HEADER TRANSFERASE 09-FEB-23 8CIE TITLE CRYSTAL STRUCTURE OF THE HUMAN CDKL5 KINASE DOMAIN WITH COMPOUND YL- TITLE 2 354 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE-LIKE 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SERINE/THREONINE-PROTEIN KINASE 9; COMPND 5 EC: 2.7.11.22; 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: CDKL5, STK9; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.RICHARDSON,X.CHEN,J.A.NEWMAN,S.BAKSHI,B.LAKSHMINARAYANA,L.BROOKE, AUTHOR 2 A.N.BULLOCK REVDAT 2 27-MAR-24 8CIE 1 JRNL REVDAT 1 14-JUN-23 8CIE 0 JRNL AUTH H.W.ONG,Y.LIANG,W.RICHARDSON,E.R.LOWRY,C.I.WELLS,X.CHEN, JRNL AUTH 2 M.SILVESTRE,K.DEMPSTER,J.A.SILVAROLI,J.L.SMITH,H.WICHTERLE, JRNL AUTH 3 N.S.PABLA,S.K.ULTANIR,A.N.BULLOCK,D.H.DREWRY,A.D.AXTMAN JRNL TITL DISCOVERY OF A POTENT AND SELECTIVE CDKL5/GSK3 CHEMICAL JRNL TITL 2 PROBE THAT IS NEUROPROTECTIVE. JRNL REF ACS CHEM NEUROSCI V. 14 1672 2023 JRNL REFN ESSN 1948-7193 JRNL PMID 37084253 JRNL DOI 10.1021/ACSCHEMNEURO.3C00135 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.289 REMARK 3 R VALUE (WORKING SET) : 0.288 REMARK 3 FREE R VALUE : 0.310 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 786 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.3300 - 4.0000 1.00 2761 121 0.2507 0.2580 REMARK 3 2 4.0000 - 3.1700 1.00 2557 139 0.2689 0.3234 REMARK 3 3 3.1700 - 2.7700 1.00 2539 118 0.3267 0.3541 REMARK 3 4 2.7700 - 2.5200 1.00 2505 133 0.3352 0.3202 REMARK 3 5 2.5200 - 2.3400 1.00 2450 153 0.3496 0.3374 REMARK 3 6 2.3400 - 2.2000 0.99 2473 122 0.3646 0.3788 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.356 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.331 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 2270 REMARK 3 ANGLE : 0.904 3080 REMARK 3 CHIRALITY : 0.057 346 REMARK 3 PLANARITY : 0.007 395 REMARK 3 DIHEDRAL : 6.202 1377 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 14 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.7582 21.1414 8.6682 REMARK 3 T TENSOR REMARK 3 T11: 0.5036 T22: 0.4522 REMARK 3 T33: 0.3484 T12: 0.0218 REMARK 3 T13: 0.1672 T23: 0.0492 REMARK 3 L TENSOR REMARK 3 L11: 9.4602 L22: 8.8675 REMARK 3 L33: 7.2303 L12: 1.0223 REMARK 3 L13: -4.7650 L23: 0.3823 REMARK 3 S TENSOR REMARK 3 S11: -0.7313 S12: -1.0723 S13: -0.4769 REMARK 3 S21: 0.2234 S22: 0.1349 S23: -0.5392 REMARK 3 S31: 1.0797 S32: 0.7483 S33: 0.5953 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 67 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6751 9.5578 -1.9660 REMARK 3 T TENSOR REMARK 3 T11: 1.2458 T22: 0.4619 REMARK 3 T33: 0.7743 T12: 0.0930 REMARK 3 T13: 0.3550 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: -0.0293 L22: 2.4895 REMARK 3 L33: 4.5232 L12: -0.7479 REMARK 3 L13: -0.9717 L23: 2.8223 REMARK 3 S TENSOR REMARK 3 S11: -0.9299 S12: 0.0246 S13: -0.7128 REMARK 3 S21: -0.6928 S22: -0.1847 S23: 0.5060 REMARK 3 S31: 1.3956 S32: -0.0312 S33: 0.8450 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 68 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.6112 16.3482 -0.6652 REMARK 3 T TENSOR REMARK 3 T11: 