HEADER TRANSFERASE 30-NOV-11 4AAA
TITLE CRYSTAL STRUCTURE OF THE HUMAN CDKL2 KINASE DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE-LIKE 2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 1-308;
COMPND 5 SYNONYM: PROTEIN KINASE P56 KKIAMRE, SERINE/THREONINE-PROTEIN KINASE
COMPND 6 KKIAMRE;
COMPND 7 EC: 2.7.11.22;
COMPND 8 ENGINEERED: YES;
COMPND 9 MUTATION: YES;
COMPND 10 OTHER_DETAILS: HIS85 CONFORMATION B AND ASP84 CONFORMATION A MAY NOT
COMPND 11 BE OCCUPIED SIMULTANEOUSLY.
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
KEYWDS TRANSFERASE, PHOSPHO-MIMETIC
EXPDTA X-RAY DIFFRACTION
AUTHOR P.CANNING,M.VOLLMAR,C.D.O.COOPER,P.MAHAJAN,N.DAGA,G.BERRIDGE,
AUTHOR 2 N.BURGESS-BROWN,J.R.C.MUNIZ,T.KROJER,F.VON DELFT,J.WEIGELT,
AUTHOR 3 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,A.BULLOCK
REVDAT 4 20-DEC-23 4AAA 1 REMARK
REVDAT 3 30-MAR-22 4AAA 1 JRNL REMARK
REVDAT 2 24-JAN-18 4AAA 1 AUTHOR
REVDAT 1 21-DEC-11 4AAA 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. 1.53 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) : 1.53
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.78
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0
REMARK 3 NUMBER OF REFLECTIONS : 56974
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) : 0.182
REMARK 3 R VALUE (WORKING SET) : 0.180
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 3041
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) : 1.53
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3479
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.63
REMARK 3 BIN R VALUE (WORKING SET) : 0.3950
REMARK 3 BIN FREE R VALUE SET COUNT : 174
REMARK 3 BIN FREE R VALUE : 0.3960
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2393
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 52
REMARK 3 SOLVENT ATOMS : 259
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.67
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.55000
REMARK 3 B22 (A**2) : 1.14000
REMARK 3 B33 (A**2) : -0.59000
REMARK 3 B12 (A**2) : 0.00000
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): 0.070
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.880
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2639 ; 0.014 ; 0.020
REMARK 3 BOND LENGTHS OTHERS (A): 1865 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3576 ; 1.563 ; 1.976
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4554 ; 0.935 ; 2.997
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 5.509 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;37.518 ;24.286
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;13.981 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;19.580 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 378 ; 0.098 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2921 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 548 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 797 ; 0.275 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1838 ; 0.178 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1259 ; 0.182 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 1258 ; 0.088 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 46 ; 0.146 ; 0.200
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): 41 ; 0.301 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 59 ; 0.213 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.161 ; 0.200
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): 5 ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7 ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 9 ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 11 ; 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 : 4
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 -4 A 34
REMARK 3 ORIGIN FOR THE GROUP (A): 29.6913 -0.3418 78.4371
REMARK 3 T TENSOR
REMARK 3 T11: 0.0637 T22: 0.0487
REMARK 3 T33: 0.1753 T12: -0.0036
REMARK 3 T13: -0.0031 T23: -0.0498
REMARK 3 L TENSOR
REMARK 3 L11: 0.2865 L22: 0.2296
REMARK 3 L33: 0.6576 L12: 0.1649
REMARK 3 L13: 0.3267 L23: 0.3761
REMARK 3 S TENSOR
REMARK 3 S11: 0.0241 S12: 0.0941 S13: -0.1880
REMARK 3 S21: -0.0020 S22: 0.0841 S23: -0.0286
REMARK 3 S31: -0.0330 S32: 0.1439 S33: -0.1083
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 85
REMARK 3 ORIGIN FOR THE GROUP (A): 42.1659 1.5063 78.6955
REMARK 3 T TENSOR
REMARK 3 T11: 0.0730 T22: 0.1328
REMARK 3 T33: 0.1132 T12: -0.0222
REMARK 3 T13: 0.0112 T23: -0.0798
REMARK 3 L TENSOR
REMARK 3 L11: 1.6067 L22: 0.3998
REMARK 3 L33: 0.0824 L12: 0.4730
REMARK 3 L13: 0.3204 L23: 0.1624
REMARK 3 S TENSOR
REMARK 3 S11: -0.0520 S12: 0.3794 S13: -0.3801
REMARK 3 S21: 0.1083 S22: 0.1173 S23: -0.0811
REMARK 3 S31: 0.0192 S32: 0.0788 S33: -0.0653
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 86 A 165
