HEADER CELL CYCLE 30-NOV-23 8R9U TITLE A SOAKABLE CRYSTAL FORM OF HUMAN CDK7 IN COMPLEX WITH AMP-PNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 7; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CDK7; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: 6 KEYWDS SERINE-THREONINE KINASE, PHOSPHORYLATION, CELL CYCLE PROGRESSION, ATP KEYWDS 2 BINDING, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR M.MUKHERJEE,A.CLEASBY REVDAT 2 26-JUN-24 8R9U 1 JRNL REVDAT 1 29-MAY-24 8R9U 0 JRNL AUTH M.MUKHERJEE,P.J.DAY,D.LAVERTY,J.A.BUEREN-CALABUIG, JRNL AUTH 2 A.J.WOODHEAD,C.GRIFFITHS-JONES,S.HISCOCK,C.EAST,S.BOYD, JRNL AUTH 3 M.O'REILLY JRNL TITL PROTEIN ENGINEERING ENABLES A SOAKABLE CRYSTAL FORM OF HUMAN JRNL TITL 2 CDK7 PRIMED FOR HIGH-THROUGHPUT CRYSTALLOGRAPHY AND JRNL TITL 3 STRUCTURE-BASED DRUG DESIGN. JRNL REF STRUCTURE 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38870939 JRNL DOI 10.1016/J.STR.2024.05.011 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.8 (16-JUL-2021) 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 50.6 REMARK 3 NUMBER OF REFLECTIONS : 28311 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) : 0.278 REMARK 3 R VALUE (WORKING SET) : 0.275 REMARK 3 FREE R VALUE : 0.340 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1386 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 51 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 4.10 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 567 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3263 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 545 REMARK 3 BIN R VALUE (WORKING SET) : 0.3259 REMARK 3 BIN FREE R VALUE : 0.3358 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.88 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 : 4490 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 294 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.57510 REMARK 3 B22 (A**2) : -2.19280 REMARK 3 B33 (A**2) : 5.76790 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.390 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.558 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.349 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 : 0.846 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.802 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 9578 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 17431 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2106 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1497 ; 16.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 9578 ; 10.000 ; HARMONIC 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 : 616 ; 5.000 ; SEMIHARMONIC 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 : 7438 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.17 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 7.09 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.77 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|10 - A|95 } REMARK 3 ORIGIN FOR THE GROUP (A): 14.5211 13.2441 -34.7171 REMARK 3 T TENSOR REMARK 3 T11: -0.0263 T22: -0.1496 REMARK 3 T33: 0.1153 T12: 0.1045 REMARK 3 T13: -0.0835 T23: 0.0953 REMARK 3 L TENSOR REMARK 3 L11: 1.5213 L22: 2.1565 REMARK 3 L33: 4.2412 L12: 0.9228 REMARK 3 L13: -0.7304 L23: 0.1629 REMARK 3 S TENSOR REMARK 3 S11: -0.1899 S12: 0.2187 S13: 0.1572 REMARK 3 S21: -0.1603 S22: 0.0468 S23: 0.0131 REMARK 3 S31: -0.4927 S32: -0.3302 S33: 0.1431 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|96 - A|311 } REMARK 3 ORIGIN FOR THE GROUP (A): 21.1339 -11.7712 -31.5473 REMARK 3 T TENSOR REMARK 3 T11: -0.0999 T22: -0.0711 REMARK 3 T33: 0.0987 T12: -0.0098 REMARK 3 T13: -0.0210 T23: 0.0390 REMARK 3 L TENSOR REMARK 3 L11: 0.6702 L22: 0.3438 REMARK 3 L33: 1.8895 L12: 0.1136 REMARK 3 L13: 0.1154 L23: 0.9278 REMARK 3 S TENSOR REMARK 3 S11: -0.0907 S12: -0.0057 S13: 0.0771 REMARK 3 S21: 0.0346 S22: 0.0492 S23: 0.0210 REMARK 3 S31: 0.2427 S32: -0.0129 S33: 0.0415 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|10 - B|95 } REMARK 3 ORIGIN FOR THE GROUP (A): 26.0160 14.1924 -66.3998 REMARK 3 T TENSOR REMARK 3 T11: -0.1742 T22: 0.0634 REMARK 3 T33: 0.0891 T12: -0.0659 REMARK 3 T13: 0.0382 T23: -0.1520 REMARK 3 L TENSOR REMARK 3 L11: 0.7116 L22: 3.8770 REMARK 3 L33: 0.0000 L12: -0.5690 REMARK 3 L13: -0.7347 L23: 0.7775 REMARK 3 S TENSOR REMARK 3 S11: -0.0549 S12: -0.1893 S13: 0.0630 REMARK 3 S21: -0.0483 S22: 0.1438 S23: 0.0822 REMARK 3 S31: -0.3215 S32: 0.5369 S33: -0.0889 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { B|96 - B|311 } REMARK 3 ORIGIN FOR THE GROUP (A): 18.9834 -10.6993 -70.8902 REMARK 3 T TENSOR REMARK 3 T11: -0.1514 T22: -0.0103 REMARK 3 T33: 0.1001 T12: -0.0375 REMARK 3 T13: 0.0063 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.6143 L22: 0.5052 REMARK 3 L33: 1.7808 L12: -0.3699 REMARK 3 L13: -0.0215 L23: -0.9212 REMARK 3 S TENSOR REMARK 3 S11: 0.0644 S12: -0.1351 S13: -0.0248 REMARK 3 S21: -0.1722 S22: -0.0634 S23: 0.1165 REMARK 3 S31: 0.1671 S32: 0.0520 S33: -0.0010 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS WERE FULLY REFINED REMARK 3 WITH FULL OCCUPANCY AT NUCLEAR POSITION. REMARK 4 REMARK 4 8R9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292135010. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-20 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 : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9998 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 : 28311 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 71.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 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 : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: BUSTER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M (NH4)3 CITRATE 15% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 20.15150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.34200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.85550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.34200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.15150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.85550 