, JRNL AUTH 3 S.LI,X.LI,Y.LIU,T.B.NGUYEN,N.O'CONNELL,E.RIVERS,D.W.ROBBINS, JRNL AUTH 4 R.TOMLINSON,T.YAO,X.ZHU,A.D.FERGUSON,M.L.LAMB, JRNL AUTH 5 J.I.MANCHESTER,S.GUICHARD JRNL TITL STRUCTURE-BASED DESIGN OF SELECTIVE NONCOVALENT CDK12 JRNL TITL 2 INHIBITORS. JRNL REF CHEMMEDCHEM V. 13 231 2018 JRNL REFN ESSN 1860-7187 JRNL PMID 29266803 JRNL DOI 10.1002/CMDC.201700695 REMARK 2 REMARK 2 RESOLUTION. 3.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 22813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9030 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.77 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : NULL ; NULL ; NULL REMARK 3 BOND ANGLES : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : NULL ; NULL ; NULL REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6B3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000230194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22962 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.060 REMARK 200 RESOLUTION RANGE LOW (A) : 88.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.52800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 4NST REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 6.5, 20.5% PEG REMARK 280 3350, 0.4 M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 2200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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 GLN A 797 REMARK 465 ASP A 798 REMARK 465 ALA A 799 REMARK 465 LEU A 800 REMARK 465 ASP A 801 REMARK 465 PHE A 802 REMARK 465 LYS A 803 REMARK 465 LYS A 804 REMARK 465 ASP A 805 REMARK 465 LYS A 806 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 GLN B 260 REMARK 465 GLY B 261 REMARK 465 LYS B 262 REMARK 465 GLN B 263 REMARK 465 GLN B 264 REMARK 465 MET B 265 REMARK 465 PRO B 266 REMARK 465 HIS B 267 REMARK 465 SER C 717 REMARK 465 ASP C 718 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 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 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 TYR D 231 C - N - CA ANGL. DEV. = 20.1 DEGREES REMARK 500 ARG D 233 C - N - CA ANGL. DEV. = 20.2 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 ASN A 854 34.79 73.48 REMARK 500 ASP A 859 37.77 -151.51 REMARK 500 ASP A 877 79.81 59.35 REMARK 500 ILE A 897 131.42 76.06 REMARK 500 ARG A 912 63.54 -116.19 REMARK 500 PRO A 974 175.24 -59.95 REMARK 500 ASN C 854 36.19 73.01 REMARK 500 ASP C 859 39.74 -152.36 REMARK 500 ASP C 877 80.64 57.69 REMARK 500 ILE C 897 130.48 78.03 REMARK 500 ARG C 912 63.63 -117.89 REMARK 500 ASP C1032 76.23 -100.08 REMARK 500 MET D 230 -71.39 -36.30 REMARK 500 TYR D 231 -35.72 1.20 REMARK 500 ARG D 232 -174.91 101.82 REMARK 500 ARG D 233 108.40 70.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 859 OD2 REMARK 620 2 ASP A 877 OD2 91.