HEADER STRUCTURAL PROTEIN 20-SEP-23 8WFP TITLE CRYSTAL STRUCTURE OF POLO-LIKE KINASE(PLK1)PBD IN COMPLEX WITH DD-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: POLO-LIKE KINASE 1,PLK-1,SERINE/THREONINE-PROTEIN KINASE 13, COMPND 5 STPK13; COMPND 6 EC: 2.7.11.21; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DD-1; COMPND 10 CHAIN: C, D; COMPND 11 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS INHIBITOR, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.PARK,Y.K.LA,J.K.BANG,S.J.LEE REVDAT 1 25-SEP-24 8WFP 0 JRNL AUTH P.GUNASEKARAN,Y.S.HWANG,G.H.LEE,J.PARK,J.G.KIM,Y.K.LA, JRNL AUTH 2 N.Y.PARK,R.KOTHANDARAMAN,M.S.YIM,J.CHOI,H.N.KIM,I.Y.PARK, JRNL AUTH 3 S.J.LEE,M.H.KIM,H.CHA-MOLSTAD,S.Y.SHIN,E.K.RYU,J.K.BANG JRNL TITL DEGRADATION OF POLO-LIKE KINASE 1 BY THE NOVEL POLY-ARGININE JRNL TITL 2 N-DEGRON PATHWAY PROTAC REGULATES TUMOR GROWTH IN NONSMALL JRNL TITL 3 CELL LUNG CANCER. JRNL REF J.MED.CHEM. V. 67 3307 2024 JRNL REFN ISSN 0022-2623 JRNL PMID 38105611 JRNL DOI 10.1021/ACS.JMEDCHEM.3C01493 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 35270 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.630 REMARK 3 FREE R VALUE TEST SET COUNT : 1987 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 35.3700 - 4.7900 0.95 2468 157 0.1976 0.2371 REMARK 3 2 4.7900 - 3.8000 0.99 2481 140 0.1630 0.1749 REMARK 3 3 3.8000 - 3.3200 0.96 2372 139 0.1797 0.2222 REMARK 3 4 3.3200 - 3.0200 0.99 2452 145 0.2042 0.2175 REMARK 3 5 3.0200 - 2.8000 0.97 2376 142 0.2089 0.2089 REMARK 3 6 2.8000 - 2.6400 0.96 2377 141 0.2268 0.2523 REMARK 3 7 2.6400 - 2.5000 0.98 2373 137 0.2123 0.2567 REMARK 3 8 2.5000 - 2.4000 0.98 2429 145 0.2116 0.2252 REMARK 3 9 2.4000 - 2.3000 0.96 2350 140 0.2179 0.2629 REMARK 3 10 2.3000 - 2.2200 0.95 2286 138 0.2235 0.3052 REMARK 3 11 2.2200 - 2.1500 0.97 2372 140 0.2211 0.2549 REMARK 3 12 2.1500 - 2.0900 0.97 2342 142 0.2120 0.2619 REMARK 3 13 2.0900 - 2.0400 0.96 2356 142 0.2209 0.2554 REMARK 3 14 2.0400 - 1.9900 0.93 2249 139 0.2591 0.3395 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.140 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 : 0.014 NULL REMARK 3 ANGLE : 2.166 NULL REMARK 3 CHIRALITY : 0.202 569 REMARK 3 PLANARITY : 0.012 653 REMARK 3 DIHEDRAL : 14.643 551 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 8WFP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300041157. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : M 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35270 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 35.