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A -24 REMARK 465 SER A -23 REMARK 465 TYR A -22 REMARK 465 TYR A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 ASP A -14 REMARK 465 TYR A -13 REMARK 465 ASP A -12 REMARK 465 ILE A -11 REMARK 465 PRO A -10 REMARK 465 THR A -9 REMARK 465 THR A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 ASP A 4 REMARK 465 VAL A 5 REMARK 465 LYS A 6 REMARK 465 SER A 7 REMARK 465 ARG A 8 REMARK 465 ALA A 9 REMARK 465 LYS A 44 REMARK 465 LEU A 45 REMARK 465 GLY A 46 REMARK 465 HIS A 47 REMARK 465 ARG A 48 REMARK 465 SER A 49 REMARK 465 GLU A 50 REMARK 465 ALA A 51 REMARK 465 LYS A 52 REMARK 465 ASP A 53 REMARK 465 GLY A 54 REMARK 465 ILE A 55 REMARK 465 HIS A 83 REMARK 465 LYS A 84 REMARK 465 ARG A 167 REMARK 465 ALA A 168 REMARK 465 TYR A 169 REMARK 465 GLU A 170 REMARK 465 HIS A 171 REMARK 465 GLN A 172 REMARK 465 CYS A 312 REMARK 465 PRO A 313 REMARK 465 VAL A 314 REMARK 465 GLU A 315 REMARK 465 THR A 316 REMARK 465 LEU A 317 REMARK 465 LYS A 318 REMARK 465 GLU A 319 REMARK 465 GLN A 320 REMARK 465 SER A 321 REMARK 465 ASN A 322 REMARK 465 PRO A 323 REMARK 465 ALA A 324 REMARK 465 LEU A 325 REMARK 465 ALA A 326 REMARK 465 ILE A 327 REMARK 465 LYS A 328 REMARK 465 ARG A 329 REMARK 465 LYS A 330 REMARK 465 ARG A 331 REMARK 465 THR A 332 REMARK 465 GLU A 333 REMARK 465 ALA A 334 REMARK 465 LEU A 335 REMARK 465 GLU A 336 REMARK 465 GLN A 337 REMARK 465 GLY A 338 REMARK 465 GLY A 339 REMARK 465 LEU A 340 REMARK 465 PRO A 341 REMARK 465 LYS A 342 REMARK 465 LYS A 343 REMARK 465 LEU A 344 REMARK 465 ILE A 345 REMARK 465 PHE A 346 REMARK 465 MET B -24 REMARK 465 SER B -23 REMARK 465 TYR B -22 REMARK 465 TYR B -21 REMARK 465 HIS B -20 REMARK 465 HIS B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 ASP B -14 REMARK 465 TYR B -13 REMARK 465 ASP B -12 REMARK 465 ILE B -11 REMARK 465 PRO B -10 REMARK 465 THR B -9 REMARK 465 THR B -8 REMARK 465 GLU B -7 REMARK 465 ASN B -6 REMARK 465 LEU B -5 REMARK 465 TYR B -4 REMARK 465 PHE B -3 REMARK 465 GLN B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 LEU B 3 REMARK 465 ASP B 4 REMARK 465 VAL B 5 REMARK 465 LYS B 6 REMARK 465 SER B 7 REMARK 465 ARG B 8 REMARK 465 ALA B 9 REMARK 465 LYS B 44 REMARK 465 LEU B 45 REMARK 465 GLY B 46 REMARK 465 HIS B 47 REMARK 465 ARG B 48 REMARK 465 SER B 49 REMARK 465 GLU B 50 REMARK 465 ALA B 51 REMARK 465 LYS B 52 REMARK 465 ASP B 53 REMARK 465 GLY B 54 REMARK 465 ILE B 55 REMARK 465 HIS B 83 REMARK 465 LYS B 84 REMARK 465 ARG B 167 REMARK 465 ALA B 168 REMARK 465 TYR B 169 REMARK 465 GLU B 170 REMARK 465 HIS B 171 REMARK 465 GLN B 172 REMARK 465 CYS B 312 REMARK 465 PRO B 313 REMARK 465 VAL B 314 REMARK 465 GLU B 315 REMARK 465 THR B 316 REMARK 465 LEU B 317 REMARK 465 LYS B 318 REMARK 465 GLU B 319 REMARK 465 GLN B 320 REMARK 465 SER B 321 REMARK 465 ASN B 322 REMARK 465 PRO B 323 REMARK 465 ALA B 324 REMARK 