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C1101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 859 OD2 REMARK 620 2 ASP C 877 OD2 77.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CJM A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CJM C 1103 DBREF 6B3E A 717 1036 UNP Q9NYV4 CDK12_HUMAN 717 1036 DBREF 6B3E B 1 267 UNP O75909 CCNK_HUMAN 1 267 DBREF 6B3E C 717 1036 UNP Q9NYV4 CDK12_HUMAN 717 1036 DBREF 6B3E D 1 267 UNP O75909 CCNK_HUMAN 1 267 SEQRES 1 A 320 SER ASP TRP GLY LYS ARG CYS VAL ASP LYS PHE ASP ILE SEQRES 2 A 320 ILE GLY ILE ILE GLY GLU GLY THR TYR GLY GLN VAL TYR SEQRES 3 A 320 LYS ALA LYS ASP LYS ASP THR GLY GLU LEU VAL ALA LEU SEQRES 4 A 320 LYS LYS VAL ARG LEU ASP ASN GLU LYS GLU GLY PHE PRO SEQRES 5 A 320 ILE THR ALA ILE ARG GLU ILE LYS ILE LEU ARG GLN LEU SEQRES 6 A 320 ILE HIS ARG SER VAL VAL ASN MET LYS GLU ILE VAL THR SEQRES 7 A 320 ASP LYS GLN ASP ALA LEU ASP PHE LYS LYS ASP LYS GLY SEQRES 8 A 320 ALA PHE TYR LEU VAL PHE GLU TYR MET ASP HIS ASP LEU SEQRES 9 A 320 MET GLY LEU LEU GLU SER GLY LEU VAL HIS PHE SER GLU SEQRES 10 A 320 ASP HIS ILE LYS SER PHE MET LYS GLN LEU MET GLU GLY SEQRES 11 A 320 LEU GLU TYR CYS HIS LYS LYS ASN PHE LEU HIS ARG ASP SEQRES 12 A 320 ILE LYS CYS SER ASN ILE LEU LEU ASN ASN SER GLY GLN SEQRES 13 A 320 ILE LYS LEU ALA ASP PHE GLY LEU ALA ARG LEU TYR ASN SEQRES 14 A 320 SER GLU GLU SER ARG PRO TYR TPO ASN LYS VAL ILE THR SEQRES 15 A 320 LEU TRP TYR ARG PRO PRO GLU LEU LEU LEU GLY GLU GLU SEQRES 16 A 320 ARG TYR THR PRO ALA ILE ASP VAL TRP SER CYS GLY CYS SEQRES 17 A 320 ILE LEU GLY GLU LEU PHE THR LYS LYS PRO ILE PHE GLN SEQRES 18 A 320 ALA ASN LEU GLU LEU ALA GLN LEU GLU LEU ILE SER ARG SEQRES 19 A 320 LEU CYS GLY SER PRO CYS PRO ALA VAL TRP PRO ASP VAL SEQRES 20 A 320 ILE LYS LEU PRO TYR PHE ASN THR MET LYS PRO LYS LYS SEQRES 21 A 320 GLN TYR ARG ARG ARG LEU ARG GLU GLU PHE SER PHE ILE SEQRES 22 A 320 PRO SER ALA ALA LEU ASP LEU LEU ASP HIS MET LEU THR SEQRES 23 A 320 LEU ASP PRO SER LYS ARG CYS THR ALA GLU GLN THR LEU SEQRES 24 A 320 GLN SER ASP PHE LEU LYS ASP VAL GLU LEU SER LYS MET SEQRES 25 A 320 ALA PRO PRO ASP LEU PRO HIS TRP SEQRES 1 B 267 MET LYS GLU ASN LYS GLU ASN SER SER PRO SER VAL THR SEQRES 2 B 267 SER ALA ASN LEU ASP HIS THR LYS PRO CYS TRP TYR TRP SEQRES 3 B 267 ASP LYS LYS ASP LEU ALA HIS THR PRO SER GLN LEU GLU SEQRES 4 B 267 GLY LEU ASP PRO ALA THR GLU ALA ARG TYR ARG ARG GLU SEQRES 5 B 267 GLY ALA ARG PHE ILE PHE ASP VAL GLY THR ARG LEU GLY SEQRES 6 B 267 LEU HIS TYR ASP THR LEU ALA THR GLY ILE ILE TYR PHE SEQRES 7 B 267 HIS ARG PHE TYR MET PHE HIS SER PHE LYS GLN PHE PRO SEQRES 8 B 267 ARG TYR VAL THR GLY ALA CYS CYS LEU PHE LEU ALA GLY SEQRES 9 B 267 LYS VAL GLU GLU THR PRO LYS LYS CYS LYS ASP ILE ILE SEQRES 10 B 267 LYS THR ALA ARG SER LEU LEU ASN ASP VAL GLN PHE GLY SEQRES 