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.79 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: PHENIX REMARK 200 STARTING MODEL: 4O9W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 3350, 10% TACSIMATE PH 8.0, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 0.00000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 ALA A 596 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 LYS A 574 CG CD CE NZ REMARK 470 LYS B 420 CG CD CE NZ REMARK 470 GLN B 536 CG CD OE1 NE2 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 N LEU B 505 N ALA B 506 1.66 REMARK 500 OG SER A 592 O HOH A 601 1.90 REMARK 500 O HOH A 630 O HOH A 690 2.02 REMARK 500 OG1 THR A 513 O HOH A 602 2.04 REMARK 500 OE1 GLU A 460 NH2 ARG A 507 2.08 REMARK 500 NH2 ARG A 456 O HOH A 603 2.10 REMARK 500 O HOH A 609 O HOH A 708 2.13 REMARK 500 OD1 ASP B 416 OG SER B 418 2.13 REMARK 500 OG1 THR B 459 O HOH B 601 2.13 REMARK 500 OG SER B 592 O HOH B 602 2.16 REMARK 500 OD1 ASP A 416 OG SER A 418 2.18 REMARK 500 NH1 ARG A 507 O HOH A 604 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 568 NZ LYS B 474 2555 1.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 399 CB GLU B 399 CG -0.126 REMARK 500 GLU B 399 CG GLU B 399 CD -0.125 REMARK 500 GLU B 488 CD GLU B 488 OE2 0.136 REMARK 500 GLU B 504 CG GLU B 504 CD 0.157 REMARK 500 ACE C 1 C PRO C 2 N 0.139 REMARK 500 PRO C 2 CD PRO C 2 N -0.128 REMARK 500 LEU C 3 C HIS C 4 N 0.156 REMARK 500 ACE D 1 C PRO D 2 N 0.146 REMARK 500 PRO D 2 CD PRO D 2 N -0.128 REMARK 500 PRO D 2 C LEU D 3 N 0.140 REMARK 500 LEU D 3 C HIS D 4 N 0.157 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 505 CA - CB - CG ANGL. DEV. = 34.8 DEGREES REMARK 500 LEU A 505 CD1 - CG - CD2 ANGL. DEV. = -20.5 DEGREES REMARK 500 LEU A 505 CB - CG - CD1 ANGL. DEV. = -28.2 DEGREES REMARK 500 LEU A 505 CB - CG - CD2 ANGL. DEV. = 48.9 DEGREES REMARK 500 LYS B 474 CD - CE - NZ ANGL. DEV. = -30.8 DEGREES REMARK 500 GLU B 488 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 GLU B 504 CA - CB - CG ANGL. DEV. = 18.1 DEGREES REMARK 500 GLU B 504 OE1 - CD - OE2 ANGL. DEV. = -49.1 DEGREES REMARK 500 GLU B 504 CG - CD - OE1 ANGL. DEV. = 35.7 DEGREES REMARK 500 GLU B 504 CG - CD - OE2 ANGL. DEV. = -36.3 DEGREES REMARK 500 GLU B 504 N - CA - C ANGL. DEV. = -17.3 DEGREES REMARK 500 LEU B 505 N - CA - CB ANGL. DEV. = 14.6 DEGREES REMARK 500 LEU B 505 CA - CB - CG ANGL. DEV. = 15.6 DEGREES REMARK 500 LEU B 505 CB - CG - CD2 ANGL. DEV. = 17.4 DEGREES REMARK 500 LEU B 505 N - CA - C ANGL. DEV. = -35.7 DEGREES REMARK 500 ALA B 506 C - N - CA ANGL. DEV. = 20.9 DEGREES 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 ASP A 402 88.10 -151.77 REMARK 500 GLU A 504 6.40 -53.27 REMARK 500 ASP B 402 89.95 -150.16 REMARK 500 ASP B 449 -30.63 -133.87 REMARK 500 GLU B 501 -107.41 -106.31 REMARK 500 LEU B 505 -4.24 -167.48 REMARK 500 ALA B 506 -57.72 83.03 REMARK 500 ARG B 507 87.19 58.05 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 ASP B 503 GLU B 504 -128.76 REMARK 500 GLU B 504 LEU B 505 103.