HEADER TRANSFERASE 10-MAR-17 5NEI TITLE THE STRUCTURE OF THE POLO-BOX DOMAIN (PBD) OF POLO-LIKE KINASE 1 TITLE 2 (PLK1) IN COMPLEX WITH JES107 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES POLO-BOX DOMAIN, 371-603; COMPND 5 SYNONYM: POLO-LIKE KINASE 1,PLK-1,SERINE/THREONINE-PROTEIN KINASE 13, COMPND 6 STPK13; COMPND 7 EC: 2.7.11.21; COMPND 8 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: PLK1, PLK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS PLK1, PBD1, MITOSIS, SMALL MOLECULE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.L.KUNCIW,M.ROSSMANN,J.E.STOKES,C.DE FUSCO,D.R.SPRING,M.HYVONEN REVDAT 2 07-FEB-24 5NEI 1 HETSYN REVDAT 1 21-FEB-18 5NEI 0 JRNL AUTH D.L.KUNCIW,C.DE FUSCO,M.ROSSMANN,J.E.STOKES,A.RENZETTI, JRNL AUTH 2 H.F.SORE,M.HYVONEN,D.R.SPRING JRNL TITL A FRAGMENT-BASED APPROACH TO DEVELOPING INHIBITORS OF THE JRNL TITL 2 CRYPTIC POCKET OF THE POLO-LIKE KINASE 1 POLO-BOX DOMAIN. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 5947 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.520 REMARK 3 FREE R VALUE TEST SET COUNT : 269 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 45.6866 - 3.3766 0.99 2843 131 0.1873 0.2240 REMARK 3 2 3.3766 - 2.6802 0.99 2835 138 0.2288 0.3026 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1832 REMARK 3 ANGLE : 1.126 2488 REMARK 3 CHIRALITY : 0.068 275 REMARK 3 PLANARITY : 0.008 316 REMARK 3 DIHEDRAL : 17.473 681 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 5NEI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003980. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-13 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) : 0.983 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5948 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 REMARK 200 RESOLUTION RANGE LOW (A) : 91.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 9.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47000 REMARK 200 FOR SHELL : 2.190 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: 3P2W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 100 MM NA/K TARTRATE, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 292K 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 45.68000 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 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: 11150 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 GLY A 367 REMARK 465 ALA A 368 REMARK 465 HIS A 369 REMARK 465 MET A 370 REMARK 465 PRO A 499 REMARK 465 ARG A 500 REMARK 465 GLU A 501 REMARK 465 GLY A 502 REMARK 465 ASP A 503 REMARK 465 GLU A 504 REMARK 465 LEU A 505 REMARK 465 ALA A 506 REMARK 465 SER A 595 REMARK 465 ALA A 596 REMARK 465 SER A 597 REMARK 465 ASN A 598 REMARK 465 ARG A 599 REMARK 465 LEU A 600 REMARK 465 LYS A 601 REMARK 465 ALA A 602 REMARK 465 SER A 603 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 GLN A 536 CG CD OE1 NE2 REMARK 470 GLU A 555 CG CD OE1 OE2 REMARK 470 LYS A 556 CG CD CE NZ REMARK 470 ARG A 557 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 574 CG CD CE NZ 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 CYS A 372 O HOH A 801 2.02 REMARK 500 OD1 ASN A 446 O HOH A 802 2.11 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 