HEADER TRANSCRIPTION 22-MAR-20 6W9E TITLE CRYSTAL STRUCTURE OF HUMAN CDK9/CYCLINT1 IN COMPLEX WITH MC180295 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C-2K,CELL DIVISION CYCLE 2-LIKE PROTEIN KINASE 4,CELL COMPND 5 DIVISION PROTEIN KINASE 9,SERINE/THREONINE-PROTEIN KINASE PITALRE, COMPND 6 TAT-ASSOCIATED KINASE COMPLEX CATALYTIC SUBUNIT; COMPND 7 EC: 2.7.11.22,2.7.11.23; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CYCLIN-T1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: CYCLIN-T; COMPND 13 ENGINEERED: YES; COMPND 14 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: CDK9, CDC2L4, TAK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CCNT1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS CDK9, CYCLIN T1, MC180295, COMPLEX, TRANSCRIPTIONAL REGULATOR, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR P.ZHANG,J.WU REVDAT 2 18-OCT-23 6W9E 1 REMARK REVDAT 1 01-SEP-21 6W9E 0 JRNL AUTH P.KIRUBAKARAN,G.MORTON,P.ZHANG,H.ZHANG,M.ABOU-GHARBIA, JRNL AUTH 2 J.ISSA,J.WU,W.CHILDERS,J.KARANICOLAS JRNL TITL COMPARATIVE MODELING OF CDK9 INHIBITORS TO EXPLORE JRNL TITL 2 SELECTIVITY AND STRUCTURE-ACTIVITY RELATIONSHIPS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 86.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 18780 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1014 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1349 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4555 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 107.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.93000 REMARK 3 B22 (A**2) : -0.93000 REMARK 3 B33 (A**2) : 3.03000 REMARK 3 B12 (A**2) : -0.47000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 7.028 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.348 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.298 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.092 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4774 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4581 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6492 ; 2.052 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10523 ; 1.087 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 559 ; 6.940 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 215 ;40.301 ;23.907 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 823 ;18.686 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.938 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 724 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5284 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1103 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 4 REMARK 4 6W9E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000246601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI (111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19797 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 86.