HEADER TRANSFERASE 30-NOV-12 3ZDU TITLE CRYSTAL STRUCTURE OF THE HUMAN CDKL3 KINASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE-LIKE 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 1-324; COMPND 5 SYNONYM: SERINE/THREONINE-PROTEIN KINASE NKIAMRE; COMPND 6 EC: 2.7.11.22; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: TWO PHOSPHOMIMETIC POINT MUTATIONS INTRODUCED, T158D COMPND 10 AND Y160E SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE; SOURCE 11 OTHER_DETAILS: SITE-DIRECTED MUTAGENESIS KEYWDS TRANSFERASE, PHOSPHO-MIMETIC EXPDTA X-RAY DIFFRACTION AUTHOR P.CANNING,J.M.ELKINS,S.GOUBIN,P.MAHAJAN,A.C.W.PIKE,A.QUIGLEY, AUTHOR 2 A.MACKENZIE,E.P.CARPENTER,F.VON DELFT,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 3 C.BOUNTRA,A.BULLOCK REVDAT 4 20-DEC-23 3ZDU 1 REMARK REVDAT 3 30-MAR-22 3ZDU 1 JRNL REMARK LINK REVDAT 2 24-JAN-18 3ZDU 1 AUTHOR JRNL REVDAT 1 20-MAR-13 3ZDU 0 JRNL AUTH P.CANNING,K.PARK,J.GONCALVES,C.LI,C.J.HOWARD,T.D.SHARPE, JRNL AUTH 2 L.J.HOLT,L.PELLETIER,A.N.BULLOCK,M.R.LEROUX JRNL TITL CDKL FAMILY KINASES HAVE EVOLVED DISTINCT STRUCTURAL JRNL TITL 2 FEATURES AND CILIARY FUNCTION. JRNL REF CELL REP V. 22 885 2018 JRNL REFN ESSN 2211-1247 JRNL PMID 29420175 JRNL DOI 10.1016/J.CELREP.2017.12.083 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 18821 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1013 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1056 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.6280 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.7000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2319 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.27000 REMARK 3 B22 (A**2) : 1.27000 REMARK 3 B33 (A**2) : -4.11000 REMARK 3 B12 (A**2) : 1.27000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.260 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.919 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2414 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2298 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3261 ; 1.510 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5257 ; 0.793 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 294 ; 6.554 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;38.150 ;23.861 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 397 ;14.956 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;24.066 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 371 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2675 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 556 ; 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): 1185 ; 1.143 ; 1.999 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1184 ; 1.142 ; 1.997 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1476 ; 1.823 ; 2.995 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1227 ; 1.763 ; 2.126 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 : 5 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 1 A 34 REMARK 3 ORIGIN FOR THE GROUP (A): 17.8190 25.5512 57.4661 REMARK 3 T TENSOR REMARK 3 T11: 0.7106 T22: 0.4851 REMARK 3 T33: 0.5841 T12: 0.2165 REMARK 3 T13: -0.0044 T23: 0.0154 REMARK 3 L TENSOR REMARK 3 L11: 9.7144 L22: 8.6422 REMARK 3 L33: 0.2499 L12: -7.1114 REMARK 3 L13: 0.9855 L23: -0.2517 REMARK 3 S TENSOR REMARK 3 S11: -0.1024 S12: 0.4717 S13: -0.1950 REMARK 3 S21: -0.1274 S22: -0.1059 S23: 1.5142 REMARK 3 S31: -0.0903 S32: -0.1103 S33: 0.2083 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 35 A 60 REMARK 3 ORIGIN FOR THE GROUP (A): 