HEADER CELL CYCLE 30-NOV-23 8R9O 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: 9 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 8R9O 1 JRNL REVDAT 1 29-MAY-24 8R9O 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. 2.22 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 43.1 REMARK 3 NUMBER OF REFLECTIONS : 15530 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) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.344 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 795 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 : 40 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 3.04 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 399 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2767 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 380 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE : 0.4024 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.76 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 : 4454 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.34400 REMARK 3 B22 (A**2) : -0.25180 REMARK 3 B33 (A**2) : 3.59570 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) : 0.420 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.555 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 : 0.877 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.795 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 9367 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 17016 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2061 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 14 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1464 ; 16.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 9367 ; 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 : 601 ; 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 : 7332 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.12 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 7.79 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.80 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): 53.9404 -14.8887 70.0010 REMARK 3 T TENSOR REMARK 3 T11: -0.0329 T22: -0.0186 REMARK 3 T33: 0.0287 T12: -0.1211 REMARK 3 T13: 0.0151 T23: 0.0289 REMARK 3 L TENSOR REMARK 3 L11: 4.8284 L22: 2.5008 REMARK 3 L33: 3.4324 L12: -1.2454 REMARK 3 L13: 2.4380 L23: -2.2443 REMARK 3 S TENSOR REMARK 3 S11: -0.0174 S12: -0.5081 S13: -0.5442 REMARK 3 S21: 0.0858 S22: -0.1851 S23: 0.1087 REMARK 3 S31: 0.2001 S32: -0.5442 S33: 0.2025 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|96 - A|312 } REMARK 3 ORIGIN FOR THE GROUP (A): 61.5641 10.5960 67.4695 REMARK 3 T TENSOR REMARK 3 T11: -0.1331 T22: 0.0799 REMARK 3 T33: 0.0136 T12: -0.0065 REMARK 3 T13: -0.0091 T23: -0.1307 REMARK 3 L TENSOR REMARK 3 L11: 0.8028 L22: 0.3768 REMARK 3 L33: 2.2020 L12: -0.3950 REMARK 3 L13: -0.0856 L23: 0.6089 REMARK 3 S TENSOR REMARK 3 S11: -0.0393 S12: -0.2336 S13: -0.0117 REMARK 3 S21: -0.1726 S22: 0.0577 S23: 0.0661 REMARK 3 S31: -0.2057 S32: 0.0815 S33: -0.0184 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|10 - B|95 } REMARK 3 ORIGIN FOR THE GROUP (A): 53.9400 47.4621 109.3780 REMARK 3 T TENSOR REMARK 3 T11: -0.0918 T22: 0.0372 REMARK 3 T33: 0.0264 T12: -0.0612 REMARK 3 T13: -0.0121 T23: 0.0664 REMARK 3 L TENSOR REMARK 3 L11: 3.2096 L22: 1.4348 REMARK 3 L33: 4.7052 L12: -2.7247 REMARK 3 L13: -0.3382 L23: -1.3252 REMARK 3 S TENSOR REMARK 3 S11: -0.1387 S12: -0.5442 S13: -0.4360 REMARK 3 S21: -0.4580 S22: 0.4055 S23: 0.5020 REMARK 3 S31: 0.4624 S32: -0.1933 S33: -0.2668 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { B|96 - B|312 } REMARK 3 ORIGIN FOR THE GROUP (A): 61.1042 73.0195 106.6640 REMARK 3 T TENSOR REMARK 3 T11: -0.1002 T22: 0.0714 REMARK 3 T33: -0.0618 T12: 0.0190 REMARK 3 T13: 0.0178 T23: -0.0363 REMARK 3 L TENSOR REMARK 3 L11: 1.4833 L22: 1.1360 REMARK 3 L33: 1.2805 L12: 0.4120 REMARK 3 L13: 0.1868 L23: 