HEADER TRANSFERASE 11-APR-19 6RCB TITLE HUMAN PROTEIN KINASE CK2 ALPHA IN COMPLEX WITH 2-CYANO-2-PROPENAMIDE TITLE 2 COMPOUND 14 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASEIN KINASE II SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN (RESIDUES 1-337); COMPND 5 SYNONYM: CK II ALPHA; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CSNK2A1, CK2A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.DALLE VEDOVE,G.LOLLI REVDAT 3 24-JAN-24 6RCB 1 REMARK REVDAT 2 22-APR-20 6RCB 1 JRNL REVDAT 1 08-APR-20 6RCB 0 JRNL AUTH A.DALLE VEDOVE,F.ZONTA,E.ZANFORLIN,N.DEMITRI,G.RIBAUDO, JRNL AUTH 2 G.CAZZANELLI,A.ONGARO,S.SARNO,G.ZAGOTTO,R.BATTISTUTTA, JRNL AUTH 3 M.RUZZENE,G.LOLLI JRNL TITL A NOVEL CLASS OF SELECTIVE CK2 INHIBITORS TARGETING ITS OPEN JRNL TITL 2 HINGE CONFORMATION. JRNL REF EUR.J.MED.CHEM. V. 195 12267 2020 JRNL REFN ISSN 0223-5234 JRNL PMID 32283296 JRNL DOI 10.1016/J.EJMECH.2020.112267 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.6523 - 3.9199 0.99 2621 156 0.1625 0.1751 REMARK 3 2 3.9199 - 3.1120 1.00 2599 141 0.1634 0.1934 REMARK 3 3 3.1120 - 2.7188 1.00 2577 118 0.2083 0.2791 REMARK 3 4 2.7188 - 2.4703 0.99 2574 129 0.2242 0.2778 REMARK 3 5 2.4703 - 2.2933 1.00 2547 124 0.2151 0.3009 REMARK 3 6 2.2933 - 2.1581 1.00 2568 127 0.2230 0.2626 REMARK 3 7 2.1581 - 2.0501 0.99 2555 137 0.2435 0.3028 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.63 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 : 0.003 2884 REMARK 3 ANGLE : 0.581 3902 REMARK 3 CHIRALITY : 0.043 400 REMARK 3 PLANARITY : 0.003 500 REMARK 3 DIHEDRAL : 7.318 1709 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 6RCB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19012 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 45.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.58400 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: 4KWP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% PEG4000, 0.2 M LITHIUM SULFATE, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.91600 REMARK 290 SMTRY3 2 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLN A 331 REMARK 465 ALA A 332 REMARK 465 ARG A 333 REMARK 465 MET A 334 REMARK 465 GLY A 335 REMARK 465 SER A 336 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 ASP A 156 42.91 -147.87 REMARK 500 ASP A 175 70.70 53.58 REMARK 500 ALA A 193 156.94 65.07 REMARK 500 ASP A 210 -157.02 -157.19 REMARK 500 HIS A 234 70.70 -106.40 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 JYZ A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6RB1 RELATED DB: PDB REMARK 900 6RB1 CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR INHIBITOR DBREF 6RCB A 1 336 UNP P68400 CSK21_HUMAN 1 336 SEQRES 1 A 336 MET SER GLY PRO VAL PRO SER ARG ALA ARG VAL TYR THR SEQRES 2 A 336 ASP VAL ASN THR HIS ARG PRO ARG GLU TYR TRP ASP TYR SEQRES 3 A 336 GLU SER HIS VAL VAL GLU TRP GLY ASN GLN ASP ASP TYR SEQRES 4 A 336 GLN LEU VAL ARG LYS LEU GLY ARG GLY LYS TYR SER GLU SEQRES 5 A 336 VAL PHE GLU ALA ILE ASN ILE THR ASN ASN GLU LYS VAL SEQRES 6 A 336 VAL VAL LYS ILE LEU LYS PRO VAL LYS LYS LYS LYS ILE SEQRES 7 A 336 LYS ARG GLU ILE LYS ILE LEU GLU ASN LEU ARG GLY GLY SEQRES 8 A 336 PRO ASN ILE ILE THR LEU ALA ASP ILE VAL LYS ASP PRO SEQRES 9 A 336 VAL SER ARG THR PRO ALA LEU VAL PHE GLU