11 B 267 GLN PHE GLY ASP ASP PRO LYS GLU GLU VAL MET VAL LEU SEQRES 12 B 267 GLU ARG ILE LEU LEU GLN THR ILE LYS PHE ASP LEU GLN SEQRES 13 B 267 VAL GLU HIS PRO TYR GLN PHE LEU LEU LYS TYR ALA LYS SEQRES 14 B 267 GLN LEU LYS GLY ASP LYS ASN LYS ILE GLN LYS LEU VAL SEQRES 15 B 267 GLN MET ALA TRP THR PHE VAL ASN ASP SER LEU CYS THR SEQRES 16 B 267 THR LEU SER LEU GLN TRP GLU PRO GLU ILE ILE ALA VAL SEQRES 17 B 267 ALA VAL MET TYR LEU ALA GLY ARG LEU CYS LYS PHE GLU SEQRES 18 B 267 ILE GLN GLU TRP THR SER LYS PRO MET TYR ARG ARG TRP SEQRES 19 B 267 TRP GLU GLN PHE VAL GLN ASP VAL PRO VAL ASP VAL LEU SEQRES 20 B 267 GLU ASP ILE CYS HIS GLN ILE LEU ASP LEU TYR SER GLN SEQRES 21 B 267 GLY LYS GLN GLN MET PRO HIS SEQRES 1 C 320 SER ASP TRP GLY LYS ARG CYS VAL ASP LYS PHE ASP ILE SEQRES 2 C 320 ILE GLY ILE ILE GLY GLU GLY THR TYR GLY GLN VAL TYR SEQRES 3 C 320 LYS ALA LYS ASP LYS ASP THR GLY GLU LEU VAL ALA LEU SEQRES 4 C 320 LYS LYS VAL ARG LEU ASP ASN GLU LYS GLU GLY PHE PRO SEQRES 5 C 320 ILE THR ALA ILE ARG GLU ILE LYS ILE LEU ARG GLN LEU SEQRES 6 C 320 ILE HIS ARG SER VAL VAL ASN MET LYS GLU ILE VAL THR SEQRES 7 C 320 ASP LYS GLN ASP ALA LEU ASP PHE LYS LYS ASP LYS GLY SEQRES 8 C 320 ALA PHE TYR LEU VAL PHE GLU TYR MET ASP HIS ASP LEU SEQRES 9 C 320 MET GLY LEU LEU GLU SER GLY LEU VAL HIS PHE SER GLU SEQRES 10 C 320 ASP HIS ILE LYS SER PHE MET LYS GLN LEU MET GLU GLY SEQRES 11 C 320 LEU GLU TYR CYS HIS LYS LYS ASN PHE LEU HIS ARG ASP SEQRES 12 C 320 ILE LYS CYS SER ASN ILE LEU LEU ASN ASN SER GLY GLN SEQRES 13 C 320 ILE LYS LEU ALA ASP PHE GLY LEU ALA ARG LEU TYR ASN SEQRES 14 C 320 SER GLU GLU SER ARG PRO TYR TPO ASN LYS VAL ILE THR SEQRES 15 C 320 LEU TRP TYR ARG PRO PRO GLU LEU LEU LEU GLY GLU GLU SEQRES 16 C 320 ARG TYR THR PRO ALA ILE ASP VAL TRP SER CYS GLY CYS SEQRES 17 C 320 ILE LEU GLY GLU LEU PHE THR LYS LYS PRO ILE PHE GLN SEQRES 18 C 320 ALA ASN LEU GLU LEU ALA GLN LEU GLU LEU ILE SER ARG SEQRES 19 C 320 LEU CYS GLY SER PRO CYS PRO ALA VAL TRP PRO ASP VAL SEQRES 20 C 320 ILE LYS LEU PRO TYR PHE ASN THR MET LYS PRO LYS LYS SEQRES 21 C 320 GLN TYR ARG ARG ARG LEU ARG GLU GLU PHE SER PHE ILE SEQRES 22 C 320 PRO SER ALA ALA LEU ASP LEU LEU ASP HIS MET LEU THR SEQRES 23 C 320 LEU ASP PRO SER LYS ARG CYS THR ALA GLU GLN THR LEU SEQRES 24 C 320 GLN SER ASP PHE LEU LYS ASP VAL GLU LEU SER LYS MET SEQRES 25 C 320 ALA PRO PRO ASP LEU PRO HIS TRP SEQRES 1 D 267 MET LYS GLU ASN LYS GLU ASN SER SER PRO SER VAL THR SEQRES 2 D 267 SER ALA ASN LEU ASP HIS THR LYS PRO CYS TRP TYR TRP SEQRES 3 D 267 ASP LYS LYS ASP LEU ALA HIS THR PRO SER GLN LEU GLU SEQRES 4 D 267 GLY LEU ASP PRO ALA THR GLU ALA ARG TYR ARG ARG GLU SEQRES 5 D 267 GLY ALA ARG PHE ILE PHE ASP VAL GLY THR ARG LEU GLY SEQRES 6 D 267 LEU HIS TYR ASP THR LEU ALA THR GLY ILE ILE TYR PHE SEQRES 7 D 267 HIS