1.2002 REMARK 3 S TENSOR REMARK 3 S11: 0.0687 S12: -0.0826 S13: -0.0057 REMARK 3 S21: 0.0158 S22: 0.0458 S23: -0.0630 REMARK 3 S31: -0.0898 S32: -0.0394 S33: -0.1145 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS WERE FULLY REFINED REMARK 3 WITH FULL OCCUPANCY AT NUCLEAR POSITION. REMARK 4 REMARK 4 8R9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292134990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-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) : 0.9999 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 : 15530 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 56.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.4 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 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 : 1.700 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 (%): 41.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 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 20.06900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.09850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.86950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.09850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.06900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.86950 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 42 REMARK 465 ILE A 43 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 GLY A 82 REMARK 465 HIS A 83 REMARK 465 LYS A 84 REMARK 465 ASP A 164 REMARK 465 PRO A 165 REMARK 465 ASN A 166 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 VAL A 173 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 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 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 PHE A 23 CG CD1 CD2 CE1 CE2 CZ 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 OD2 ASP A 155 H3 YN3 A 401 1.40 REMARK 500 OD2 ASP B 155 H3 YN3 B 401 1.58 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 ALA A 24 -160.93 58.95 REMARK 500 ASP A 155 81.61 74.99 REMARK 500 PHE A 156 34.08 -97.15 REMARK 500 TRP A 237 104.68 -173.52 REMARK 500 ASP A 239 49.70 -109.95 REMARK 500 PHE A 261 76.94 -106.17 REMARK 500 LEU B 15 -61.33 -122.27 REMARK 500 LYS B 32 -8.82 -58.04 REMARK 500 ASN B 35 8.87 54.26 REMARK 500 ARG B 57 -44.01 -137.82 REMARK 500 ASP B 137 37.52 -146.72 REMARK 500 ASP B 155 80.71 67.98 REMARK 500 PHE B 156 34.33 -96.95 REMARK 500 PHE B 261 77.20 -106.55 REMARK 500 LYS B 291 20.85 -75.64 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 PHE B 23 ALA B 24 -149.94 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 573 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH A 574 DISTANCE = 9.17 ANGSTROMS REMARK 525 HOH B 563 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH B 564 DISTANCE = 7.87 ANGSTROMS REMARK 525 HOH B 565 DISTANCE = 7.89 ANGSTROMS DBREF 8R9O A 1 346 UNP P50613 CDK7_HUMAN 1 346 DBREF 8R9O B 1 346 UNP P50613 CDK7_HUMAN 1 346 SEQADV 8R9O MET A -24 UNP P50613 INITIATING METHIONINE SEQADV 8R9O SER A -23 UNP P50613 EXPRESSION TAG SEQADV 8R9O TYR A -22 UNP P50613 EXPRESSION TAG SEQADV 8R9O TYR A -21 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS A -20 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS A -19 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS A -18 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS A -17 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS A -16 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS A -15 UNP P50613 EXPRESSION TAG SEQADV 8R9O ASP A -14 UNP P50613 EXPRESSION TAG SEQADV 8R9O TYR A -13 UNP P50613 EXPRESSION TAG SEQADV 8R9O ASP A -12 UNP P50613 EXPRESSION TAG SEQADV 8R9O ILE A -11 UNP P50613 EXPRESSION TAG SEQADV 8R9O PRO A -10 UNP P50613 EXPRESSION TAG SEQADV 8R9O THR A -9 UNP P50613 EXPRESSION TAG SEQADV 8R9O THR A -8 UNP P50613 EXPRESSION TAG SEQADV 8R9O GLU A -7 UNP P50613 EXPRESSION TAG SEQADV 8R9O ASN A -6 UNP P50613 