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 417 0.07 SIDE CHAIN 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 B 703 DISTANCE = 5.88 ANGSTROMS DBREF 8WFP A 373 596 UNP P53350 PLK1_HUMAN 373 596 DBREF 8WFP B 373 596 UNP P53350 PLK1_HUMAN 373 596 DBREF 8WFP C 1 7 PDB 8WFP 8WFP 1 7 DBREF 8WFP D 1 7 PDB 8WFP 8WFP 1 7 SEQADV 8WFP ALA A 371 UNP P53350 EXPRESSION TAG SEQADV 8WFP ALA A 372 UNP P53350 EXPRESSION TAG SEQADV 8WFP ALA B 371 UNP P53350 EXPRESSION TAG SEQADV 8WFP ALA B 372 UNP P53350 EXPRESSION TAG SEQRES 1 A 226 ALA ALA HIS LEU SER ASP MET LEU GLN GLN LEU HIS SER SEQRES 2 A 226 VAL ASN ALA SER LYS PRO SER GLU ARG GLY LEU VAL ARG SEQRES 3 A 226 GLN GLU GLU ALA GLU ASP PRO ALA CYS ILE PRO ILE PHE SEQRES 4 A 226 TRP VAL SER LYS TRP VAL ASP TYR SER ASP LYS TYR GLY SEQRES 5 A 226 LEU GLY TYR GLN LEU CYS ASP ASN SER VAL GLY VAL LEU SEQRES 6 A 226 PHE ASN ASP SER THR ARG LEU ILE LEU TYR ASN ASP GLY SEQRES 7 A 226 ASP SER LEU GLN TYR ILE GLU ARG ASP GLY THR GLU SER SEQRES 8 A 226 TYR LEU THR VAL SER SER HIS PRO ASN SER LEU MET LYS SEQRES 9 A 226 LYS ILE THR LEU LEU LYS TYR PHE ARG ASN TYR MET SER SEQRES 10 A 226 GLU HIS LEU LEU LYS ALA GLY ALA ASN ILE THR PRO ARG SEQRES 11 A 226 GLU GLY ASP GLU LEU ALA ARG LEU PRO TYR LEU ARG THR SEQRES 12 A 226 TRP PHE ARG THR ARG SER ALA ILE ILE LEU HIS LEU SER SEQRES 13 A 226 ASN GLY SER VAL GLN ILE ASN PHE PHE GLN ASP HIS THR SEQRES 14 A 226 LYS LEU ILE LEU CYS PRO LEU MET ALA ALA VAL THR TYR SEQRES 15 A 226 ILE ASP GLU LYS ARG ASP PHE ARG THR TYR ARG LEU SER SEQRES 16 A 226 LEU LEU GLU GLU TYR GLY CYS CYS LYS GLU LEU ALA SER SEQRES 17 A 226 ARG LEU ARG TYR ALA ARG THR MET VAL ASP LYS LEU LEU SEQRES 18 A 226 SER SER ARG SER ALA SEQRES 1 B 226 ALA ALA HIS LEU SER ASP MET LEU GLN GLN LEU HIS SER SEQRES 2 B 226 VAL ASN ALA SER LYS PRO SER GLU ARG GLY LEU VAL ARG SEQRES 3 B 226 GLN GLU GLU ALA GLU ASP PRO ALA CYS ILE PRO ILE PHE SEQRES 4 B 226 TRP VAL SER LYS TRP VAL ASP TYR SER ASP LYS TYR GLY SEQRES 5 B 226 LEU GLY TYR GLN LEU CYS ASP ASN SER VAL GLY VAL LEU SEQRES 6 B 226 PHE ASN ASP SER THR ARG LEU ILE LEU TYR ASN ASP GLY SEQRES 7 B 226 ASP SER LEU GLN TYR ILE GLU ARG ASP GLY THR GLU SER SEQRES 8 B 226 TYR LEU THR VAL SER SER HIS PRO ASN SER LEU MET LYS SEQRES 9 B 226 LYS ILE THR LEU LEU LYS TYR PHE ARG ASN TYR MET SER SEQRES 10 B 226 GLU HIS LEU LEU LYS ALA GLY ALA ASN ILE THR PRO ARG SEQRES 11 B 226 GLU GLY ASP GLU LEU ALA ARG LEU PRO TYR LEU ARG THR SEQRES 12 B 226 TRP PHE ARG THR ARG SER ALA ILE ILE LEU HIS LEU SER SEQRES 13 B 226 ASN GLY SER VAL GLN ILE ASN PHE PHE GLN ASP