17.9462 16.7333 72.0421 REMARK 3 T TENSOR REMARK 3 T11: 2.0469 T22: 1.5519 REMARK 3 T33: 0.4267 T12: 1.5132 REMARK 3 T13: 0.2741 T23: 0.1527 REMARK 3 L TENSOR REMARK 3 L11: 1.7654 L22: 12.8234 REMARK 3 L33: 0.7605 L12: 0.6072 REMARK 3 L13: -0.2830 L23: -1.4743 REMARK 3 S TENSOR REMARK 3 S11: -0.6263 S12: 0.2342 S13: 0.1460 REMARK 3 S21: 0.2212 S22: 0.9286 S23: 1.1553 REMARK 3 S31: -0.9654 S32: -1.0206 S33: -0.3024 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 61 A 159 REMARK 3 ORIGIN FOR THE GROUP (A): 29.7899 16.5263 66.8983 REMARK 3 T TENSOR REMARK 3 T11: 0.4545 T22: 0.2068 REMARK 3 T33: 0.2373 T12: 0.0881 REMARK 3 T13: 0.1338 T23: 0.0270 REMARK 3 L TENSOR REMARK 3 L11: 0.9742 L22: 4.0969 REMARK 3 L33: 3.6202 L12: -1.2624 REMARK 3 L13: 1.3157 L23: -0.1263 REMARK 3 S TENSOR REMARK 3 S11: -0.1042 S12: -0.1322 S13: -0.0222 REMARK 3 S21: 0.1730 S22: 0.1913 S23: 0.4565 REMARK 3 S31: -0.5113 S32: -0.3617 S33: -0.0872 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 160 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): 37.5172 -0.1157 69.6608 REMARK 3 T TENSOR REMARK 3 T11: 0.1973 T22: 0.1359 REMARK 3 T33: 0.0280 T12: 0.0359 REMARK 3 T13: 0.0127 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.5598 L22: 4.8450 REMARK 3 L33: 2.8972 L12: 0.9680 REMARK 3 L13: -0.4422 L23: 0.5160 REMARK 3 S TENSOR REMARK 3 S11: -0.0688 S12: -0.0314 S13: -0.1725 REMARK 3 S21: 0.0837 S22: 0.0981 S23: -0.1455 REMARK 3 S31: 0.1344 S32: 0.0201 S33: -0.0294 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 303 A 309 REMARK 3 ORIGIN FOR THE GROUP (A): 36.1528 35.2414 70.9341 REMARK 3 T TENSOR REMARK 3 T11: 0.7594 T22: 0.6347 REMARK 3 T33: 0.7342 T12: 0.0032 REMARK 3 T13: 0.0115 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.2484 L22: 0.9283 REMARK 3 L33: 22.5698 L12: -0.1673 REMARK 3 L13: -5.0580 L23: -0.6586 REMARK 3 S TENSOR REMARK 3 S11: -0.1697 S12: 0.0389 S13: -0.0340 REMARK 3 S21: 0.6633 S22: 0.2254 S23: 0.2885 REMARK 3 S31: -0.4309 S32: -0.5585 S33: -0.0557 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 3ZDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1290054956. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-12 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 : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9611 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20446 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 54.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: ENSEMBLE OF PDB ENTRIES 4AGU AND 4AAA REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03M ZN CL, 30% PEG_6000, 5% ETHYLENE REMARK 280 GLYCOL, MES PH5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.54333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 109.08667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 109.08667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.54333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -152.7 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 109.08667 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 A2079 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 0 REMARK 465 GLU A 37 REMARK 465 ARG A 38 REMARK 465 PRO A 39 REMARK 465 GLU A 40 REMARK 465 GLN A 41 REMARK 465 SER A 42 REMARK 465 VAL A 43 REMARK 465 LEU A 150 REMARK 465 ALA A 151 REMARK 465 ALA A 152 REMARK 465 PRO A 153 REMARK 465 GLY A 154 REMARK 465 ASN A 310 REMARK 465 SER A 311 REMARK 465 LEU A 312 REMARK 465 ILE A 313 REMARK 465 LYS A 314 REMARK 465 PRO A 315 REMARK 465 LYS A 316 REMARK 465 GLU A 317 REMARK 465 SER