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.88500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.13 REMARK 200 STARTING MODEL: 3BLQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA/K PHOSPHATE PH6.2, 200MM NACL, REMARK 280 4MM TCEP AND 1~6% PEG1000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 86.67000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.03895 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.45600 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 86.67000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 50.03895 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.45600 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 86.67000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 50.03895 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.45600 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 100.07790 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 64.91200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 100.07790 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 64.91200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 100.07790 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 64.91200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 GLN A 4 REMARK 465 TYR A 5 REMARK 465 ASP A 6 REMARK 465 PRO A 91 REMARK 465 TYR A 92 REMARK 465 ASN A 93 REMARK 465 ARG A 94 REMARK 465 CYS A 95 REMARK 465 ALA A 177 REMARK 465 LYS A 178 REMARK 465 ASN A 179 REMARK 465 SER A 180 REMARK 465 MET A 327 REMARK 465 LEU A 328 REMARK 465 SER A 329 REMARK 465 THR A 330 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 3 REMARK 465 GLU B 4 REMARK 465 ARG B 5 REMARK 465 LYS B 6 REMARK 465 ASN B 7 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 88 CG CD CE NZ REMARK 470 LYS A 264 CG CD CE NZ REMARK 470 GLU A 266 CG CD OE1 OE2 REMARK 470 LYS A 269 CG CD CE NZ REMARK 470 GLN A 271 CG CD OE1 NE2 REMARK 470 LYS A 272 CG CD CE NZ 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 CYS A 10 61.51 -153.44 REMARK 500 SER A 17 -9.74 -58.35 REMARK 500 LEU A 22 -31.97 -142.16 REMARK 500 ALA A 23 139.09 -173.94 REMARK 500 GLN A 27 52.12 35.60 REMARK 500 HIS A 75 139.99 -170.53 REMARK 500 ASP A 149 42.69 -164.61 REMARK 500 ASP A 167 81.04 61.13 REMARK 500 TPO A 186 133.26 -38.08 REMARK 500 VAL A 190 139.44 76.33 REMARK 500 LEU A 201 28.81 -68.40 REMARK 500 ARG A 225 12.24 54.38 REMARK 500 LEU A 244 -43.29 -144.14 REMARK 500 ASN A 255 12.61 90.68 REMARK 500 ASN A 258 -7.47 -46.50 REMARK 500 LEU A 261 12.52 -67.92 REMARK 500 LYS A 264 -157.11 -78.84 REMARK 500 GLU A 266 94.23 -32.19 REMARK 500 LEU A 267 94.00 -52.19 REMARK 500 LYS A 269 -62.76 163.54 REMARK 500 LYS A 272 -150.97 -97.64 REMARK 500 ARG A 273 -64.56 -127.22 REMARK 500 LYS A 325 -56.90 -136.51 REMARK 500 ASN B 21 53.15 -92.62 REMARK 500 GLN B 97 52.38 -119.77 REMARK 500 THR B 121 16.56 -69.88 REMARK 500 PHE B 146 23.78 41.68 REMARK 500 ARG B 165 58.61 33.38 REMARK 500 GLN B 190 -31.62 -133.24 REMARK 500 ASN B 250 -9.43 58.32 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 GLU A 263 LYS A 264 143.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TO7 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TO7 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TOJ A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TOJ A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 301 DBREF 6W9E A 1 330 UNP P50750 CDK9_HUMAN 1 330 DBREF 6W9E B 1 259 UNP O60563 CCNT1_HUMAN 1 259 SEQADV 6W9E ARG B 77 UNP O60563 GLN 77 ENGINEERED MUTATION SEQADV 6W9E GLY B 96 UNP O60563 GLU 96 ENGINEERED MUTATION SEQADV 6W9E LEU B 241 UNP O60563 PHE 241 ENGINEERED MUTATION SEQRES 1 A 330 MET ALA LYS GLN TYR ASP SER VAL GLU CYS PRO PHE CYS SEQRES 2 A 330 ASP GLU VAL SER LYS