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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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