465 LEU B 325 REMARK 465 ALA B 326 REMARK 465 ILE B 327 REMARK 465 LYS B 328 REMARK 465 ARG B 329 REMARK 465 LYS B 330 REMARK 465 ARG B 331 REMARK 465 THR B 332 REMARK 465 GLU B 333 REMARK 465 ALA B 334 REMARK 465 LEU B 335 REMARK 465 GLU B 336 REMARK 465 GLN B 337 REMARK 465 GLY B 338 REMARK 465 GLY B 339 REMARK 465 LEU B 340 REMARK 465 PRO B 341 REMARK 465 LYS B 342 REMARK 465 LYS B 343 REMARK 465 LEU B 344 REMARK 465 ILE B 345 REMARK 465 PHE B 346 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 O HOH A 517 O HOH A 544 2.17 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 GLN A 22 57.25 -98.40 REMARK 500 PHE A 23 -61.23 -163.84 REMARK 500 ARG A 136 18.68 54.29 REMARK 500 ASP A 137 32.91 -148.98 REMARK 500 ASP A 155 71.88 64.26 REMARK 500 PHE A 156 35.40 -94.29 REMARK 500 VAL A 174 162.87 -33.61 REMARK 500 TYR A 190 -176.49 -172.45 REMARK 500 PHE A 261 71.61 -111.43 REMARK 500 PHE B 23 71.47 49.84 REMARK 500 ALA B 24 104.93 -174.93 REMARK 500 LYS B 41 53.83 -115.44 REMARK 500 LYS B 42 90.85 -37.97 REMARK 500 HIS B 71 143.09 -171.23 REMARK 500 ASP B 137 30.60 -145.96 REMARK 500 ASP B 155 73.42 67.08 REMARK 500 PHE B 156 34.81 -94.57 REMARK 500 SER B 161 136.99 -30.52 REMARK 500 VAL B 174 159.48 -49.58 REMARK 500 TYR B 190 -176.34 -173.22 REMARK 500 VAL B 192 -52.50 -24.63 REMARK 500 THR B 248 102.42 -59.54 REMARK 500 LYS B 250 116.04 -38.39 REMARK 500 PHE B 261 71.68 -111.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 61 GLU A 62 144.88 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 A 648 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 649 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A 650 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A 651 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 652 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 653 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH A 654 DISTANCE = 7.93 ANGSTROMS REMARK 525 HOH A 655 DISTANCE = 7.93 ANGSTROMS REMARK 525 HOH A 656 DISTANCE = 8.21 ANGSTROMS REMARK 525 HOH A 657 DISTANCE = 9.43 ANGSTROMS REMARK 525 HOH A 658 DISTANCE = 10.30 ANGSTROMS REMARK 525 HOH A 659 DISTANCE = 12.29 ANGSTROMS REMARK 525 HOH B 631 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH B 632 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH B 633 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH B 634 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH B 635 DISTANCE = 7.42 ANGSTROMS DBREF 8R9U A 1 346 UNP P50613 CDK7_HUMAN 1 346 DBREF 8R9U B 1 346 UNP P50613 CDK7_HUMAN 1 346 SEQADV 8R9U MET A -24 UNP P50613 INITIATING METHIONINE SEQADV 8R9U SER A -23 UNP P50613 EXPRESSION TAG SEQADV 8R9U TYR A -22 UNP P50613 EXPRESSION TAG SEQADV 8R9U TYR A -21 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS A -20 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS A -19 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS A -18 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS A -17 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS A -16 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS A -15 UNP P50613 EXPRESSION TAG SEQADV 8R9U ASP A -14 UNP P50613 EXPRESSION TAG SEQADV 8R9U TYR A -13 UNP P50613 EXPRESSION TAG SEQADV 8R9U ASP A -12 UNP P50613 EXPRESSION TAG SEQADV 8R9U ILE A -11 UNP P50613 EXPRESSION TAG SEQADV 8R9U PRO A -10 UNP P50613 EXPRESSION TAG SEQADV 8R9U THR A -9 UNP P50613 EXPRESSION TAG SEQADV 8R9U THR A -8 UNP P50613 EXPRESSION TAG SEQADV 8R9U GLU A -7 UNP P50613 EXPRESSION TAG SEQADV 8R9U ASN A -6 UNP P50613 EXPRESSION TAG SEQADV 8R9U LEU A -5 UNP P50613 EXPRESSION TAG SEQADV 8R9U TYR A -4 UNP P50613 EXPRESSION TAG SEQADV 8R9U PHE A -3 UNP P50613 EXPRESSION TAG SEQADV 8R9U GLN A -2 UNP P50613 EXPRESSION TAG SEQADV 8R9U GLY A -1 UNP P50613 EXPRESSION TAG SEQADV 8R9U SER A 0 UNP P50613 EXPRESSION TAG SEQADV 8R9U ARG A 132 UNP P50613 TRP 132 ENGINEERED MUTATION SEQADV 8R9U ASP A 164 UNP P50613 SER 164 ENGINEERED MUTATION SEQADV 8R9U GLU A 170 UNP P50613 THR 170 ENGINEERED MUTATION SEQADV 8R9U MET B -24 UNP P50613 INITIATING METHIONINE SEQADV 8R9U SER B -23 UNP P50613 EXPRESSION TAG SEQADV 8R9U TYR B -22 UNP P50613 EXPRESSION TAG SEQADV 8R9U TYR B -21 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS B -20 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS B -19 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS B -18 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS B -17 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS B -16 UNP P50613 EXPRESSION TAG SEQADV 8R9U HIS B -15 UNP P50613 EXPRESSION TAG SEQADV 8R9U ASP B -14 UNP P50613 EXPRESSION TAG SEQADV 8R9U TYR B -13 UNP P50613 EXPRESSION TAG SEQADV 8R9U ASP B -12 UNP P50613 EXPRESSION TAG SEQADV 8R9U ILE B -11 UNP P50613 EXPRESSION TAG SEQADV 8R9U PRO B -10 UNP P50613 EXPRESSION TAG SEQADV 8R9U THR B -9 UNP P50613 EXPRESSION TAG SEQADV 8R9U THR B -8 UNP P50613 EXPRESSION TAG SEQADV 8R9U GLU B -7 UNP P50613 EXPRESSION TAG SEQADV 8R9U ASN B -6 UNP P50613 EXPRESSION TAG SEQADV 8R9U LEU B -5 UNP P50613 EXPRESSION TAG SEQADV 8R9U TYR B -4 UNP P50613 EXPRESSION TAG SEQADV 8R9U PHE B -3 UNP P50613 EXPRESSION TAG SEQADV 8R9U GLN B -2 UNP P50613 EXPRESSION TAG SEQADV 8R9U GLY B -1 UNP P50613 EXPRESSION TAG SEQADV 8R9U SER B 0 UNP P50613 EXPRESSION TAG SEQADV 8R9U ARG B 132 UNP P50613 TRP 132 ENGINEERED MUTATION SEQADV 8R9U ASP B 164 UNP P50613 SER 164 ENGINEERED MUTATION SEQADV 8R9U GLU B 170 UNP P50613 THR 170 ENGINEERED MUTATION SEQRES 1 A 371 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 A 371 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY SER MET SEQRES 3 A 371 ALA LEU ASP VAL LYS SER ARG ALA LYS ARG TYR GLU LYS SEQRES 4 A 371 LEU ASP PHE LEU GLY GLU GLY GLN PHE ALA THR VAL TYR SEQRES 5 A 371 LYS ALA ARG ASP LYS ASN THR ASN GLN ILE VAL ALA ILE SEQRES 6 A 371 LYS LYS ILE LYS LEU GLY HIS ARG SER GLU ALA LYS ASP SEQRES 7 A 371 GLY ILE ASN ARG THR ALA LEU ARG GLU ILE LYS LEU LEU SEQRES 8 A 371 GLN GLU LEU SER HIS PRO ASN ILE ILE GLY LEU LEU ASP SEQRES 