HEADER TRANSFERASE 26-MAY-20 6Z54 TITLE CRYSTAL STRUCTURE OF CLK3 IN COMPLEX WITH MACROCYCLE ODS2003178 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY PROTEIN KINASE CLK3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CDC-LIKE KINASE 3; COMPND 5 EC: 2.7.12.1; COMPND 6 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: CLK3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: -R3-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS KINASE, KINASE INHIBITOR, CLK3, MACROCYCLE, NANOCYCLIC, STRUCTURAL KEYWDS 2 GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAIKUAD,P.BENDERITTER,J.HOFLACK,A.DENIS,S.KNAPP,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 2 24-JAN-24 6Z54 1 REMARK REVDAT 1 03-JUN-20 6Z54 0 JRNL AUTH A.CHAIKUAD,P.BENDERITTER,J.HOFLACK,A.DENIS,S.KNAPP, JRNL AUTH 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF CLK3 IN COMPLEX WITH MACROCYCLE JRNL TITL 2 ODS2003178 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 40311 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2157 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2672 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 187 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2899 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 407 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : -0.34000 REMARK 3 B33 (A**2) : -0.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.104 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.063 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3176 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2258 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4284 ; 1.603 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5478 ; 0.911 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 384 ; 5.764 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;34.647 ;23.620 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 567 ;13.392 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.383 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 445 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3578 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 680 ; 0.001 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 134 A 207 REMARK 3 ORIGIN FOR THE GROUP (A): 47.5590 28.5585 17.6675 REMARK 3 T TENSOR REMARK 3 T11: 0.0644 T22: 0.1110 REMARK 3 T33: 0.0853 T12: -0.0415 REMARK 3 T13: 0.0138 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 2.2571 L22: 1.4722 REMARK 3 L33: 3.6385 L12: 0.1659 REMARK 3 L13: 0.8390 L23: 0.5377 REMARK 3 S TENSOR REMARK 3 S11: -0.0353 S12: 0.1733 S13: 0.0320 REMARK 3 S21: 0.0717 S22: -0.0079 S23: -0.1593 REMARK 3 S31: -0.2038 S32: 0.2512 S33: 0.0433 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 208 A 372 REMARK 3 ORIGIN FOR THE GROUP (A): 26.3379 26.1201 17.3771 REMARK 3 T TENSOR REMARK 3 T11: 0.0886 T22: 0.0849 REMARK 3 T33: 0.0323 T12: -0.0131 REMARK 3 T13: -0.0015 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 1.6578 L22: 0.5885 REMARK 3 L33: 0.6567 L12: 0.2208 REMARK 3 L13: -0.5237 L23: -0.0775 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: 0.2893 S13: 0.0373 REMARK 3 S21: -0.1500 S22: -0.0123 S23: -0.0413 REMARK 3 S31: -0.0433 S32: -0.0121 S33: 0.0052 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 373 A 484 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7640 23.9487 28.5423 REMARK 3 T TENSOR REMARK 3 T11: 0.0054 T22: 0.0623 REMARK 3 T33: 0.0813 T12: -0.0141 REMARK 3 T13: 0.0002 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.9678 L22: 1.5373 REMARK 3 L33: 2.4014 L12: -0.3769 REMARK 3 L13: -0.0765 L23: 1.0786 REMARK 3 S TENSOR REMARK 3 S11: -0.0478 S12: 0.1871 S13: -0.0661 REMARK 3 S21: -0.0289 S22: 0.0150 S23: 0.1887 REMARK 3 S31: -0.0285 S32: -0.1214 S33: 0.0327 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 6Z54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108926. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42478 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 50.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : 0.51000 REMARK 200 FOR SHELL : 2.400 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: 2EU9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 3350, 0.2M POTASSIUM/SODIUM REMARK 280 PHOSPHATE, 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 3555 X+1/2,Y+1/2,Z 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 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 SMTRY1 3 1.000000 0.000000 0.000000 44.38000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.38000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.13000 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: 2510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 31.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1000 LIES ON A SPECIAL POSITION. 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 SER A 125 REMARK 465 MET A 126 REMARK 465 GLN A 127 REMARK 465 SER A 128 REMARK 465 SER A 129 REMARK 465 LYS A 130 REMARK 465 ARG A 131 REMARK 465 SER A 132 REMARK 465 SER A 133 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 ARG A 134 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 196 CD OE1 OE2 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 LEU A 221 O HOH A 601 2.13 REMARK 500 O HOH A 616 O HOH A 922 2.19 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 HIS A 328 CG HIS A 328 CD2 0.061 REMARK 500 HIS A 377 CG HIS A 377 CD2 0.055 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 MET A 263 CG - SD - CE ANGL. DEV. = -13.9 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 ARG A 155 -54.63 -157.03 REMARK 500 ARG A 155 -49.62 -148.06 REMARK 500 THR A 282 -14.79 79.09 REMARK 500 ASP A 320 75.24 68.73 REMARK 500 ALA A 336 152.33 77.41 REMARK 500 ALA A 352 -151.90 -156.00 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 EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Q7H A 515 DBREF 6Z54 A 127 484 UNP P49761 CLK3_HUMAN 127 484 SEQADV 6Z54 SER A 125 UNP P49761 EXPRESSION TAG SEQADV 6Z54 MET A 126 UNP P49761 EXPRESSION TAG SEQRES 1 A 360 SER MET GLN SER SER LYS ARG SER SER ARG SER VAL GLU SEQRES 2 A 360 ASP ASP LYS GLU GLY HIS LEU VAL CYS ARG ILE GLY ASP SEQRES 3 A 360 TRP LEU GLN GLU ARG TYR GLU ILE VAL GLY ASN LEU GLY SEQRES 4 A 360 GLU GLY THR PHE GLY LYS VAL VAL GLU CYS LEU ASP HIS SEQRES 5 A 360 ALA ARG GLY LYS SER GLN VAL ALA LEU LYS ILE ILE ARG SEQRES 6 A 360 ASN VAL GLY LYS TYR ARG GLU ALA ALA ARG LEU GLU ILE SEQRES 7 A 360 ASN VAL LEU LYS LYS ILE LYS GLU LYS ASP LYS GLU ASN SEQRES 8 A 360 LYS PHE LEU CYS VAL LEU MET SER ASP TRP PHE ASN PHE SEQRES 9 A 360 HIS GLY HIS MET CYS ILE ALA PHE GLU LEU LEU GLY LYS SEQRES 10 A 360 ASN THR PHE GLU PHE LEU LYS GLU ASN ASN PHE GLN PRO SEQRES 11 A 360 TYR PRO LEU PRO HIS VAL ARG HIS MET ALA TYR GLN LEU SEQRES 12 A 360 CYS HIS ALA LEU ARG PHE LEU HIS GLU ASN GLN LEU THR SEQRES 13 A 360 HIS THR ASP LEU LYS PRO GLU ASN ILE LEU PHE VAL ASN SEQRES 14 A 360 SER GLU PHE GLU THR LEU TYR ASN GLU HIS LYS SER CYS SEQRES 15 A 360 GLU GLU LYS SER VAL LYS ASN THR SER ILE ARG VAL ALA SEQRES 16 A 360 ASP PHE GLY SER ALA THR PHE ASP HIS GLU HIS HIS THR SEQRES 17 A 360 THR ILE VAL ALA THR ARG HIS TYR ARG PRO PRO GLU VAL SEQRES 18 A 360 ILE LEU GLU LEU GLY TRP ALA GLN PRO CYS ASP VAL TRP SEQRES 19 A 360 SER ILE GLY CYS ILE LEU PHE GLU TYR TYR ARG GLY PHE SEQRES 20 A 360 THR LEU PHE GLN THR HIS GLU ASN ARG GLU HIS LEU VAL SEQRES 21 A 360 MET MET GLU LYS ILE LEU GLY PRO ILE PRO SER HIS MET SEQRES 22 A 360 ILE HIS ARG THR ARG LYS GLN LYS TYR PHE TYR LYS GLY SEQRES 23 A 360 