EXPRESSION TAG SEQADV 8R9O LEU A -5 UNP P50613 EXPRESSION TAG SEQADV 8R9O TYR A -4 UNP P50613 EXPRESSION TAG SEQADV 8R9O PHE A -3 UNP P50613 EXPRESSION TAG SEQADV 8R9O GLN A -2 UNP P50613 EXPRESSION TAG SEQADV 8R9O GLY A -1 UNP P50613 EXPRESSION TAG SEQADV 8R9O SER A 0 UNP P50613 EXPRESSION TAG SEQADV 8R9O ARG A 132 UNP P50613 TRP 132 ENGINEERED MUTATION SEQADV 8R9O ASP A 164 UNP P50613 SER 164 ENGINEERED MUTATION SEQADV 8R9O GLU A 170 UNP P50613 THR 170 ENGINEERED MUTATION SEQADV 8R9O MET B -24 UNP P50613 INITIATING METHIONINE SEQADV 8R9O SER B -23 UNP P50613 EXPRESSION TAG SEQADV 8R9O TYR B -22 UNP P50613 EXPRESSION TAG SEQADV 8R9O TYR B -21 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS B -20 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS B -19 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS B -18 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS B -17 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS B -16 UNP P50613 EXPRESSION TAG SEQADV 8R9O HIS B -15 UNP P50613 EXPRESSION TAG SEQADV 8R9O ASP B -14 UNP P50613 EXPRESSION TAG SEQADV 8R9O TYR B -13 UNP P50613 EXPRESSION TAG SEQADV 8R9O ASP B -12 UNP P50613 EXPRESSION TAG SEQADV 8R9O ILE B -11 UNP P50613 EXPRESSION TAG SEQADV 8R9O PRO B -10 UNP P50613 EXPRESSION TAG SEQADV 8R9O THR B -9 UNP P50613 EXPRESSION TAG SEQADV 8R9O THR B -8 UNP P50613 EXPRESSION TAG SEQADV 8R9O GLU B -7 UNP P50613 EXPRESSION TAG SEQADV 8R9O ASN B -6 UNP P50613 EXPRESSION TAG SEQADV 8R9O LEU B -5 UNP P50613 EXPRESSION TAG SEQADV 8R9O TYR B -4 UNP P50613 EXPRESSION TAG SEQADV 8R9O PHE B -3 UNP P50613 EXPRESSION TAG SEQADV 8R9O GLN B -2 UNP P50613 EXPRESSION TAG SEQADV 8R9O GLY B -1 UNP P50613 EXPRESSION TAG SEQADV 8R9O SER B 0 UNP P50613 EXPRESSION TAG SEQADV 8R9O ARG B 132 UNP P50613 TRP 132 ENGINEERED MUTATION SEQADV 8R9O ASP B 164 UNP P50613 SER 164 ENGINEERED MUTATION SEQADV 8R9O 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 YN3 A 401 73 HET YN3 B 401 73 HETNAM YN3 ~{N}-[(1~{S})-2-(DIMETHYLAMINO)-1-PHENYL-ETHYL]-6,6- HETNAM 2 YN3 DIMETHYL-3-[[4-(PROPANOYLAMINO)PHENYL]CARBONYLAMINO]- HETNAM 3 YN3 1,4-DIHYDROPYRROLO[3,4-C]PYRAZOLE-5-CARBOXAMIDE FORMUL 3 YN3 2(C28 H35 N7 O3) FORMUL 5 HOH *139(H2 O) HELIX 1 AA1 ARG A 57 LEU A 69 1 13 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 GLY A 186 1 7 HELIX 7 AA7 VAL A 192 ARG A 209 1 18 HELIX 8 AA8 SER A 217 LEU A 229 1 13 HELIX 9 AA9 PRO A 256 PHE A 261 1 6 HELIX 10 AB1 GLY A 265 PHE A 276 1 12 HELIX 11 AB2 THR A 285 LYS A 291 1 7 HELIX 12 AB3 MET A 292 ASN A 297 1 6 HELIX 13 AB4 PRO A 303 LEU A 307 5 5 HELIX 14 AB5 THR B 58 LEU B 69 1 12 HELIX 15 AB6 LEU B 98 ASP B 104 1 7 HELIX 16 AB7 THR B 110 HIS B 131 1 22 HELIX 17 AB8 LYS B 139 ASN B 141 5 3 HELIX 18 AB9 THR B 175 ARG B 179 5 5 HELIX 19 AC1 ALA B 180 PHE B 185 1 6 HELIX 20 AC2 VAL B 192 ARG B 209 1 18 HELIX 21 AC3 SER B 217 GLY B 230 1 14 HELIX 22 AC4 TRP B 237 LEU B 243 5 7 HELIX 23 AC5 PRO B 256 PHE B 261 1 6 HELIX 24 AC6 GLY B 265 PHE B 276 1 12 HELIX 25 AC7 THR B 285 LYS B 291 1 7 HELIX 26 AC8 MET B 292 ASN B 297 1 6 HELIX 27 AC9 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 LYS A 28 N LEU A 15 SHEET 3 AA1 5 ILE A 37 ILE A 40 -1 O VAL A 38 N ALA A 29 SHEET 4 AA1 5 LEU A 89 ASP A 92 -1 O PHE A 91 N ALA A 39 SHEET 5 AA1 5 LEU A 77 ALA A 80 -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 LYS B 28 N LEU B 15 SHEET 3 AA4 5 ILE B 37 LYS B 42 -1 O VAL B 38 N ALA B 29 SHEET 4 AA4 5 LEU B 89 ASP B 92 -1 O PHE B 91 N ALA B 39 SHEET 5 AA4 5 ASP B 79 ALA B 80 -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 LINK SG CYS A 312 C26 YN3 A 401 1555 1555 1.82 LINK SG CYS B 312 C26 YN3 B 401 1555 1555 1.82 CISPEP 1 ARG A 298 PRO A 299 0 -7.80 CISPEP 2 ARG B 298 PRO B 299 0 -8.47 CRYST1 40.138 123.739 142.197 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 0.024914 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007032 0.00000