REMARK 3 ORIGIN FOR THE GROUP (A): 34.9948 21.4350 80.3436
REMARK 3 T TENSOR
REMARK 3 T11: 0.0494 T22: 0.0467
REMARK 3 T33: 0.0380 T12: -0.0032
REMARK 3 T13: 0.0021 T23: -0.0044
REMARK 3 L TENSOR
REMARK 3 L11: 0.4510 L22: 0.3923
REMARK 3 L33: 0.0312 L12: 0.2257
REMARK 3 L13: 0.0044 L23: -0.0889
REMARK 3 S TENSOR
REMARK 3 S11: 0.0219 S12: -0.0450 S13: 0.0161
REMARK 3 S21: -0.0198 S22: -0.0245 S23: 0.0027
REMARK 3 S31: 0.0174 S32: -0.0036 S33: 0.0026
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 166 A 303
REMARK 3 ORIGIN FOR THE GROUP (A): 42.7036 32.9002 73.0624
REMARK 3 T TENSOR
REMARK 3 T11: 0.0410 T22: 0.0479
REMARK 3 T33: 0.0343 T12: -0.0063
REMARK 3 T13: -0.0042 T23: 0.0182
REMARK 3 L TENSOR
REMARK 3 L11: 0.1987 L22: 0.1512
REMARK 3 L33: 0.8190 L12: -0.0279
REMARK 3 L13: 0.0659 L23: -0.1553
REMARK 3 S TENSOR
REMARK 3 S11: 0.0082 S12: 0.0155 S13: 0.0705
REMARK 3 S21: 0.0115 S22: -0.0449 S23: -0.0142
REMARK 3 S31: -0.0222 S32: 0.0156 S33: 0.0368
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. RESIDUES 149 TO 160 ARE
REMARK 3 DISORDERED RESIDUE HIS85 CONFORMATION B AND ASP84 CONFORMATION A
REMARK 3 MAY NOT BE OCCUPIED SIMULTANEOUSLY.
REMARK 4
REMARK 4 4AAA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-11.
REMARK 100 THE DEPOSITION ID IS D_1290050527.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-OCT-11
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 : 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 : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53461
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
REMARK 200 RESOLUTION RANGE LOW (A) : 42.140
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 13.70
REMARK 200 R MERGE (I) : 0.14000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.90
REMARK 200 R MERGE FOR SHELL (I) : 1.14000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100
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: PDB ENTRY 3NIZ
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL, 0.1M TRIS PH 8.5; 25% PEG
REMARK 280 3350.
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 33.90950
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.83000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.11000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.83000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.90950
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.11000
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 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 400
REMARK 400 COMPOUND
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, THR 159 TO ASP
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, TYR 161 TO GLU
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 MET A -22
REMARK 465 GLY A -21
REMARK 465 HIS A -20
REMARK 465 HIS A -19
REMARK 465 HIS A -18
REMARK 465 HIS A -17
REMARK 465 HIS A -16
REMARK 465 HIS A -15
REMARK 465 SER A -14
REMARK 465 SER A -13
REMARK 465 GLY A -12
REMARK 465 VAL A -11
REMARK 465 ASP A -10
REMARK 465 LEU A -9
REMARK 465 GLY A -8
REMARK 465 THR A -7
REMARK 465 GLU A -6
REMARK 465 ASN A -5
REMARK 465 ARG A 149
REMARK 465 THR A 150
REMARK 465 LEU A 151
REMARK 465 ALA A 152
REMARK 465 ALA A 153
REMARK 465 PRO A 154
REMARK 465 GLY A 155
REMARK 465 GLU A 156
REMARK 465 VAL A 157
REMARK 465 TYR A 158
REMARK 465 ASP A 159
REMARK 465 ASP A 160
REMARK 465 LYS A 303
REMARK 465 VAL A 304
REMARK 465 GLN A 305
REMARK 465 LYS A 306
REMARK 465 ASP A 307
REMARK 465 ALA A 308
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 LYS A 33 CD CE NZ
REMARK 470 LYS A 42 CD CE NZ
REMARK 470 LYS A 53 CD CE NZ
REMARK 470 LYS A 71 CE NZ
REMARK 470 ARG A 125 CZ NH1 NH2
REMARK 470 GLU A 161 CG CD OE1 OE2
REMARK 470 VAL A 162 CG1 CG2
REMARK 470 LYS A 244 CE NZ
REMARK 470 LEU A 302 CG CD1 CD2
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 2062 O HOH A 2070 1.64
REMARK 500 O HOH A 2073 O HOH A 2081 2.10
REMARK 500 O HOH A 2089 O HOH A 2090 2.12
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 CD2 HIS A 85 O HOH A 2136 4457 2.09
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 60 CG HIS A 60 CD2 0.057
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 41 96.11 -68.88
REMARK 500 LYS A 73 -117.94 56.60
REMARK 500 ARG A 125 -14.07 82.36
REMARK 500 LEU A 268 30.71 -99.23
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 5-AMINO-3-((4-(AMINOSULFONYL)PHENYL)AMINO)-N-(2,
REMARK 600 6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE
REMARK 600 (DKI): CDK12 INHIBITOR III
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DKI A 500
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 506
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 TWO PHOSPHO-MIMETIC ACTIVATING MUTATIONS INTRODUCED.