HIS VAL ASN SEQRES 10 A 336 ASN THR ASP PHE LYS GLN LEU TYR GLN THR LEU THR ASP SEQRES 11 A 336 TYR ASP ILE ARG PHE TYR MET TYR GLU ILE LEU LYS ALA SEQRES 12 A 336 LEU ASP TYR CYS HIS SER MET GLY ILE MET HIS ARG ASP SEQRES 13 A 336 VAL LYS PRO HIS ASN VAL MET ILE ASP HIS GLU HIS ARG SEQRES 14 A 336 LYS LEU ARG LEU ILE ASP TRP GLY LEU ALA GLU PHE TYR SEQRES 15 A 336 HIS PRO GLY GLN GLU TYR ASN VAL ARG VAL ALA SER ARG SEQRES 16 A 336 TYR PHE LYS GLY PRO GLU LEU LEU VAL ASP TYR GLN MET SEQRES 17 A 336 TYR ASP TYR SER LEU ASP MET TRP SER LEU GLY CYS MET SEQRES 18 A 336 LEU ALA SER MET ILE PHE ARG LYS GLU PRO PHE PHE HIS SEQRES 19 A 336 GLY HIS ASP ASN TYR ASP GLN LEU VAL ARG ILE ALA LYS SEQRES 20 A 336 VAL LEU GLY THR GLU ASP LEU TYR ASP TYR ILE ASP LYS SEQRES 21 A 336 TYR ASN ILE GLU LEU ASP PRO ARG PHE ASN ASP ILE LEU SEQRES 22 A 336 GLY ARG HIS SER ARG LYS ARG TRP GLU ARG PHE VAL HIS SEQRES 23 A 336 SER GLU ASN GLN HIS LEU VAL SER PRO GLU ALA LEU ASP SEQRES 24 A 336 PHE LEU ASP LYS LEU LEU ARG TYR ASP HIS GLN SER ARG SEQRES 25 A 336 LEU THR ALA ARG GLU ALA MET GLU HIS PRO TYR PHE TYR SEQRES 26 A 336 THR VAL VAL LYS ASP GLN ALA ARG MET GLY SER HET JYZ A 401 23 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HETNAM JYZ (~{E})-2-CYANO-~{N}-(2-HYDROXYPHENYL)-3-(3-METHOXY-4- HETNAM 2 JYZ OXIDANYL-PHENYL)PROP-2-ENAMIDE HETNAM SO4 SULFATE ION FORMUL 2 JYZ C17 H14 N2 O4 FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *224(H2 O) HELIX 1 AA1 ASP A 14 ARG A 19 1 6 HELIX 2 AA2 PRO A 20 ASP A 25 1 6 HELIX 3 AA3 TYR A 26 HIS A 29 5 4 HELIX 4 AA4 ASN A 35 ASP A 37 5 3 HELIX 5 AA5 LYS A 74 ARG A 89 1 16 HELIX 6 AA6 ASP A 120 LEU A 128 1 9 HELIX 7 AA7 THR A 129 MET A 150 1 22 HELIX 8 AA8 LYS A 158 HIS A 160 5 3 HELIX 9 AA9 SER A 194 LYS A 198 5 5 HELIX 10 AB1 GLY A 199 VAL A 204 1 6 HELIX 11 AB2 TYR A 211 PHE A 227 1 17 HELIX 12 AB3 ASP A 237 GLY A 250 1 14 HELIX 13 AB4 GLY A 250 TYR A 261 1 12 HELIX 14 AB5 ASP A 266 ILE A 272 5 7 HELIX 15 AB6 ARG A 280 VAL A 285 5 6 HELIX 16 AB7 ASN A 289 VAL A 293 5 5 HELIX 17 AB8 SER A 294 LEU A 305 1 12 HELIX 18 AB9 ASP A 308 ARG A 312 5 5 HELIX 19 AC1 THR A 314 GLU A 320 1 7 HELIX 20 AC2 HIS A 321 TYR A 325 5 5 SHEET 1 AA1 5 TYR A 39 ARG A 47 0 SHEET 2 AA1 5 SER A 51 ASN A 58 -1 O VAL A 53 N LEU A 45 SHEET 3 AA1 5 LYS A 64 LEU A 70 -1 O VAL A 65 N ALA A 56 SHEET 4 AA1 5 THR A 108 GLU A 114 -1 O LEU A 111 N LYS A 68 SHEET 5 AA1 5 LEU A 97 ASP A 103 -1 N VAL A 101 O ALA A 110 SHEET 1 AA2 2 ILE A 152 MET A 153 0 SHEET 2 AA2 2 GLU A 180 PHE A 181 -1 O GLU A 180 N MET A 153 SHEET 1 AA3 2 VAL A 162 ASP A 165 0 SHEET 2 AA3 2 LYS A 170 LEU A 173 -1 O ARG A 172 N MET A 163 CISPEP 1 GLU A 230 PRO A 231 0 -7.69 SITE 1 AC1 13 LEU A 45 VAL A 53 VAL A 66 LYS A 68 SITE 2 AC1 13 GLU A 81 PHE A 113 VAL A 116 ASN A 118 SITE 3 AC1 13 MET A 163 ILE A 174 ASP A 175 HOH A 527 SITE 4 AC1 13 HOH A 623 SITE 1 AC2 8 ASP A 253 ARG A 278 ARG A 306 TYR A 307 SITE 2 AC2 8 ASP A 308 HOH A 529 HOH A 577 HOH A 621 SITE 1 AC3 4 ARG A 80 ARG A 155 ASN A 189 HOH A 567 SITE 1 AC4 4 ARG A 191 LYS A 198 ASN A 238 HOH A 504 CRYST1 57.451 45.832 62.326 90.00 112.27 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017406 0.000000 0.007130 0.00000 SCALE2 0.000000 0.021819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017338 0.00000