9 A 371 ALA PHE GLY HIS LYS SER ASN ILE SER LEU VAL PHE ASP SEQRES 10 A 371 PHE MET GLU THR ASP LEU GLU VAL ILE ILE LYS ASP ASN SEQRES 11 A 371 SER LEU VAL LEU THR PRO SER HIS ILE LYS ALA TYR MET SEQRES 12 A 371 LEU MET THR LEU GLN GLY LEU GLU TYR LEU HIS GLN HIS SEQRES 13 A 371 ARG ILE LEU HIS ARG ASP LEU LYS PRO ASN ASN LEU LEU SEQRES 14 A 371 LEU ASP GLU ASN GLY VAL LEU LYS LEU ALA ASP PHE GLY SEQRES 15 A 371 LEU ALA LYS SER PHE GLY ASP PRO ASN ARG ALA TYR GLU SEQRES 16 A 371 HIS GLN VAL VAL THR ARG TRP TYR ARG ALA PRO GLU LEU SEQRES 17 A 371 LEU PHE GLY ALA ARG MET TYR GLY VAL GLY VAL ASP MET SEQRES 18 A 371 TRP ALA VAL GLY CYS ILE LEU ALA GLU LEU LEU LEU ARG SEQRES 19 A 371 VAL PRO PHE LEU PRO GLY ASP SER ASP LEU ASP GLN LEU SEQRES 20 A 371 THR ARG ILE PHE GLU THR LEU GLY THR PRO THR GLU GLU SEQRES 21 A 371 GLN TRP PRO ASP MET CYS SER LEU PRO ASP TYR VAL THR SEQRES 22 A 371 PHE LYS SER PHE PRO GLY ILE PRO LEU HIS HIS ILE PHE SEQRES 23 A 371 SER ALA ALA GLY ASP ASP LEU LEU ASP LEU ILE GLN GLY SEQRES 24 A 371 LEU PHE LEU PHE ASN PRO CYS ALA ARG ILE THR ALA THR SEQRES 25 A 371 GLN ALA LEU LYS MET LYS TYR PHE SER ASN ARG PRO GLY SEQRES 26 A 371 PRO THR PRO GLY CYS GLN LEU PRO ARG PRO ASN CYS PRO SEQRES 27 A 371 VAL GLU THR LEU LYS GLU GLN SER ASN PRO ALA LEU ALA SEQRES 28 A 371 ILE LYS ARG LYS ARG THR GLU ALA LEU GLU GLN GLY GLY SEQRES 29 A 371 LEU PRO LYS LYS LEU ILE PHE SEQRES 1 B 371 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 B 371 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY SER MET SEQRES 3 B 371 ALA LEU ASP VAL LYS SER ARG ALA LYS ARG TYR GLU LYS SEQRES 4 B 371 LEU ASP PHE LEU GLY GLU GLY GLN PHE ALA THR VAL TYR SEQRES 5 B 371 LYS ALA ARG ASP LYS ASN THR ASN GLN ILE VAL ALA ILE SEQRES 6 B 371 LYS LYS ILE LYS LEU GLY HIS ARG SER GLU ALA LYS ASP SEQRES 7 B 371 GLY ILE ASN ARG THR ALA LEU ARG GLU ILE LYS LEU LEU SEQRES 8 B 371 GLN GLU LEU SER HIS PRO ASN ILE ILE GLY LEU LEU ASP SEQRES 9 B 371 ALA PHE GLY HIS LYS SER ASN ILE SER LEU VAL PHE ASP SEQRES 10 B 371 PHE MET GLU THR ASP LEU GLU VAL ILE ILE LYS ASP ASN SEQRES 11 B 371 SER LEU VAL LEU THR PRO SER HIS ILE LYS ALA TYR MET SEQRES 12 B 371 LEU MET THR LEU GLN GLY LEU GLU TYR LEU HIS GLN HIS SEQRES 13 B 371 ARG ILE LEU HIS ARG ASP LEU LYS PRO ASN ASN LEU LEU SEQRES 14 B 371 LEU ASP GLU ASN GLY VAL LEU LYS LEU ALA ASP PHE GLY SEQRES 15 B 371 LEU ALA LYS SER PHE GLY ASP PRO ASN ARG ALA TYR GLU SEQRES 16 B 371 HIS GLN VAL VAL THR ARG TRP TYR ARG ALA PRO GLU LEU SEQRES 17 B 371 LEU PHE GLY ALA ARG MET TYR GLY VAL GLY VAL ASP MET SEQRES 18 B 371 TRP ALA VAL GLY CYS ILE LEU ALA GLU LEU LEU LEU ARG SEQRES 19 B 371 VAL PRO PHE LEU PRO GLY ASP SER ASP LEU ASP GLN LEU SEQRES 20 B 371 THR ARG ILE PHE GLU THR LEU GLY THR PRO THR GLU GLU SEQRES 21 B 371 GLN TRP PRO ASP MET CYS SER LEU PRO ASP TYR VAL THR SEQRES 22 B 371 PHE LYS SER PHE PRO GLY ILE PRO LEU HIS HIS ILE PHE SEQRES 23 B 371 SER ALA ALA GLY ASP ASP LEU LEU ASP LEU ILE GLN GLY SEQRES 24 B 371 LEU PHE LEU PHE ASN