ARG PHE TYR MET PHE HIS SER PHE LYS GLN PHE PRO SEQRES 8 D 267 ARG TYR VAL THR GLY ALA CYS CYS LEU PHE LEU ALA GLY SEQRES 9 D 267 LYS VAL GLU GLU THR PRO LYS LYS CYS LYS ASP ILE ILE SEQRES 10 D 267 LYS THR ALA ARG SER LEU LEU ASN ASP VAL GLN PHE GLY SEQRES 11 D 267 GLN PHE GLY ASP ASP PRO LYS GLU GLU VAL MET VAL LEU SEQRES 12 D 267 GLU ARG ILE LEU LEU GLN THR ILE LYS PHE ASP LEU GLN SEQRES 13 D 267 VAL GLU HIS PRO TYR GLN PHE LEU LEU LYS TYR ALA LYS SEQRES 14 D 267 GLN LEU LYS GLY ASP LYS ASN LYS ILE GLN LYS LEU VAL SEQRES 15 D 267 GLN MET ALA TRP THR PHE VAL ASN ASP SER LEU CYS THR SEQRES 16 D 267 THR LEU SER LEU GLN TRP GLU PRO GLU ILE ILE ALA VAL SEQRES 17 D 267 ALA VAL MET TYR LEU ALA GLY ARG LEU CYS LYS PHE GLU SEQRES 18 D 267 ILE GLN GLU TRP THR SER LYS PRO MET TYR ARG ARG TRP SEQRES 19 D 267 TRP GLU GLN PHE VAL GLN ASP VAL PRO VAL ASP VAL LEU SEQRES 20 D 267 GLU ASP ILE CYS HIS GLN ILE LEU ASP LEU TYR SER GLN SEQRES 21 D 267 GLY LYS GLN GLN MET PRO HIS MODRES 6B3E TPO A 893 THR MODIFIED RESIDUE MODRES 6B3E TPO C 893 THR MODIFIED RESIDUE HET TPO A 893 11 HET TPO C 893 11 HET MG A1101 1 HET CJM A1102 33 HET EDO B 301 4 HET EDO B 302 4 HET MG C1101 1 HET EDO C1102 4 HET CJM C1103 33 HETNAM TPO PHOSPHOTHREONINE HETNAM MG MAGNESIUM ION HETNAM CJM 2-[(2S)-1-(6-{[(4,5-DIFLUORO-1H-BENZIMIDAZOL-2-YL) HETNAM 2 CJM METHYL]AMINO}-9-ETHYL-9H-PURIN-2-YL)PIPERIDIN-2- HETNAM 3 CJM YL]ETHAN-1-OL HETNAM EDO 1,2-ETHANEDIOL HETSYN TPO PHOSPHONOTHREONINE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 TPO 2(C4 H10 N O6 P) FORMUL 5 MG 2(MG 2+) FORMUL 6 CJM 2(C22 H26 F2 N8 O) FORMUL 7 EDO 3(C2 H6 O2) FORMUL 12 HOH *9(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 GLY A 827 1 8 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 THR A 898 ARG A 902 5 5 HELIX 7 AA7 PRO A 903 LEU A 908 1 6 HELIX 8 AA8 PRO A 915 LYS A 932 1 18 HELIX 9 AA9 LEU A 940 GLY A 953 1 14 HELIX 10 AB1 TRP A 960 LEU A 966 5 7 HELIX 11 AB2 ARG A 981 PHE A 986 1 6 HELIX 12 AB3 PRO A 990 LEU A 1001 1 12 HELIX 13 AB4 THR A 1010 LEU A 1015 1 6 HELIX 14 AB5 SER A 1017 ASP A 1022 1 6 HELIX 15 AB6 ASP B 27 ALA B 32 1 6 HELIX 16 AB7 THR B 34 GLU B 39 1 6 HELIX 17 AB8 ASP B 42 LEU B 64 1 23 HELIX 18 AB9 HIS B 67 TYR B 82 1 16 HELIX 19 AC1 PRO B 91 GLU B 107 1 17 HELIX 20 AC2 LYS B 112 LEU B 124 1 13 HELIX 21 AC3 ASN B 125 GLY B 130 1 6 HELIX 22 AC4 GLN B 131 GLY B 133 5 3 HELIX 23 AC5 ASP B 135 ILE B 151 1 17 HELIX 24 AC6 HIS B 159 GLN B 170 1 12 HELIX 25 AC7 ASP B 174 LEU B 193 1 20 HELIX 26 AC8 CYS B 194 GLN B 200 5 7 HELIX 27 AC9 GLU B 202 LYS B 219 1 18 HELIX 28 AD1 GLU B 221 THR B 226 5 6 HELIX 29 AD2 ARG B 233 PHE B 238 5 6 HELIX 30 AD3 PRO B 243 ASP B 256 1 14 HELIX 31 AD4 CYS C 723 ASP C 725 5 3 HELIX 32 AD5 PRO C 768 ARG C 779 1 12 HELIX 33 AD6 LEU C 820 GLY C 827 1 8 HELIX 34 AD7 SER C 832 