GLY LEU VAL TRP ASP GLU ASN SER SER ASP GLY ARG TYR SEQRES 24 A 360 VAL LYS GLU ASN CYS LYS PRO LEU LYS SER TYR MET LEU SEQRES 25 A 360 GLN ASP SER LEU GLU HIS VAL GLN LEU PHE ASP LEU MET SEQRES 26 A 360 ARG ARG MET LEU GLU PHE ASP PRO ALA GLN ARG ILE THR SEQRES 27 A 360 LEU ALA GLU ALA LEU LEU HIS PRO PHE PHE ALA GLY LEU SEQRES 28 A 360 THR PRO GLU GLU ARG SER PHE HIS THR HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 509 4 HET EDO A 510 4 HET EDO A 511 4 HET EDO A 512 4 HET EDO A 513 8 HET PO4 A 514 5 HET Q7H A 515 35 HETNAM EDO 1,2-ETHANEDIOL HETNAM PO4 PHOSPHATE ION HETNAM Q7H 11,15-DIMETHYL-6-(OXAN-4-YLOXY)-8-OXA-2,11,15,19,21,23- HETNAM 2 Q7H HEXAZATETRACYCLO[15.6.1.13,7.020,24]PENTACOSA-1(23), HETNAM 3 Q7H 3(25),4,6,17,20(24),21-HEPTAEN-10-ONE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 13(C2 H6 O2) FORMUL 15 PO4 O4 P 3- FORMUL 16 Q7H C25 H30 N6 O4 FORMUL 17 HOH *407(H2 O) HELIX 1 AA1 VAL A 191 ASP A 212 1 22 HELIX 2 AA2 ASN A 242 ASN A 250 1 9 HELIX 3 AA3 PRO A 256 ASN A 277 1 22 HELIX 4 AA4 LYS A 285 GLU A 287 5 3 HELIX 5 AA5 THR A 337 ARG A 341 5 5 HELIX 6 AA6 PRO A 342 LEU A 347 1 6 HELIX 7 AA7 GLN A 353 GLY A 370 1 18 HELIX 8 AA8 GLU A 378 GLY A 391 1 14 HELIX 9 AA9 PRO A 394 THR A 401 1 8 HELIX 10 AB1 LYS A 403 LYS A 405 5 3 HELIX 11 AB2 SER A 418 CYS A 428 1 11 HELIX 12 AB3 PRO A 430 MET A 435 5 6 HELIX 13 AB4 SER A 439 LEU A 453 1 15 HELIX 14 AB5 THR A 462 LEU A 467 1 6 HELIX 15 AB6 LEU A 468 LEU A 475 5 8 HELIX 16 AB7 THR A 476 SER A 481 1 6 SHEET 1 AA1 6 TRP A 151 LEU A 152 0 SHEET 2 AA1 6 TYR A 156 GLY A 165 -1 O TYR A 156 N LEU A 152 SHEET 3 AA1 6 GLY A 168 ASP A 175 -1 O GLY A 168 N GLY A 165 SHEET 4 AA1 6 GLN A 182 ILE A 188 -1 O LEU A 185 N VAL A 171 SHEET 5 AA1 6 HIS A 231 GLU A 237 -1 O MET A 232 N ILE A 188 SHEET 6 AA1 6 MET A 222 PHE A 228 -1 N PHE A 226 O CYS A 233 SHEET 1 AA2 2 LEU A 279 THR A 280 0 SHEET 2 AA2 2 THR A 325 PHE A 326 -1 O THR A 325 N THR A 280 SHEET 1 AA3 2 ILE A 289 PHE A 291 0 SHEET 2 AA3 2 ILE A 316 VAL A 318 -1 O ARG A 317 N LEU A 290 SHEET 1 AA4 2 PHE A 296 TYR A 300 0 SHEET 2 AA4 2 GLU A 307 VAL A 311 -1 O GLU A 308 N LEU A 299 SHEET 1 AA5 2 PHE A 407 TYR A 408 0 SHEET 2 AA5 2 GLY A 411 LEU A 412 -1 O GLY A 411 N TYR A 408 SITE 1 AC1 8 THR A 372 GLN A 375 HIS A 399 THR A 401 SITE 2 AC1 8 HOH A 606 HOH A 637 HOH A 699 HOH A 808 SITE 1 AC2 7 HIS A 331 GLY A 350 TRP A 351 ARG A 422 SITE 2 AC2 7 LYS A 425 EDO A 513 HOH A 681 SITE 1 AC3 5 SER A 419 PRO A 457 HOH A 610 HOH A 623 SITE 2 AC3 5 HOH A 688 SITE 1 AC4 7 LEU A 412 VAL A 413 TRP A 414 GLU A 416 SITE 2 AC4 7 HOH A 616 HOH A 663 HOH A 738 SITE 1 AC5 5 GLU A 381 TRP A 414 ASP A 415 SER A 418 SITE 2 AC5 5 HOH A 629 SITE 1 AC6 4 ASP A 447 ARG A 450 ARG A 451 GLU A 454 SITE 1 AC7 4 VAL A 145 ARG A 147 ASP A 150 HOH A 706 SITE 1 AC8 3 ARG A 189 LYS A 193 TYR A 194 SITE 1 AC9 8 THR A 372 LEU A 373 ILE A 389 CYS A 428 SITE 2 AC9 8 TYR A 434 HOH A 606 HOH A 614 HOH A 652 SITE 1 AD1 5 LYS A 140 PRO A 394 SER A 395 HIS A 396 SITE 2 AD1 5 HOH A 810 SITE 1 AD2 5 LYS A 432 ARG A 450 HOH A 603 HOH A 626 SITE 2 AD2 5 HOH A 712 SITE 1 AD3 4 GLU A 387 LYS A 388 HOH A 603 HOH A 657 SITE 1 AD4 9 HIS A 330 HIS A 331 LYS A 425 EDO A 502 SITE 2 AD4 9 HOH A 613 HOH A 619 HOH A 644 HOH A 658 SITE 3 AD4 9 HOH A 937 SITE 1 AD5 5 ARG A 195 ARG A 199 LYS A 403 LYS A 405 SITE 2 AD5 5 HOH A 722 SITE 1 AD6 14 LEU A 162 PHE A 167 ALA A 184 PHE A 236 SITE 2 AD6 14 GLU A 237 LEU A 239 ASN A 242 GLU A 245 SITE 3 AD6 14 GLU A 287 ASN A 288 LEU A 290 ASP A 320 SITE 4 AD6 14 HOH A 691 HOH A 721 CRYST1 88.760 62.260 75.700 90.00 97.61 90.00 C 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 0.011266 0.000000 0.001505 0.00000 SCALE2 0.000000 0.016062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013327 0.00000