DBREF 4AAA A 1 308 UNP Q92772 CDKL2_HUMAN 1 308
SEQADV 4AAA MET A -22 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA GLY A -21 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA HIS A -20 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA HIS A -19 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA HIS A -18 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA HIS A -17 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA HIS A -16 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA HIS A -15 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA SER A -14 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA SER A -13 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA GLY A -12 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA VAL A -11 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA ASP A -10 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA LEU A -9 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA GLY A -8 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA THR A -7 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA GLU A -6 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA ASN A -5 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA LEU A -4 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA TYR A -3 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA PHE A -2 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA GLN A -1 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA SER A 0 UNP Q92772 EXPRESSION TAG
SEQADV 4AAA ASP A 159 UNP Q92772 THR 159 ENGINEERED MUTATION
SEQADV 4AAA GLU A 161 UNP Q92772 TYR 161 ENGINEERED MUTATION
SEQRES 1 A 331 MET GLY HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP
SEQRES 2 A 331 LEU GLY THR GLU ASN LEU TYR PHE GLN SER MET GLU LYS
SEQRES 3 A 331 TYR GLU ASN LEU GLY LEU VAL GLY GLU GLY SER TYR GLY
SEQRES 4 A 331 MET VAL MET LYS CYS ARG ASN LYS ASP THR GLY ARG ILE
SEQRES 5 A 331 VAL ALA ILE LYS LYS PHE LEU GLU SER ASP ASP ASP LYS
SEQRES 6 A 331 MET VAL LYS LYS ILE ALA MET ARG GLU ILE LYS LEU LEU
SEQRES 7 A 331 LYS GLN LEU ARG HIS GLU ASN LEU VAL ASN LEU LEU GLU
SEQRES 8 A 331 VAL CYS LYS LYS LYS LYS ARG TRP TYR LEU VAL PHE GLU
SEQRES 9 A 331 PHE VAL ASP HIS THR ILE LEU ASP ASP LEU GLU LEU PHE
SEQRES 10 A 331 PRO ASN GLY LEU ASP TYR GLN VAL VAL GLN LYS TYR LEU
SEQRES 11 A 331 PHE GLN ILE ILE ASN GLY ILE GLY PHE CYS HIS SER HIS
SEQRES 12 A 331 ASN ILE ILE HIS ARG ASP ILE LYS PRO GLU ASN ILE LEU
SEQRES 13 A 331 VAL SER GLN SER GLY VAL VAL LYS LEU CYS ASP PHE GLY
SEQRES 14 A 331 PHE ALA ARG THR LEU ALA ALA PRO GLY GLU VAL TYR ASP
SEQRES 15 A 331 ASP GLU VAL ALA THR ARG TRP TYR ARG ALA PRO GLU LEU
SEQRES 16 A 331 LEU VAL GLY ASP VAL LYS TYR GLY LYS ALA VAL ASP VAL
SEQRES 17 A 331 TRP ALA ILE GLY CYS LEU VAL THR GLU MET PHE MET GLY
SEQRES 18 A 331 GLU PRO LEU PHE PRO GLY ASP SER ASP ILE ASP GLN LEU