HIS A 373 45.43 -79.36 REMARK 500 ASP A 376 -21.70 100.77 REMARK 500 LYS A 388 71.13 64.82 REMARK 500 TYR A 417 39.17 -147.36 REMARK 500 LYS A 420 -66.00 -136.32 REMARK 500 ASP A 449 -46.73 -159.49 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 8VB A 701 DBREF 5NEI A 371 603 UNP P53350 PLK1_HUMAN 371 603 SEQADV 5NEI GLY A 367 UNP P53350 EXPRESSION TAG SEQADV 5NEI ALA A 368 UNP P53350 EXPRESSION TAG SEQADV 5NEI HIS A 369 UNP P53350 EXPRESSION TAG SEQADV 5NEI MET A 370 UNP P53350 EXPRESSION TAG SEQRES 1 A 237 GLY ALA HIS MET ASP CYS HIS LEU SER ASP MET LEU GLN SEQRES 2 A 237 GLN LEU HIS SER VAL ASN ALA SER LYS PRO SER GLU ARG SEQRES 3 A 237 GLY LEU VAL ARG GLN GLU GLU ALA GLU ASP PRO ALA CYS SEQRES 4 A 237 ILE PRO ILE PHE TRP VAL SER LYS TRP VAL ASP TYR SER SEQRES 5 A 237 ASP LYS TYR GLY LEU GLY TYR GLN LEU CYS ASP ASN SER SEQRES 6 A 237 VAL GLY VAL LEU PHE ASN ASP SER THR ARG LEU ILE LEU SEQRES 7 A 237 TYR ASN ASP GLY ASP SER LEU GLN TYR ILE GLU ARG ASP SEQRES 8 A 237 GLY THR GLU SER TYR LEU THR VAL SER SER HIS PRO ASN SEQRES 9 A 237 SER LEU MET LYS LYS ILE THR LEU LEU LYS TYR PHE ARG SEQRES 10 A 237 ASN TYR MET SER GLU HIS LEU LEU LYS ALA GLY ALA ASN SEQRES 11 A 237 ILE THR PRO ARG GLU GLY ASP GLU LEU ALA ARG LEU PRO SEQRES 12 A 237 TYR LEU ARG THR TRP PHE ARG THR ARG SER ALA ILE ILE SEQRES 13 A 237 LEU HIS LEU SER ASN GLY SER VAL GLN ILE ASN PHE PHE SEQRES 14 A 237 GLN ASP HIS THR LYS LEU ILE LEU CYS PRO LEU MET ALA SEQRES 15 A 237 ALA VAL THR TYR ILE ASP GLU LYS ARG ASP PHE ARG THR SEQRES 16 A 237 TYR ARG LEU SER LEU LEU GLU GLU TYR GLY CYS CYS LYS SEQRES 17 A 237 GLU LEU ALA SER ARG LEU ARG TYR ALA ARG THR MET VAL SEQRES 18 A 237 ASP LYS LEU LEU SER SER ARG SER ALA SER ASN ARG LEU SEQRES 19 A 237 LYS ALA SER HET 8VB A 701 31 HETNAM 8VB 2-[[3-[[5-(3-IODANYLPHENYL)CARBONYLTHIOPHEN-2- HETNAM 2 8VB YL]CARBONYLAMINO]PHENYL]METHYL]PROPANEDIOIC ACID HETSYN 8VB JES107; POLOTYRIN FORMUL 2 8VB C22 H16 I N O6 S FORMUL 3 HOH *11(H2 O) HELIX 1 AA1 ASP A 376 LYS A 388 1 13 HELIX 2 AA2 ARG A 396 GLU A 401 5 6 HELIX 3 AA3 ASP A 402 ILE A 406 5 5 HELIX 4 AA4 LEU A 472 LEU A 490 1 19 HELIX 5 AA5 LEU A 564 GLY A 571 1 8 HELIX 6 AA6 CYS A 573 SER A 592 1 20 SHEET 1 AA1 6 VAL A 411 ASP A 416 0 SHEET 2 AA1 6 GLY A 422 LEU A 427 -1 O GLY A 424 N VAL A 415 SHEET 3 AA1 6 VAL A 432 PHE A 436 -1 O LEU A 435 N LEU A 423 SHEET 4 AA1 6 ARG A 441 LEU A 444 -1 O LEU A 444 N VAL A 432 SHEET 5 AA1 6 SER A 450 ILE A 454 -1 O ILE A 454 N ARG A 441 SHEET 6 AA1 6 GLU A 460 THR A 464 -1 O LEU A 463 N LEU A 451 SHEET 1 AA2 6 LEU A 511 ARG A 516 0 SHEET 2 AA2 6 ALA A 520 LEU A 525 -1 O ILE A 522 N PHE A 515 SHEET 3 AA2 6 VAL A 530 PHE A 534 -1 O GLN A 531 N LEU A 523 SHEET 4 AA2 6 THR A 539 CYS A 544 -1 O THR A 539 N PHE A 534 SHEET 5 AA2 6 ALA A 549 ILE A 553 -1 O ALA A 549 N CYS A 544 SHEET 6 AA2 6 PHE A 559 ARG A 563 -1 O TYR A 562 N VAL A 550 SITE 1 AC1 7 TYR A 417 TYR A 421 PRO A 469 ASN A 470 SITE 2 AC1 7 SER A 471 TYR A 481 PHE A 482 CRYST1 33.350 91.360 35.940 90.00 99.71 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 0.029985 0.000000 0.005131 0.00000 SCALE2 0.000000 0.010946 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028229 0.00000