PRO CYS ALA ARG ILE THR ALA THR SEQRES 25 B 371 GLN ALA LEU LYS MET LYS TYR PHE SER ASN ARG PRO GLY SEQRES 26 B 371 PRO THR PRO GLY CYS GLN LEU PRO ARG PRO ASN CYS PRO SEQRES 27 B 371 VAL GLU THR LEU LYS GLU GLN SER ASN PRO ALA LEU ALA SEQRES 28 B 371 ILE LYS ARG LYS ARG THR GLU ALA LEU GLU GLN GLY GLY SEQRES 29 B 371 LEU PRO LYS LYS LEU ILE PHE HET YNK A 401 61 HET YNK B 401 61 HETNAM YNK 7-DIMETHYLPHOSPHORYL-3-[2-[[(3~{S})-6,6- HETNAM 2 YNK DIMETHYLPIPERIDIN-3-YL]AMINO]-5-(TRIFLUOROMETHYL) HETNAM 3 YNK PYRIMIDIN-4-YL]-1~{H}-INDOLE-6-CARBONITRILE FORMUL 3 YNK 2(C23 H26 F3 N6 O P) FORMUL 5 HOH *294(H2 O) HELIX 1 AA1 ALA A 59 GLN A 67 1 9 HELIX 2 AA2 LEU A 98 ASP A 104 1 7 HELIX 3 AA3 THR A 110 HIS A 131 1 22 HELIX 4 AA4 LYS A 139 ASN A 141 5 3 HELIX 5 AA5 THR A 175 ARG A 179 5 5 HELIX 6 AA6 ALA A 180 PHE A 185 1 6 HELIX 7 AA7 GLY A 191 ARG A 209 1 19 HELIX 8 AA8 SER A 217 GLY A 230 1 14 HELIX 9 AA9 TRP A 237 LEU A 243 5 7 HELIX 10 AB1 PRO A 256 PHE A 261 1 6 HELIX 11 AB2 GLY A 265 PHE A 276 1 12 HELIX 12 AB3 THR A 285 LYS A 291 1 7 HELIX 13 AB4 MET A 292 SER A 296 5 5 HELIX 14 AB5 PRO A 303 LEU A 307 5 5 HELIX 15 AB6 ARG B 57 LEU B 69 1 13 HELIX 16 AB7 LEU B 98 ASP B 104 1 7 HELIX 17 AB8 THR B 110 HIS B 131 1 22 HELIX 18 AB9 LYS B 139 ASN B 141 5 3 HELIX 19 AC1 THR B 175 ARG B 179 5 5 HELIX 20 AC2 ALA B 180 PHE B 185 1 6 HELIX 21 AC3 VAL B 192 ARG B 209 1 18 HELIX 22 AC4 SER B 217 GLY B 230 1 14 HELIX 23 AC5 TRP B 237 LEU B 243 5 7 HELIX 24 AC6 PRO B 256 PHE B 261 1 6 HELIX 25 AC7 GLY B 265 PHE B 276 1 12 HELIX 26 AC8 THR B 285 LYS B 291 1 7 HELIX 27 AC9 MET B 292 ASN B 297 1 6 HELIX 28 AD1 PRO B 303 LEU B 307 5 5 SHEET 1 AA1 5 TYR A 12 GLU A 20 0 SHEET 2 AA1 5 THR A 25 ASP A 31 -1 O VAL A 26 N GLY A 19 SHEET 3 AA1 5 ILE A 37 ILE A 43 -1 O VAL A 38 N ALA A 29 SHEET 4 AA1 5 ILE A 87 ASP A 92 -1 O PHE A 91 N ALA A 39 SHEET 5 AA1 5 LEU A 77 PHE A 81 -1 N LEU A 78 O VAL A 90 SHEET 1 AA2 3 THR A 96 ASP A 97 0 SHEET 2 AA2 3 LEU A 143 LEU A 145 -1 O LEU A 145 N THR A 96 SHEET 3 AA2 3 LEU A 151 LEU A 153 -1 O LYS A 152 N LEU A 144 SHEET 1 AA3 2 ILE A 133 LEU A 134 0 SHEET 2 AA3 2 LYS A 160 SER A 161 -1 O LYS A 160 N LEU A 134 SHEET 1 AA4 5 TYR B 12 GLU B 20 0 SHEET 2 AA4 5 THR B 25 ASP B 31 -1 O VAL B 26 N GLY B 19 SHEET 3 AA4 5 ILE B 37 ILE B 40 -1 O VAL B 38 N ALA B 29 SHEET 4 AA4 5 SER B 88 ASP B 92 -1 O PHE B 91 N ALA B 39 SHEET 5 AA4 5 LEU B 77 PHE B 81 -1 N ASP B 79 O VAL B 90 SHEET 1 AA5 3 THR B 96 ASP B 97 0 SHEET 2 AA5 3 LEU B 143 LEU B 145 -1 O LEU B 145 N THR B 96 SHEET 3 AA5 3 LEU B 151 LEU B 153 -1 O LYS B 152 N LEU B 144 SHEET 1 AA6 2 ILE B 133 LEU B 134 0 SHEET 2 AA6 2 LYS B 160 SER B 161 -1 O LYS B 160 N LEU B 134 CISPEP 1 ARG A 298 PRO A 299 0 5.86 CISPEP 2 ARG B 298 PRO B 299 0 6.14 CRYST1 40.303 127.711 142.684 90.00 90.00 90.00 P 21 21 21 8 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 0.024812 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007830 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007008 0.00000