LYS C 853 1 22 HELIX 35 AD8 LYS C 861 SER C 863 5 3 HELIX 36 AD9 THR C 898 ARG C 902 5 5 HELIX 37 AE1 PRO C 903 LEU C 908 1 6 HELIX 38 AE2 PRO C 915 LYS C 932 1 18 HELIX 39 AE3 LEU C 940 GLY C 953 1 14 HELIX 40 AE4 TRP C 960 LEU C 966 5 7 HELIX 41 AE5 ARG C 981 PHE C 986 1 6 HELIX 42 AE6 PRO C 990 LEU C 1001 1 12 HELIX 43 AE7 THR C 1010 GLN C 1016 1 7 HELIX 44 AE8 SER C 1017 ASP C 1022 1 6 HELIX 45 AE9 ASP D 27 ALA D 32 1 6 HELIX 46 AF1 THR D 34 GLU D 39 1 6 HELIX 47 AF2 ASP D 42 LEU D 64 1 23 HELIX 48 AF3 HIS D 67 TYR D 82 1 16 HELIX 49 AF4 PRO D 91 GLU D 107 1 17 HELIX 50 AF5 LYS D 112 LEU D 124 1 13 HELIX 51 AF6 ASN D 125 GLY D 130 1 6 HELIX 52 AF7 GLN D 131 GLY D 133 5 3 HELIX 53 AF8 ASP D 135 ILE D 151 1 17 HELIX 54 AF9 HIS D 159 GLN D 170 1 12 HELIX 55 AG1 ASP D 174 LEU D 193 1 20 HELIX 56 AG2 CYS D 194 GLN D 200 5 7 HELIX 57 AG3 GLU D 202 LYS D 219 1 18 HELIX 58 AG4 GLU D 221 THR D 226 5 6 HELIX 59 AG5 ARG D 233 PHE D 238 5 6 HELIX 60 AG6 PRO D 243 ASP D 256 1 14 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 GLY A 731 SHEET 3 AA1 5 LEU A 752 VAL A 758 -1 O LEU A 755 N TYR A 742 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 LYS A 790 O VAL A 812 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 GLY C 734 0 SHEET 2 AA4 5 VAL C 741 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 LYS C 790 O VAL C 812 SHEET 1 AA5 3 HIS C 818 ASP C 819 0 SHEET 2 AA5 3 ILE C 865 LEU C 867 -1 O LEU C 867 N HIS C 818 SHEET 3 AA5 3 ILE C 873 LEU C 875 -1 O LYS C 874 N LEU C 866 SHEET 1 AA6 2 PHE C 855 LEU C 856 0 SHEET 2 AA6 2 ARG C 882 LEU C 883 -1 O ARG C 882 N LEU C 856 LINK C TYR A 892 N TPO A 893 1555 1555 1.34 LINK C TPO A 893 N ASN A 894 1555 1555 1.34 LINK C TYR C 892 N TPO C 893 1555 1555 1.35 LINK C TPO C 893 N ASN C 894 1555 1555 1.34 LINK OD2 ASP A 859 MG MG A1101 1555 1555 2.73 LINK OD2 ASP A 877 MG MG A1101 1555 1555 2.15 LINK OD2 ASP C 859 MG MG C1101 1555 1555 2.94 LINK OD2 ASP C 877 MG MG C1101 1555 1555 2.62 SITE 1 AC1 2 ASP A 859 ASP A 877 SITE 1 AC2 12 ILE A 733 GLY A 734 ALA A 754 VAL A 787 SITE 2 AC2 12 GLU A 814 TYR A 815 MET A 816 HIS A 818 SITE 3 AC2 12 ASP A 819 SER A 863 LEU A 866 ALA A 876 SITE 1 AC3 4 HIS B 67 TYR B 68 ASP B 69 THR B 70 SITE 1 AC4 4 ASP B 69 GLU B 107 VAL B 157 GLU B 158 SITE 1 AC5 2 ASP C 859 ASP C 877 SITE 1 AC6 7 LYS C 756 GLU C 774 VAL C 787 PHE C 813 SITE 2 AC6 7 ASP C 877 PHE C 878 CJM C1103 SITE 1 AC7 14 ILE C 733 GLY C 734 ALA C 754 VAL C 787 SITE 2 AC7 14 GLU C 814 TYR C 815 MET C 816 HIS C 818 SITE 3 AC7 14 ASP C 819 SER C 863 ASN C 864 LEU C 866 SITE 4 AC7 14 ALA C 876 EDO C1102 CRYST1 50.140 77.260 90.640 76.53 85.28 78.22 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 0.019944 -0.004159 -0.000744 0.00000 SCALE2 0.000000 0.013222 -0.003004 0.00000 SCALE3 0.000000 0.000000 0.011352 0.00000