HEADER TRANSFERASE 07-SEP-21 7VDS TITLE THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 5 (CDK5) IN COMPLEX WITH P25 TITLE 2 AND COMPOUND 24 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT-LIKE KINASE 5, P25; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CELL DIVISION PROTEIN KINASE 5; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CYCLIN-DEPENDENT KINASE 5 ACTIVATOR 1; COMPND 9 CHAIN: C, D; COMPND 10 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: CDK5, CDKN5; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; 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: PFASTBAC1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: CDK5R1, CDK5R, NCK5A; SOURCE 16 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PFASTBAC1 KEYWDS CDK5, P25, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.MALOJCIC,S.L.CLUGSTON,M.DANIELS,J.C.HARMANGE,M.LEDEBORER REVDAT 2 29-NOV-23 7VDS 1 REMARK REVDAT 1 09-MAR-22 7VDS 0 JRNL AUTH M.H.DANIELS,G.MALOJCIC,S.L.CLUGSTON,B.WILLIAMS, JRNL AUTH 2 M.COEFFET-LE GAL,X.R.PAN-ZHOU,S.VENKATACHALAN,J.C.HARMANGE, JRNL AUTH 3 M.LEDEBOER JRNL TITL DISCOVERY AND OPTIMIZATION OF HIGHLY SELECTIVE INHIBITORS OF JRNL TITL 2 CDK5. JRNL REF J.MED.CHEM. V. 65 3575 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35143203 JRNL DOI 10.1021/ACS.JMEDCHEM.1C02069 REMARK 2 REMARK 2 RESOLUTION. 3.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22918 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1207 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) : 3.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1692 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6952 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 183 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 133.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.44000 REMARK 3 B12 (A**2) : -0.07000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.473 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.408 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.569 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7268 ; 0.003 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6994 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9795 ; 1.244 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16125 ; 1.048 ; 1.586 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 860 ; 6.043 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 377 ;33.246 ;21.936 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1263 ;15.435 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 49 ;16.620 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 890 ; 0.047 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7979 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1654 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 11 287 B 4 287 8275 0.130 0.050 REMARK 3 2 C 147 292 D 147 292 4395 0.140 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7VDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300024447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12713 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24161 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050 REMARK 200 RESOLUTION RANGE LOW (A) : 48.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.10 REMARK 200 R MERGE (I) : 0.14400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 18.60 REMARK 200 R MERGE FOR SHELL (I) : 2.56500 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: PHASER REMARK 200 STARTING MODEL: 3O0G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 5.5, 0.3M MGCL2, 20% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 102.46000 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 51.23000 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 51.23000 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 102.46000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 8610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -140.