0.7107 T22: 0.5380 REMARK 3 T33: 0.4853 T12: 0.2190 REMARK 3 T13: 0.1820 T23: 0.0740 REMARK 3 L TENSOR REMARK 3 L11: 2.0492 L22: 5.3079 REMARK 3 L33: 4.8783 L12: -2.3719 REMARK 3 L13: 3.0145 L23: -2.6432 REMARK 3 S TENSOR REMARK 3 S11: -0.5325 S12: -0.3542 S13: -0.6095 REMARK 3 S21: 0.0302 S22: -0.1029 S23: -0.2689 REMARK 3 S31: 1.6887 S32: 1.4797 S33: 0.6041 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 130 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1361 27.9841 -13.6656 REMARK 3 T TENSOR REMARK 3 T11: 0.2969 T22: 0.2567 REMARK 3 T33: 0.2382 T12: -0.0731 REMARK 3 T13: 0.0466 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 4.9894 L22: 2.4874 REMARK 3 L33: 7.2362 L12: 0.6025 REMARK 3 L13: -1.3329 L23: -2.4590 REMARK 3 S TENSOR REMARK 3 S11: -0.0877 S12: -0.4037 S13: 0.2316 REMARK 3 S21: -0.0743 S22: -0.0601 S23: -0.3069 REMARK 3 S31: 0.0227 S32: 0.8492 S33: 0.1936 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 131 THROUGH 172 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0023 17.2861 -10.2288 REMARK 3 T TENSOR REMARK 3 T11: 0.9115 T22: 0.2538 REMARK 3 T33: 0.4695 T12: -0.0421 REMARK 3 T13: 0.2492 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 5.3428 L22: 2.7423 REMARK 3 L33: 4.9981 L12: -1.7156 REMARK 3 L13: -2.5272 L23: 0.2992 REMARK 3 S TENSOR REMARK 3 S11: -0.6901 S12: -0.5379 S13: -1.0645 REMARK 3 S21: -0.0773 S22: -0.0855 S23: 0.3950 REMARK 3 S31: 1.7202 S32: 0.1221 S33: 0.5042 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 173 THROUGH 228 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1875 23.9192 -20.4310 REMARK 3 T TENSOR REMARK 3 T11: 0.6097 T22: 0.5384 REMARK 3 T33: 0.3936 T12: -0.3308 REMARK 3 T13: 0.0842 T23: -0.1514 REMARK 3 L TENSOR REMARK 3 L11: 2.0802 L22: 4.5654 REMARK 3 L33: 7.6656 L12: -0.8065 REMARK 3 L13: -0.2231 L23: 0.7574 REMARK 3 S TENSOR REMARK 3 S11: -0.3537 S12: 0.4583 S13: -0.3136 REMARK 3 S21: -0.2581 S22: 0.1742 S23: 0.2616 REMARK 3 S31: 0.6984 S32: -1.8763 S33: 0.1917 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 229 THROUGH 262 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.4393 22.8166 -28.5993 REMARK 3 T TENSOR REMARK 3 T11: 0.9349 T22: 1.2056 REMARK 3 T33: 0.5419 T12: -0.7495 REMARK 3 T13: -0.0778 T23: -0.0701 REMARK 3 L TENSOR REMARK 3 L11: 2.6873 L22: 1.8587 REMARK 3 L33: 0.2710 L12: 0.3253 REMARK 3 L13: 0.9410 L23: 0.0641 REMARK 3 S TENSOR REMARK 3 S11: 0.0593 S12: 0.6491 S13: -0.1970 REMARK 3 S21: -0.5366 S22: 0.3474 S23: 0.6690 REMARK 3 S31: 0.8773 S32: -1.8805 S33: -0.1565 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 263 THROUGH 304 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0856 26.9978 -27.7495 REMARK 3 T TENSOR REMARK 3 T11: 0.5145 T22: 0.2765 REMARK 3 T33: 0.3824 T12: -0.1152 REMARK 3 T13: 0.1502 T23: -0.0363 REMARK 3 L TENSOR REMARK 3 L11: 4.2398 L22: 5.5656 REMARK 3 L33: 3.3135 L12: 0.6451 REMARK 3 L13: 1.0009 L23: -0.0928 REMARK 3 S TENSOR REMARK 3 S11: -0.3641 S12: 0.4303 S13: -0.3005 REMARK 3 S21: -0.4839 S22: 0.2393 S23: -0.3526 REMARK 3 S31: 0.4315 S32: 0.0639 S33: 0.1273 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8CIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128581. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-22 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) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16108 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 39.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 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) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRI-SODIUM CITRATE, 1.1 M REMARK 280 LITHIUM SULFATE, 0.4 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.75650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.75650 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 65.75650 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 65.75650 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 65.75650 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 65.75650 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 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 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 ILE A 3 REMARK 465 PRO A 4 REMARK 465 ASN A 5 REMARK 465 ILE A 6 REMARK 465 GLY A 7 REMARK 465 ASN A 8 REMARK 465 VAL A 9 REMARK 465 MET A 10 REMARK 465 ASN A 11 REMARK 465 LYS A 12 REMARK 465 ASP A 46 REMARK 465 SER A 47 REMARK 465 GLU A 48 REMARK 465 GLU A 49 REMARK 465 ASN A 50 REMARK 465 GLU A 51 REMARK 465 ARG A 80 REMARK 465 ARG A 81 REMARK 465 ARG A 82 REMARK 465 GLY A 83 REMARK 465 LYS A 84 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 34 CG CD OE1 OE2 REMARK 470 HIS A 36 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 THR A 57 OG1 CG2 REMARK 470 LEU A 58 CG CD1 CD2 REMARK 470 LYS A 62 CG CD CE NZ REMARK 470 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 PHE A 79 CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 ARG A 158 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 164 CG OD1 ND2 REMARK 470 ASN A 167 CG OD1 ND2 REMARK 470 TYR A 188 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 MET A 235 SD CE REMARK 470 LYS A 236 CD CE NZ REMARK 470 ARG A 243 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 247 CG CD1 CD2 REMARK 470 ARG A 248 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 254 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 61 CA - CB - CG ANGL. DEV. = 14.6 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 GLU A 21 -71.27 -136.18 REMARK 500 LYS A 54 -66.93 10.61 REMARK 500 LEU A 67 66.65 -69.85 REMARK 500 MET A 103 79.48 -109.62 REMARK 500 ARG A 134 -5.80 79.56 REMARK 500 ASP A 135 53.72 -140.58 REMARK 500 ASP A 153 74.98 61.72 REMARK 500 GLU A 162 -124.23 47.59 REMARK 500 ALA A 166 -89.74 -106.22 REMARK 500 PRO A 250 73.00 -67.97 REMARK 500 LEU A 302 -73.25 -92.