TYR GLU LYS LEU ALA LYS ILE GLY SEQRES 3 A 330 GLN GLY THR PHE GLY GLU VAL PHE LYS ALA ARG HIS ARG SEQRES 4 A 330 LYS THR GLY GLN LYS VAL ALA LEU LYS LYS VAL LEU MET SEQRES 5 A 330 GLU ASN GLU LYS GLU GLY PHE PRO ILE THR ALA LEU ARG SEQRES 6 A 330 GLU ILE LYS ILE LEU GLN LEU LEU LYS HIS GLU ASN VAL SEQRES 7 A 330 VAL ASN LEU ILE GLU ILE CYS ARG THR LYS ALA SER PRO SEQRES 8 A 330 TYR ASN ARG CYS LYS GLY SER ILE TYR LEU VAL PHE ASP SEQRES 9 A 330 PHE CYS GLU HIS ASP LEU ALA GLY LEU LEU SER ASN VAL SEQRES 10 A 330 LEU VAL LYS PHE THR LEU SER GLU ILE LYS ARG VAL MET SEQRES 11 A 330 GLN MET LEU LEU ASN GLY LEU TYR TYR ILE HIS ARG ASN SEQRES 12 A 330 LYS ILE LEU HIS ARG ASP MET LYS ALA ALA ASN VAL LEU SEQRES 13 A 330 ILE THR ARG ASP GLY VAL LEU LYS LEU ALA ASP PHE GLY SEQRES 14 A 330 LEU ALA ARG ALA PHE SER LEU ALA LYS ASN SER GLN PRO SEQRES 15 A 330 ASN ARG TYR TPO ASN ARG VAL VAL THR LEU TRP TYR ARG SEQRES 16 A 330 PRO PRO GLU LEU LEU LEU GLY GLU ARG ASP TYR GLY PRO SEQRES 17 A 330 PRO ILE ASP LEU TRP GLY ALA GLY CYS ILE MET ALA GLU SEQRES 18 A 330 MET TRP THR ARG SER PRO ILE MET GLN GLY ASN THR GLU SEQRES 19 A 330 GLN HIS GLN LEU ALA LEU ILE SER GLN LEU CYS GLY SER SEQRES 20 A 330 ILE THR PRO GLU VAL TRP PRO ASN VAL ASP ASN TYR GLU SEQRES 21 A 330 LEU TYR GLU LYS LEU GLU LEU VAL LYS GLY GLN LYS ARG SEQRES 22 A 330 LYS VAL LYS ASP ARG LEU LYS ALA TYR VAL ARG ASP PRO SEQRES 23 A 330 TYR ALA LEU ASP LEU ILE ASP LYS LEU LEU VAL LEU ASP SEQRES 24 A 330 PRO ALA GLN ARG ILE ASP SEP ASP ASP ALA LEU ASN HIS SEQRES 25 A 330 ASP PHE PHE TRP SER ASP PRO MET PRO SER ASP LEU LYS SEQRES 26 A 330 GLY MET LEU SER THR SEQRES 1 B 259 MET GLU GLY GLU ARG LYS ASN ASN ASN LYS ARG TRP TYR SEQRES 2 B 259 PHE THR ARG GLU GLN LEU GLU ASN SER PRO SER ARG ARG SEQRES 3 B 259 PHE GLY VAL ASP PRO ASP LYS GLU LEU SER TYR ARG GLN SEQRES 4 B 259 GLN ALA ALA ASN LEU LEU GLN ASP MET GLY GLN ARG LEU SEQRES 5 B 259 ASN VAL SER GLN LEU THR ILE ASN THR ALA ILE VAL TYR SEQRES 6 B 259 MET HIS ARG PHE TYR MET ILE GLN SER PHE THR ARG PHE SEQRES 7 B 259 PRO GLY ASN SER VAL ALA PRO ALA ALA LEU PHE LEU ALA SEQRES 8 B 259 ALA LYS VAL GLU GLY GLN PRO LYS LYS LEU GLU HIS VAL SEQRES 9 B 259 ILE LYS VAL ALA HIS THR CYS LEU HIS PRO GLN GLU SER SEQRES 10 B 259 LEU PRO ASP THR ARG SER GLU ALA TYR LEU GLN GLN VAL SEQRES 11 B 259 GLN ASP LEU VAL ILE LEU GLU SER ILE ILE LEU GLN THR SEQRES 12 B 259 LEU GLY PHE GLU LEU THR ILE ASP HIS PRO HIS THR HIS SEQRES 13 B 259 VAL VAL LYS CYS THR GLN LEU VAL ARG ALA SER LYS ASP SEQRES 14 B 259 LEU ALA GLN THR SER TYR PHE MET ALA THR ASN SER LEU SEQRES 15 B 259 HIS LEU THR THR PHE SER LEU GLN TYR THR PRO PRO VAL SEQRES 16 B 259 VAL ALA CYS VAL CYS ILE HIS LEU ALA CYS LYS TRP SER SEQRES 17 B 259 ASN TRP GLU ILE PRO VAL SER THR ASP GLY LYS HIS TRP SEQRES 18 B 259 TRP GLU TYR VAL ASP ALA THR VAL THR LEU GLU LEU LEU SEQRES 19 B 259 ASP GLU LEU THR HIS GLU LEU LEU GLN ILE LEU GLU LYS SEQRES 20 B 259 THR PRO ASN ARG LEU LYS ARG ILE TRP ASN TRP ARG MODRES 6W9E TPO A 186 THR MODIFIED RESIDUE MODRES 6W9E SEP A 306 SER MODIFIED RESIDUE HET TPO A 186 11 HET SEP A 306 10 HET TO7 A 401 25 HET TO7 A 402 25 HET TOJ A 403 25 HET TOJ A 404 25 HET PO4 B 301 5 HETNAM TPO PHOSPHOTHREONINE HETNAM SEP PHOSPHOSERINE HETNAM TO7 (4-AMINO-2-{[(1S,2S,4R)-BICYCLO[2.2.1]HEPTAN-2- HETNAM 2 TO7 