SEQRES 19 A 331 TYR HIS ILE MET MET CYS LEU GLY ASN LEU ILE PRO ARG
SEQRES 20 A 331 HIS GLN GLU LEU PHE ASN LYS ASN PRO VAL PHE ALA GLY
SEQRES 21 A 331 VAL ARG LEU PRO GLU ILE LYS GLU ARG GLU PRO LEU GLU
SEQRES 22 A 331 ARG ARG TYR PRO LYS LEU SER GLU VAL VAL ILE ASP LEU
SEQRES 23 A 331 ALA LYS LYS CYS LEU HIS ILE ASP PRO ASP LYS ARG PRO
SEQRES 24 A 331 PHE CYS ALA GLU LEU LEU HIS HIS ASP PHE PHE GLN MET
SEQRES 25 A 331 ASP GLY PHE ALA GLU ARG PHE SER GLN GLU LEU GLN LEU
SEQRES 26 A 331 LYS VAL GLN LYS ASP ALA
HET DKI A 500 28
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
HETNAM DKI 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-
HETNAM 2 DKI DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN DKI CDK 1/2 INHIBITOR
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 DKI C15 H13 F2 N7 O2 S2
FORMUL 3 EDO 6(C2 H6 O2)
FORMUL 9 HOH *259(H2 O)
HELIX 1 1 SER A 0 GLU A 2 5 3
HELIX 2 2 GLY A 11 SER A 14 5 4
HELIX 3 3 ASP A 41 LEU A 58 1 18
HELIX 4 4 ILE A 87 PHE A 94 1 8
HELIX 5 5 ASP A 99 HIS A 120 1 22
HELIX 6 6 LYS A 128 GLU A 130 5 3
HELIX 7 7 ALA A 169 VAL A 174 1 6
HELIX 8 8 LYS A 181 GLY A 198 1 18
HELIX 9 9 SER A 206 GLY A 219 1 14
HELIX 10 10 ILE A 222 ASN A 232 1 11
HELIX 11 11 PRO A 233 ALA A 236 5 4
HELIX 12 12 PRO A 248 TYR A 253 1 6
HELIX 13 13 SER A 257 LEU A 268 1 12
HELIX 14 14 ASP A 271 ARG A 275 5 5
HELIX 15 15 PHE A 277 HIS A 283 5 7
HELIX 16 16 HIS A 284 MET A 289 1 6
HELIX 17 17 GLY A 291 LEU A 302 1 12
SHEET 1 AA 5 TYR A 4 LEU A 9 0
SHEET 2 AA 5 VAL A 18 ASN A 23 -1 O LYS A 20 N LEU A 7
SHEET 3 AA 5 ILE A 29 LEU A 36 -1 O VAL A 30 N CYS A 21
SHEET 4 AA 5 ARG A 75 GLU A 81 -1 O TRP A 76 N PHE A 35
SHEET 5 AA 5 LEU A 66 LYS A 72 -1 N LEU A 67 O VAL A 79
SHEET 1 AB 3 HIS A 85 THR A 86 0
SHEET 2 AB 3 ILE A 132 VAL A 134 -1 O VAL A 134 N HIS A 85
SHEET 3 AB 3 VAL A 140 LEU A 142 -1 O LYS A 141 N LEU A 133
SITE 1 AC1 19 VAL A 10 GLY A 11 TYR A 15 VAL A 18
SITE 2 AC1 19 VAL A 64 GLU A 81 PHE A 82 VAL A 83
SITE 3 AC1 19 ASP A 84 THR A 86 ASP A 89 GLU A 130
SITE 4 AC1 19 LEU A 133 CYS A 143 ASP A 144 EDO A 501
SITE 5 AC1 19 HOH A2016 HOH A2022 HOH A2024
SITE 1 AC2 7 PHE A 80 CYS A 143 ASP A 144 DKI A 500
SITE 2 AC2 7 HOH A2158 HOH A2257 HOH A2258
SITE 1 AC3 4 ASP A 89 GLU A 92 SER A 119 HIS A 120
SITE 1 AC4 5 ILE A 243 LYS A 244 ARG A 246 HOH A2199
SITE 2 AC4 5 HOH A2212
SITE 1 AC5 4 ASN A 220 LEU A 221 PRO A 223 HOH A2095
SITE 1 AC6 3 MET A 1 TYR A 4 ASN A 6
SITE 1 AC7 6 GLY A 27 ILE A 29 ASP A 273 PHE A 277
SITE 2 AC7 6 HOH A2046 HOH A2234
CRYST1 67.819 70.220 83.660 90.00 90.00 90.00 P 21 21 21 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 0.014745 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014241 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011953 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