A 318 REMARK 465 SER A 319 REMARK 465 LYS A 320 REMARK 465 GLU A 321 REMARK 465 ASN A 322 REMARK 465 GLU A 323 REMARK 465 LEU A 324 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 GLU A 2 CG CD OE1 OE2 REMARK 470 SER A 14 OG REMARK 470 LYS A 22 NZ REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 ARG A 49 NE CZ NH1 NH2 REMARK 470 LYS A 52 CE NZ REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 GLN A 56 CG CD OE1 NE2 REMARK 470 ARG A 70 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 LYS A 100 CE NZ REMARK 470 ASP A 155 CG OD1 OD2 REMARK 470 TYR A 157 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 159 CG OD1 OD2 REMARK 470 LYS A 212 CD CE NZ REMARK 470 LYS A 230 CE NZ REMARK 470 GLN A 243 CG CD OE1 NE2 REMARK 470 LYS A 246 CE NZ REMARK 470 LYS A 250 CD CE NZ REMARK 470 LYS A 254 CG CD CE NZ REMARK 470 ASP A 289 CG OD1 OD2 REMARK 470 LYS A 294 CE NZ REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 LYS A 302 CG CD CE NZ REMARK 470 GLN A 305 CG CD OE1 NE2 REMARK 470 GLU A 306 CG CD OE1 OE2 REMARK 470 LYS A 308 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 HOH A 2057 O HOH A 2141 1.92 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 GLU A 2 121.04 -36.78 REMARK 500 ARG A 124 3.99 80.42 REMARK 500 ASP A 125 47.86 -156.16 REMARK 500 ASP A 143 92.44 75.18 REMARK 500 LEU A 201 55.73 -118.69 REMARK 500 ARG A 288 -60.03 -27.81 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 A2035 DISTANCE = 7.11 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 38R: ATP-MIMETIC KINASE INHIBITOR ASC67 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 352 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 92 NE2 REMARK 620 2 HIS A 211 NE2 107.6 REMARK 620 3 HOH A2029 O 88.5 96.0 REMARK 620 4 HOH A2033 O 83.5 167.5 78.2 REMARK 620 5 HOH A2034 O 102.3 108.3 148.6 73.9 REMARK 620 6 HOH A2158 O 154.0 98.3 91.4 71.0 66.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 353 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 125 OD2 REMARK 620 2 ASP A 143 OD2 92.6 REMARK 620 3 ASP A 143 OD1 125.4 44.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 351 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 175 OD1 REMARK 620 2 HIS A 223 NE2 126.3 REMARK 620 3 HIS A 282 NE2 95.8 111.6 REMARK 620 4 HOH A2087 O 104.0 110.2 107.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 38R A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 354 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 355 DBREF 3ZDU A 1 324 UNP Q8IVW4 CDKL3_HUMAN 1 324 SEQADV 3ZDU SER A 0 UNP Q8IVW4 EXPRESSION TAG SEQADV 3ZDU ASP A 158 UNP Q8IVW4 THR 158 ENGINEERED MUTATION SEQADV 3ZDU GLU A 160 UNP Q8IVW4 TYR 160 ENGINEERED MUTATION SEQRES 1 A 325 SER MET GLU MET TYR GLU THR LEU GLY LYS VAL GLY GLU SEQRES 2 A 325 GLY SER TYR GLY THR VAL MET LYS CYS LYS HIS LYS ASN SEQRES 3 A 325 THR GLY GLN ILE VAL ALA ILE LYS ILE PHE TYR GLU ARG SEQRES 4 A 325 PRO GLU GLN SER VAL ASN LYS ILE ALA MET ARG GLU ILE SEQRES 5 A 325 LYS PHE LEU LYS GLN PHE HIS HIS GLU ASN LEU VAL ASN SEQRES 6 A 325 LEU ILE GLU VAL PHE ARG GLN LYS LYS LYS ILE HIS LEU SEQRES 7 A 325 VAL PHE GLU PHE ILE ASP HIS THR VAL LEU ASP GLU LEU SEQRES 8 A 325 GLN HIS TYR CYS HIS GLY LEU GLU SER LYS ARG LEU ARG SEQRES 9 A 325 LYS TYR LEU PHE GLN ILE LEU ARG ALA ILE ASP TYR LEU SEQRES 10 A 325 HIS SER ASN ASN ILE ILE HIS ARG ASP ILE LYS PRO GLU SEQRES 11 A 325 ASN ILE LEU VAL SER GLN SER GLY ILE THR LYS LEU CYS SEQRES 12 A 325 ASP PHE GLY PHE ALA ARG THR LEU ALA ALA PRO GLY ASP SEQRES 13 A 325 ILE TYR ASP