HEADER TRANSFERASE 06-APR-20 6YL1 TITLE CDK2(F80C) WITH COVALENT ADDUCT TK37 AT F80C COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL DIVISION PROTEIN KINASE 2,P33 PROTEIN KINASE; COMPND 5 EC: 2.7.11.22; COMPND 6 ENGINEERED: YES; COMPND 7 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: CDK2, CDKN2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COVALENT INHIBITOR, CYSTEINE MODIFICATION, KINASE, ALLOSTERIC KEYWDS 2 INHIBITOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.CRAVEN,R.M.L.MORGAN,D.J.MANN REVDAT 4 24-JAN-24 6YL1 1 REMARK REVDAT 3 16-DEC-20 6YL1 1 JRNL REVDAT 2 19-AUG-20 6YL1 1 JRNL REVDAT 1 22-JUL-20 6YL1 0 JRNL AUTH G.B.CRAVEN,D.P.AFFRON,T.KOSEL,T.L.M.WONG,Z.H.JUKES,C.T.LIU, JRNL AUTH 2 R.M.L.MORGAN,A.ARMSTRONG,D.J.MANN JRNL TITL MULTIPARAMETER KINETIC ANALYSIS FOR COVALENT FRAGMENT JRNL TITL 2 OPTIMIZATION BY USING QUANTITATIVE IRREVERSIBLE TETHERING JRNL TITL 3 (QIT). JRNL REF CHEMBIOCHEM V. 21 3417 2020 JRNL REFN ESSN 1439-7633 JRNL PMID 32659037 JRNL DOI 10.1002/CBIC.202000457 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 32893 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2352 REMARK 3 ANGLE : 0.972 3202 REMARK 3 CHIRALITY : 0.056 362 REMARK 3 PLANARITY : 0.007 407 REMARK 3 DIHEDRAL : 23.916 865 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YL1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107754. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32900 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 36.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.06219 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4EK3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 8 MG/ML IN PH 6.2 PHOSPHATE REMARK 280 BUFFER RESOVOIR: 8-12% PEG3350, HEPES 0.1 M (PH 7.5-8.5) 1:1, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 26.67000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.62000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.67000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.62000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 ASP A 38 REMARK 465 THR A 39 REMARK 465 GLU A 40 REMARK 465 THR A 41 REMARK 465 GLU A 42 REMARK 465 GLY A 43 REMARK 465 VAL A 44 REMARK 465 PRO A 45 REMARK 465 VAL A 154 REMARK 465 PRO A 155 REMARK 465 VAL A 156 REMARK 465 ARG A 157 REMARK 465 THR A 158 REMARK 465 TYR A 159 REMARK 465 THR A 160 REMARK 465 HIS A 161 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 LEU A -2 CG CD1 CD2 REMARK 470 ASN A 3 CG OD1 ND2 REMARK 470 LYS A 24 CG CD CE NZ REMARK 470 ARG A 36 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 49 CG1 CG2 CD1 REMARK 470 ARG A 50 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 ASN A 74 CG OD1 ND2 REMARK 470 LYS A 75 CG CD CE NZ REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 150 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 162 CG CD OE1 OE2 REMARK 470 ARG A 297 CG CD NE CZ NH1 NH2 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 TYR A 15 -8.59 -141.26 REMARK 500 ASN A 23 108.07 -56.37 REMARK 500 ASN A 23 108.07 -56.70 REMARK 500 ARG A 126 -17.45 85.26 REMARK 500 ASP A 127 50.35 -147.99 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 OWN A 301 DBREF 6YL1 A 1 298 UNP P24941 CDK2_HUMAN 1 298 SEQADV 6YL1 GLY A -4 UNP P24941 EXPRESSION TAG SEQADV 