YL]AMINO}-1,3-THIAZOL-5-YL)(2-NITROPHENYL)METHANONE HETNAM TOJ (4-AMINO-2-{[(1R,2R,4S)-BICYCLO[2.2.1]HEPTAN-2- HETNAM 2 TOJ YL]AMINO}-1,3-THIAZOL-5-YL)(2-NITROPHENYL)METHANONE HETNAM PO4 PHOSPHATE ION HETSYN TPO PHOSPHONOTHREONINE HETSYN SEP PHOSPHONOSERINE HETSYN TO7 MC180295 FORMUL 1 TPO C4 H10 N O6 P FORMUL 1 SEP C3 H8 N O6 P FORMUL 3 TO7 2(C17 H18 N4 O3 S) FORMUL 5 TOJ 2(C17 H18 N4 O3 S) FORMUL 7 PO4 O4 P 3- FORMUL 8 HOH *28(H2 O) HELIX 1 AA1 GLU A 15 SER A 17 5 3 HELIX 2 AA2 PRO A 60 LEU A 73 1 14 HELIX 3 AA3 LEU A 110 ASN A 116 1 7 HELIX 4 AA4 THR A 122 ASN A 143 1 22 HELIX 5 AA5 LYS A 151 ALA A 153 5 3 HELIX 6 AA6 PRO A 196 LEU A 201 1 6 HELIX 7 AA7 PRO A 208 ARG A 225 1 18 HELIX 8 AA8 THR A 233 GLY A 246 1 14 HELIX 9 AA9 LYS A 274 ALA A 281 1 8 HELIX 10 AB1 ASP A 285 LEU A 296 1 12 HELIX 11 AB2 ASP A 299 ARG A 303 5 5 HELIX 12 AB3 ASP A 305 ASN A 311 1 7 HELIX 13 AB4 HIS A 312 SER A 317 5 6 HELIX 14 AB5 THR B 15 ASN B 21 1 7 HELIX 15 AB6 SER B 22 PHE B 27 1 6 HELIX 16 AB7 ASP B 30 ASN B 53 1 24 HELIX 17 AB8 SER B 55 TYR B 70 1 16 HELIX 18 AB9 PRO B 79 GLU B 95 1 17 HELIX 19 AC1 LYS B 100 HIS B 113 1 14 HELIX 20 AC2 SER B 123 GLY B 145 1 23 HELIX 21 AC3 HIS B 152 LEU B 163 1 12 HELIX 22 AC4 SER B 167 THR B 185 1 19 HELIX 23 AC5 THR B 192 ASN B 209 1 18 HELIX 24 AC6 HIS B 220 VAL B 225 5 6 HELIX 25 AC7 THR B 230 THR B 248 1 19 HELIX 26 AC8 ASN B 250 TRP B 256 1 7 SHEET 1 AA1 5 TYR A 19 LYS A 24 0 SHEET 2 AA1 5 VAL A 33 HIS A 38 -1 O LYS A 35 N ALA A 23 SHEET 3 AA1 5 LYS A 44 LYS A 49 -1 O VAL A 45 N ALA A 36 SHEET 4 AA1 5 ILE A 99 ASP A 104 -1 O PHE A 103 N ALA A 46 SHEET 5 AA1 5 LEU A 81 ARG A 86 -1 N ILE A 82 O VAL A 102 SHEET 1 AA2 3 HIS A 108 ASP A 109 0 SHEET 2 AA2 3 VAL A 155 ILE A 157 -1 O ILE A 157 N HIS A 108 SHEET 3 AA2 3 LEU A 163 LEU A 165 -1 O LYS A 164 N LEU A 156 SHEET 1 AA3 2 ILE A 145 LEU A 146 0 SHEET 2 AA3 2 ARG A 172 ALA A 173 -1 O ARG A 172 N LEU A 146 LINK C TYR A 185 N TPO A 186 1555 1555 1.34 LINK C TPO A 186 N ASN A 187 1555 1555 1.33 LINK C ASP A 305 N SEP A 306 1555 1555 1.34 LINK C SEP A 306 N ASP A 307 1555 1555 1.34 CISPEP 1 ASP A 318 PRO A 319 0 -17.25 SITE 1 AC1 17 PHE A 30 VAL A 33 VAL A 79 PHE A 103 SITE 2 AC1 17 ASP A 104 PHE A 105 CYS A 106 GLU A 107 SITE 3 AC1 17 HIS A 108 ASP A 109 LEU A 156 ALA A 166 SITE 4 AC1 17 ASP A 167 TO7 A 402 TOJ A 403 TOJ A 404 SITE 5 AC1 17 HOH A 503 SITE 1 AC2 17 PHE A 30 VAL A 33 LYS A 48 VAL A 79 SITE 2 AC2 17 PHE A 103 ASP A 104 PHE A 105 CYS A 106 SITE 3 AC2 17 GLU A 107 HIS A 108 ASP A 109 LEU A 156 SITE 4 AC2 17 ASP A 167 TO7 A 401 TOJ A 403 TOJ A 404 SITE 5 AC2 17 HOH A 503 SITE 1 AC3 18 ILE A 25 PHE A 30 VAL A 33 ALA A 46 SITE 2 AC3 18 LYS A 48 PHE A 103 ASP A 104 PHE A 105 SITE 3 AC3 18 CYS A 106 GLU A 107 ASN A 154 LEU A 156 SITE 4 AC3 18 ALA A 166 ASP A 167 TO7 A 401 TO7 A 402 SITE 5 AC3 18 TOJ A 404 HOH A 503 SITE 1 AC4 16 PHE A 30 VAL A 33 LYS A 48 VAL A 79 SITE 2 AC4 16 PHE A 103 ASP A 104 PHE A 105 CYS A 106 SITE 3 AC4 16 GLU A 107 ASP A 109 LEU A 156 ASP A 167 SITE 4 AC4 16 TO7 A 401 TO7 A 402 TOJ A 403 HOH A 503 SITE 1 AC5 3 LYS B 99 LYS B 100 HIS B 103 CRYST1 173.340 173.340 97.368 90.00 90.00 120.00 H 3 9 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 0.005769 0.003331 0.000000 0.00000 SCALE2 0.000000 0.006661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010270 0.00000