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CIE A 1 303 UNP O76039 CDKL5_HUMAN 1 303 SEQADV 8CIE SER A 0 UNP O76039 EXPRESSION TAG SEQADV 8CIE ASP A 169 UNP O76039 THR 169 CONFLICT SEQADV 8CIE GLU A 171 UNP O76039 TYR 171 CONFLICT SEQRES 1 A 304 SER MET LYS ILE PRO ASN ILE GLY ASN VAL MET ASN LYS SEQRES 2 A 304 PHE GLU ILE LEU GLY VAL VAL GLY GLU GLY ALA TYR GLY SEQRES 3 A 304 VAL VAL LEU LYS CYS ARG HIS LYS GLU THR HIS GLU ILE SEQRES 4 A 304 VAL ALA ILE LYS LYS PHE LYS ASP SER GLU GLU ASN GLU SEQRES 5 A 304 GLU VAL LYS GLU THR THR LEU ARG GLU LEU LYS MET LEU SEQRES 6 A 304 ARG THR LEU LYS GLN GLU ASN ILE VAL GLU LEU LYS GLU SEQRES 7 A 304 ALA PHE ARG ARG ARG GLY LYS LEU TYR LEU VAL PHE GLU SEQRES 8 A 304 TYR VAL GLU LYS ASN MET LEU GLU LEU LEU GLU GLU MET SEQRES 9 A 304 PRO ASN GLY VAL PRO PRO GLU LYS VAL LYS SER TYR ILE SEQRES 10 A 304 TYR GLN LEU ILE LYS ALA ILE HIS TRP CYS HIS LYS ASN SEQRES 11 A 304 ASP ILE VAL HIS ARG ASP ILE LYS PRO GLU ASN LEU LEU SEQRES 12 A 304 ILE SER HIS ASN ASP VAL LEU LYS LEU CYS ASP PHE GLY SEQRES 13 A 304 PHE ALA ARG ASN LEU SER GLU GLY ASN ASN ALA ASN TYR SEQRES 14 A 304 ASP GLU GLU VAL ALA THR ARG TRP TYR ARG SER PRO GLU SEQRES 15 A 304 LEU LEU LEU GLY ALA PRO TYR GLY LYS SER VAL ASP MET SEQRES 16 A 304 TRP SER VAL GLY CYS ILE LEU GLY GLU LEU SER ASP GLY SEQRES 17 A 304 GLN PRO LEU PHE PRO GLY GLU SER GLU ILE ASP GLN LEU SEQRES 18 A 304 PHE THR ILE GLN LYS VAL LEU GLY PRO LEU PRO SER GLU SEQRES 19 A 304 GLN MET LYS LEU PHE TYR SER ASN PRO ARG PHE HIS GLY SEQRES 20 A 304 LEU ARG PHE PRO ALA VAL ASN HIS PRO GLN SER LEU GLU SEQRES 21 A 304 ARG ARG TYR LEU GLY ILE LEU ASN SER VAL LEU LEU ASP SEQRES 22 A 304 LEU MET LYS ASN LEU LEU LYS LEU ASP PRO ALA ASP ARG SEQRES 23 A 304 TYR LEU THR GLU GLN CYS LEU ASN HIS PRO THR PHE GLN SEQRES 24 A 304 THR GLN ARG LEU LEU HET US0 A 401 25 HET SO4 A 402 5 HETNAM US0 4-[[3,5-BIS(FLUORANYL)PHENYL]CARBONYLAMINO]-~{N}- HETNAM 2 US0 PIPERIDIN-4-YL-1~{H}-PYRAZOLE-3-CARBOXAMIDE HETNAM SO4 SULFATE ION FORMUL 2 US0 C16 H17 F2 N5 O2 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *37(H2 O) HELIX 1 AA1 THR A 56 LEU A 67 1 12 HELIX 2 AA2 MET A 96 MET A 103 1 8 HELIX 3 AA3 PRO A 108 ASN A 129 1 22 HELIX 4 AA4 LYS A 137 GLU A 139 5 3 HELIX 5 AA5 GLU A 171 TRP A 176 1 6 HELIX 6 AA6 SER A 179 GLY A 185 1 7 HELIX 7 AA7 GLY A 189 GLY A 207 1 19 HELIX 8 AA8 SER A 215 GLY A 228 1 14 HELIX 9 AA9 PRO A 231 TYR A 239 1 9 HELIX 10 AB1 SER A 240 HIS A 245 5 6 HELIX 11 AB2 SER A 257 TYR A 262 1 6 HELIX 12 AB3 ASN A 267 LEU A 278 1 12 HELIX 13 AB4 ASP A 281 ARG A 285 5 5 HELIX 14 AB5 LEU A 287 ASN A 293 1 7 HELIX 15 AB6 HIS A 294 GLN A 298 5 5 SHEET 1 AA1 5 GLU A 14 GLY A 20 0 SHEET 2 AA1 5 VAL A 26 ARG A 31 -1 O LYS A 29 N LEU A 16 SHEET 3 AA1 5 ILE A 38 LYS A 43 -1 O LYS A 43 N VAL A 26 SHEET 4 AA1 5 LEU A 87 GLU A 90 -1 O PHE A 89 N ALA A 40 SHEET 5 AA1 5 LEU A 75 ALA A 78 -1 N GLU A 77 O VAL A 88 SHEET 1 AA2 3 LYS A 94 ASN A 95 0 SHEET 2 AA2 3 LEU A 141 ILE A 143 -1 O ILE A 143 N LYS A 94 SHEET 3 AA2 3 LEU A 149 LEU A 151 -1 O LYS A 150 N LEU A 142 SHEET 1 AA3 2 ILE A 131 VAL A 132 0 SHEET 2 AA3 2 ARG A 158 ASN A 159 -1 O ARG A 158 N VAL A 132 CRYST1 88.660 88.660 131.513 90.00 90.00 120.00 P 63 2 2 12 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 0.011279 0.006512 0.000000 0.00000 SCALE2 0.000000 0.013024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007604 0.00000