6YL1 PRO A -3 UNP P24941 EXPRESSION TAG SEQADV 6YL1 LEU A -2 UNP P24941 EXPRESSION TAG SEQADV 6YL1 GLY A -1 UNP P24941 EXPRESSION TAG SEQADV 6YL1 SER A 0 UNP P24941 EXPRESSION TAG SEQADV 6YL1 CYS A 80 UNP P24941 PHE 80 ENGINEERED MUTATION SEQADV 6YL1 ALA A 177 UNP P24941 CYS 177 ENGINEERED MUTATION SEQRES 1 A 303 GLY PRO LEU GLY SER MET GLU ASN PHE GLN LYS VAL GLU SEQRES 2 A 303 LYS ILE GLY GLU GLY THR TYR GLY VAL VAL TYR LYS ALA SEQRES 3 A 303 ARG ASN LYS LEU THR GLY GLU VAL VAL ALA LEU LYS LYS SEQRES 4 A 303 ILE ARG LEU ASP THR GLU THR GLU GLY VAL PRO SER THR SEQRES 5 A 303 ALA ILE ARG GLU ILE SER LEU LEU LYS GLU LEU ASN HIS SEQRES 6 A 303 PRO ASN ILE VAL LYS LEU LEU ASP VAL ILE HIS THR GLU SEQRES 7 A 303 ASN LYS LEU TYR LEU VAL CYS GLU PHE LEU HIS GLN ASP SEQRES 8 A 303 LEU LYS LYS PHE MET ASP ALA SER ALA LEU THR GLY ILE SEQRES 9 A 303 PRO LEU PRO LEU ILE LYS SER TYR LEU PHE GLN LEU LEU SEQRES 10 A 303 GLN GLY LEU ALA PHE CYS HIS SER HIS ARG VAL LEU HIS SEQRES 11 A 303 ARG ASP LEU LYS PRO GLN ASN LEU LEU ILE ASN THR GLU SEQRES 12 A 303 GLY ALA ILE LYS LEU ALA ASP PHE GLY LEU ALA ARG ALA SEQRES 13 A 303 PHE GLY VAL PRO VAL ARG THR TYR THR HIS GLU VAL VAL SEQRES 14 A 303 THR LEU TRP TYR ARG ALA PRO GLU ILE LEU LEU GLY ALA SEQRES 15 A 303 LYS TYR TYR SER THR ALA VAL ASP ILE TRP SER LEU GLY SEQRES 16 A 303 CYS ILE PHE ALA GLU MET VAL THR ARG ARG ALA LEU PHE SEQRES 17 A 303 PRO GLY ASP SER GLU ILE ASP GLN LEU PHE ARG ILE PHE SEQRES 18 A 303 ARG THR LEU GLY THR PRO ASP GLU VAL VAL TRP PRO GLY SEQRES 19 A 303 VAL THR SER MET PRO ASP TYR LYS PRO SER PHE PRO LYS SEQRES 20 A 303 TRP ALA ARG GLN ASP PHE SER LYS VAL VAL PRO PRO LEU SEQRES 21 A 303 ASP GLU ASP GLY ARG SER LEU LEU SER GLN MET LEU HIS SEQRES 22 A 303 TYR ASP PRO ASN LYS ARG ILE SER ALA LYS ALA ALA LEU SEQRES 23 A 303 ALA HIS PRO PHE PHE GLN ASP VAL THR LYS PRO VAL PRO SEQRES 24 A 303 HIS LEU ARG LEU HET OWN A 301 22 HETNAM OWN METHYL 4-(CYCLOPROPYLMETHYL)-1-PROP-2-ENOYL-2,3- HETNAM 2 OWN DIHYDROQUINOXALINE-6-CARBOXYLATE FORMUL 2 OWN C17 H20 N2 O3 FORMUL 3 HOH *119(H2 O) HELIX 1 AA1 THR A 47 LYS A 56 1 10 HELIX 2 AA2 LEU A 87 SER A 94 1 8 HELIX 3 AA3 PRO A 100 HIS A 121 1 22 HELIX 4 AA4 LYS A 129 GLN A 131 5 3 HELIX 5 AA5 ALA A 170 LEU A 175 1 6 HELIX 6 AA6 THR A 182 ARG A 199 1 18 HELIX 7 AA7 SER A 207 GLY A 220 1 14 HELIX 8 AA8 GLY A 229 MET A 233 5 5 HELIX 9 AA9 ASP A 247 VAL A 252 1 6 HELIX 10 AB1 ASP A 256 LEU A 267 1 12 HELIX 11 AB2 SER A 276 ALA A 282 1 7 HELIX 12 AB3 HIS A 283 GLN A 287 5 5 SHEET 1 AA1 5 PHE A 4 GLU A 12 0 SHEET 2 AA1 5 VAL A 17 ASN A 23 -1 O LYS A 20 N VAL A 7 SHEET 3 AA1 5 VAL A 29 ARG A 36 -1 O LEU A 32 N TYR A 19 SHEET 4 AA1 5 LYS A 75 GLU A 81 -1 O LEU A 76 N ILE A 35 SHEET 5 AA1 5 LEU A 66 THR A 72 -1 N ASP A 68 O VAL A 79 SHEET 1 AA2 3 GLN A 85 ASP A 86 0 SHEET 2 AA2 3 LEU A 133 ILE A 135 -1 O ILE A 135 N GLN A 85 SHEET 3 AA2 3 ILE A 141 LEU A 143 -1 O LYS A 142 N LEU A 134 LINK SG CYS A 80 C13 OWN A 301 1555 1555 1.57 SITE 1 AC1 11 ILE A 10 GLU A 12 VAL A 18 ALA A 31 SITE 2 AC1 11 CYS A 80 GLU A 81 PHE A 82 LEU A 83 SITE 3 AC1 11 GLN A 131 LEU A 134 ASP A 145 CRYST1 53.340 71.240 71.870 90.00 90.00 90.00 P 21 21 21 4 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 0.018748 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013914 0.00000