ASP GLU VAL ALA THR ARG TRP TYR ARG ALA SEQRES 14 A 325 PRO GLU LEU VAL LEU LYS ASP THR SER TYR GLY LYS PRO SEQRES 15 A 325 VAL ASP ILE TRP ALA LEU GLY CYS MET ILE ILE GLU MET SEQRES 16 A 325 ALA THR GLY ASN PRO TYR LEU PRO SER SER SER ASP LEU SEQRES 17 A 325 ASP LEU LEU HIS LYS ILE VAL LEU LYS VAL GLY ASN LEU SEQRES 18 A 325 SER PRO HIS LEU GLN ASN ILE PHE SER LYS SER PRO ILE SEQRES 19 A 325 PHE ALA GLY VAL VAL LEU PRO GLN VAL GLN HIS PRO LYS SEQRES 20 A 325 ASN ALA ARG LYS LYS TYR PRO LYS LEU ASN GLY LEU LEU SEQRES 21 A 325 ALA ASP ILE VAL HIS ALA CYS LEU GLN ILE ASP PRO ALA SEQRES 22 A 325 ASP ARG ILE SER SER SER ASP LEU LEU HIS HIS GLU TYR SEQRES 23 A 325 PHE THR ARG ASP GLY PHE ILE GLU LYS PHE MET PRO GLU SEQRES 24 A 325 LEU LYS ALA LYS LEU LEU GLN GLU ALA LYS VAL ASN SER SEQRES 25 A 325 LEU ILE LYS PRO LYS GLU SER SER LYS GLU ASN GLU LEU HET 38R A 350 27 HET ZN A 351 1 HET ZN A 352 1 HET NA A 353 1 HET EDO A 354 4 HET EDO A 355 4 HETNAM 38R [4-({4-[(3-CYCLOPENTYL-1H-PYRAZOL-5-YL)AMINO]PYRIMIDIN- HETNAM 2 38R 2-YL}AMINO)PHENYL]ACETONITRILE HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 38R C20 H21 N7 FORMUL 3 ZN 2(ZN 2+) FORMUL 5 NA NA 1+ FORMUL 6 EDO 2(C2 H6 O2) FORMUL 8 HOH *159(H2 O) HELIX 1 1 ASN A 44 PHE A 57 1 14 HELIX 2 2 VAL A 86 TYR A 93 1 8 HELIX 3 3 GLU A 98 ASN A 119 1 22 HELIX 4 4 LYS A 127 GLU A 129 5 3 HELIX 5 5 GLU A 160 TRP A 165 1 6 HELIX 6 6 ALA A 168 LEU A 173 1 6 HELIX 7 7 LYS A 180 GLY A 197 1 18 HELIX 8 8 SER A 205 VAL A 217 1 13 HELIX 9 9 SER A 221 SER A 231 1 11 HELIX 10 10 PRO A 232 ALA A 235 5 4 HELIX 11 11 ASN A 247 TYR A 252 1 6 HELIX 12 12 ASN A 256 LEU A 267 1 12 HELIX 13 13 ASP A 270 ARG A 274 5 5 HELIX 14 14 SER A 276 HIS A 282 1 7 HELIX 15 15 HIS A 283 ARG A 288 1 6 HELIX 16 16 GLY A 290 VAL A 309 1 20 SHEET 1 AA 5 TYR A 4 GLY A 13 0 SHEET 2 AA 5 GLY A 16 HIS A 23 -1 O GLY A 16 N GLY A 13 SHEET 3 AA 5 ILE A 29 ILE A 34 -1 O VAL A 30 N CYS A 21 SHEET 4 AA 5 HIS A 76 GLU A 80 -1 O LEU A 77 N LYS A 33 SHEET 5 AA 5 LEU A 65 PHE A 69 -1 N ILE A 66 O VAL A 78 SHEET 1 AB 3 HIS A 84 THR A 85 0 SHEET 2 AB 3 ILE A 131 VAL A 133 -1 O VAL A 133 N HIS A 84 SHEET 3 AB 3 THR A 139 LEU A 141 -1 O LYS A 140 N LEU A 132 LINK NE2 HIS A 92 ZN ZN A 352 1555 1555 2.05 LINK OD2 ASP A 125 NA NA A 353 1555 1555 2.24 LINK OD2 ASP A 143 NA NA A 353 1555 1555 2.27 LINK OD1 ASP A 143 NA NA A 353 1555 1555 3.18 LINK OD1 ASP A 175 ZN ZN A 351 1555 1555 2.03 LINK NE2 HIS A 211 ZN ZN A 352 5555 1555 2.18 LINK NE2 HIS A 223 ZN ZN A 351 1555 1555 2.07 LINK NE2 HIS A 282 ZN ZN A 351 4546 1555 2.15 LINK ZN ZN A 351 O HOH A2087 1555 1555 2.14 LINK ZN ZN A 352 O HOH A2029 1555 1555 2.18 LINK ZN ZN A 352 O HOH A2033 1555 1555 2.67 LINK ZN ZN A 352 O HOH A2034 1555 1555 2.26 LINK ZN ZN A 352 O HOH A2158 1555 1555 1.78 SITE 1 AC1 17 VAL A 10 ALA A 31 LYS A 33 PHE A 79 SITE 2 AC1 17 GLU A 80 PHE A 81 ILE A 82 ASP A 83 SITE 3 AC1 17 HIS A 84 THR A 85 ASP A 88 GLU A 129 SITE 4 AC1 17 ASN A 130 LEU A 132 ASP A 143 HOH A2004 SITE 5 AC1 17 HOH A2028 SITE 1 AC2 4 ASP A 175 HIS A 223 HIS A 282 HOH A2087 SITE 1 AC3 6 HIS A 92 HIS A 211 HOH A2029 HOH A2033 SITE 2 AC3 6 HOH A2034 HOH A2158 SITE 1 AC4 3 ASP A 125 ASP A 143 HOH A2069 SITE 1 AC5 2 ARG A 111 HOH A2059 SITE 1 AC6 5 ILE A 275 SER A 276 ASP A 279 HOH A2057 SITE 2 AC6 5 HOH A2141 CRYST1 63.930 63.930 163.630 90.00 90.00 120.00 P 31 2 1 6 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 0.015642 0.009031 0.000000 0.00000 SCALE2 0.000000 0.018062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006111 0.00000