HIS THR SEQRES 14 B 226 LYS LEU ILE LEU CYS PRO LEU MET ALA ALA VAL THR TYR SEQRES 15 B 226 ILE ASP GLU LYS ARG ASP PHE ARG THR TYR ARG LEU SER SEQRES 16 B 226 LEU LEU GLU GLU TYR GLY CYS CYS LYS GLU LEU ALA SER SEQRES 17 B 226 ARG LEU ARG TYR ALA ARG THR MET VAL ASP LYS LEU LEU SEQRES 18 B 226 SER SER ARG SER ALA SEQRES 1 C 7 ACE PRO LEU HIS SER TPO NH2 SEQRES 1 D 7 ACE PRO LEU HIS SER TPO NH2 HET ACE C 1 3 HET TPO C 6 11 HET NH2 C 7 1 HET ACE D 1 3 HET TPO D 6 11 HET NH2 D 7 1 HETNAM ACE ACETYL GROUP HETNAM TPO PHOSPHOTHREONINE HETNAM NH2 AMINO GROUP HETSYN TPO PHOSPHONOTHREONINE FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 TPO 2(C4 H10 N O6 P) FORMUL 3 NH2 2(H2 N) FORMUL 5 HOH *232(H2 O) HELIX 1 AA1 ALA A 371 SER A 387 1 17 HELIX 2 AA2 LYS A 388 ARG A 392 5 5 HELIX 3 AA3 ARG A 396 GLU A 401 5 6 HELIX 4 AA4 ASP A 402 ILE A 406 5 5 HELIX 5 AA5 LEU A 472 LEU A 490 1 19 HELIX 6 AA6 LEU A 564 GLY A 571 1 8 HELIX 7 AA7 CYS A 573 SER A 595 1 23 HELIX 8 AA8 ALA B 372 SER B 387 1 16 HELIX 9 AA9 LYS B 388 ARG B 392 5 5 HELIX 10 AB1 ARG B 396 GLU B 401 5 6 HELIX 11 AB2 ASP B 402 ILE B 406 5 5 HELIX 12 AB3 PRO B 469 SER B 471 5 3 HELIX 13 AB4 LEU B 472 LEU B 490 1 19 HELIX 14 AB5 LEU B 564 GLY B 571 1 8 HELIX 15 AB6 CYS B 573 SER B 595 1 23 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 GLY A 433 N TYR A 425 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 LYS A 540 CYS A 544 -1 O LEU A 543 N VAL A 530 SHEET 5 AA2 6 ALA A 549 ILE A 553 -1 O ILE A 553 N LYS A 540 SHEET 6 AA2 6 PHE A 559 ARG A 563 -1 O TYR A 562 N VAL A 550 SHEET 1 AA3 6 VAL B 411 ASP B 416 0 SHEET 2 AA3 6 GLY B 422 LEU B 427 -1 O GLY B 424 N VAL B 415 SHEET 3 AA3 6 VAL B 432 PHE B 436 -1 O GLY B 433 N TYR B 425 SHEET 4 AA3 6 ARG B 441 LEU B 444 -1 O LEU B 444 N VAL B 432 SHEET 5 AA3 6 SER B 450 ILE B 454 -1 O ILE B 454 N ARG B 441 SHEET 6 AA3 6 GLU B 460 THR B 464 -1 O LEU B 463 N LEU B 451 SHEET 1 AA4 6 LEU B 511 ARG B 516 0 SHEET 2 AA4 6 ALA B 520 LEU B 525 -1 O HIS B 524 N THR B 513 SHEET 3 AA4 6 VAL B 530 PHE B 534 -1 O GLN B 531 N LEU B 523 SHEET 4 AA4 6 LYS B 540 CYS B 544 -1 O LEU B 543 N VAL B 530 SHEET 5 AA4 6 ALA B 549 ILE B 553 -1 O ILE B 553 N LYS B 540 SHEET 6 AA4 6 PHE B 559 ARG B 563 -1 O TYR B 562 N VAL B 550 LINK C ACE C 1 N PRO C 2 1555 1555 1.48 LINK C SER C 5 N TPO C 6 1555 1555 1.45 LINK C TPO C 6 N NH2 C 7 1555 1555 1.40 LINK C ACE D 1 N PRO D 2 1555 1555 1.48 LINK C SER D 5 N TPO D 6 1555 1555 1.45 LINK C TPO D 6 N NH2 D 7 1555 1555 1.40 CRYST1 77.829 35.370 95.545 90.00 89.98 90.00 P 1 2 1 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 0.012849 0.000000 -0.000004 0.00000 SCALE2 0.000000 0.028273 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010466 0.00000