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 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: 3150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 1 REMARK 465 PRO A 292 REMARK 465 SER B 1 REMARK 465 GLN B 2 REMARK 465 GLU B 8 REMARK 465 LYS B 9 REMARK 465 ILE B 10 REMARK 465 GLY B 11 REMARK 465 GLU B 12 REMARK 465 GLY B 13 REMARK 465 THR B 14 REMARK 465 TYR B 15 REMARK 465 PHE B 289 REMARK 465 CYS B 290 REMARK 465 PRO B 291 REMARK 465 PRO B 292 REMARK 465 MET C 99 REMARK 465 GLN C 100 REMARK 465 PRO C 101 REMARK 465 PRO C 102 REMARK 465 PRO C 103 REMARK 465 ALA C 104 REMARK 465 GLN C 105 REMARK 465 PRO C 106 REMARK 465 PRO C 107 REMARK 465 ALA C 108 REMARK 465 PRO C 109 REMARK 465 PRO C 110 REMARK 465 ALA C 111 REMARK 465 SER C 112 REMARK 465 GLN C 113 REMARK 465 LEU C 114 REMARK 465 SER C 115 REMARK 465 GLY C 116 REMARK 465 SER C 117 REMARK 465 GLN C 118 REMARK 465 THR C 119 REMARK 465 GLY C 120 REMARK 465 GLY C 121 REMARK 465 SER C 122 REMARK 465 SER C 123 REMARK 465 SER C 124 REMARK 465 VAL C 125 REMARK 465 LYS C 126 REMARK 465 LYS C 127 REMARK 465 ALA C 128 REMARK 465 PRO C 129 REMARK 465 HIS C 130 REMARK 465 PRO C 131 REMARK 465 ALA C 132 REMARK 465 VAL C 133 REMARK 465 THR C 134 REMARK 465 SER C 135 REMARK 465 ALA C 136 REMARK 465 GLY C 137 REMARK 465 THR C 138 REMARK 465 PRO C 139 REMARK 465 LYS C 140 REMARK 465 ARG C 141 REMARK 465 VAL C 142 REMARK 465 ILE C 143 REMARK 465 VAL C 144 REMARK 465 GLN C 145 REMARK 465 GLY C 294 REMARK 465 GLN C 295 REMARK 465 GLU C 296 REMARK 465 ASP C 297 REMARK 465 LYS C 298 REMARK 465 LYS C 299 REMARK 465 ARG C 300 REMARK 465 LEU C 301 REMARK 465 LEU C 302 REMARK 465 LEU C 303 REMARK 465 GLY C 304 REMARK 465 LEU C 305 REMARK 465 ASP C 306 REMARK 465 ARG C 307 REMARK 465 MET D 99 REMARK 465 GLN D 100 REMARK 465 PRO D 101 REMARK 465 PRO D 102 REMARK 465 PRO D 103 REMARK 465 ALA D 104 REMARK 465 GLN D 105 REMARK 465 PRO D 106 REMARK 465 PRO D 107 REMARK 465 ALA D 108 REMARK 465 PRO D 109 REMARK 465 PRO D 110 REMARK 465 ALA D 111 REMARK 465 SER D 112 REMARK 465 GLN D 113 REMARK 465 LEU D 114 REMARK 465 SER D 115 REMARK 465 GLY D 116 REMARK 465 SER D 117 REMARK 465 GLN D 118 REMARK 465 THR D 119 REMARK 465 GLY D 120 REMARK 465 GLY D 121 REMARK 465 SER D 122 REMARK 465 SER D 123 REMARK 465 SER D 124 REMARK 465 VAL D 125 REMARK 465 LYS D 126 REMARK 465 LYS D 127 REMARK 465 ALA D 128 REMARK 465 PRO D 129 REMARK 465 HIS D 130 REMARK 465 PRO D 131 REMARK 465 ALA D 132 REMARK 465 VAL D 133 REMARK 465 THR D 134 REMARK 465 SER D 135 REMARK 465 ALA D 136 REMARK 465 GLY D 137 REMARK 465 THR D 138 REMARK 465 PRO D 139 REMARK 465 LYS D 140 REMARK 465 ARG D 141 REMARK 465 VAL D 142 REMARK 465 ILE D 143 REMARK 465 VAL D 144 REMARK 465 GLN D 145 REMARK 465 ALA D 146 REMARK 465 GLY D 294 REMARK 465 GLN D 295 REMARK 465 GLU D 296 REMARK 465 ASP D 297 REMARK 465 LYS D 298 REMARK 465 LYS D 299 REMARK 465 ARG D 300 REMARK 465 LEU D 301 REMARK 465 LEU D 302 REMARK 465 LEU D 303 REMARK 465 GLY D 304 REMARK 465 LEU D 305 REMARK 465 ASP D 306 REMARK 465 ARG D 307 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 42 -166.41 -77.44 REMARK 500 ASP A 73 60.10 32.82 REMARK 500 ASP A 126 39.46 -159.28 REMARK 500 LYS A 128 157.92 175.92 REMARK 500 ASP A 144 88.94 65.97 REMARK 500 VAL A 163 134.42 77.03 REMARK 500 LEU A 165 -38.26 -38.57 REMARK 500 SER A 180 -157.37 -98.10 REMARK 500 ASN A 197 -132.41 -128.40 REMARK 500 TRP A 227 77.78 -155.17 REMARK 500 LEU A 267 43.66 -100.53 REMARK 500 ASP B 38 -71.84 -92.40 REMARK 500 ASP B 40 51.45 31.33 REMARK 500 GLU B 42 65.37 75.01 REMARK 500 ASP B 73 106.31 -28.37 REMARK 500 ASP B 126 40.93 -160.56 REMARK 500 LYS B 128 159.00 176.73 REMARK 500 ASP B 144 91.71 68.25 REMARK 500 VAL B 163 135.45 76.98 REMARK 500 LEU B 165 -39.34 -39.47 REMARK 500 SER B 180 -156.28 -99.21 REMARK 500 ASN B 197 -131.67 -127.74 REMARK 500 TRP B 227 77.93 -153.57 REMARK 500 THR B 245 44.56 -101.07 REMARK 500 SER B 247 -45.21 82.27 REMARK 500 LEU B 248 -3.94 94.79 REMARK 500 LEU B 267 43.85 -101.12 REMARK 500 CYS C 163 72.97 -100.16 REMARK 500 PRO C 171 2.41 -67.55 REMARK 500 ILE C 196 93.07 -69.56 REMARK 500 CYS C 253 97.02 -68.80 REMARK 500 SER D 170 83.11 34.65 REMARK 500 PRO D 171 6.84 -69.98 REMARK 500 ILE D 196 92.93 -68.75 REMARK 500 SER D 242 88.00 -170.02 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 A 448 DISTANCE = 6.96 ANGSTROMS DBREF 7VDS A 2 292 UNP Q00535 CDK5_HUMAN 2 292 DBREF 7VDS B 2 292 UNP Q00535 CDK5_HUMAN 2 292 DBREF 7VDS C 100 307 UNP Q15078 CD5R1_HUMAN 100 307 DBREF 7VDS D 100 307 UNP Q15078 CD5R1_HUMAN 100 307 SEQADV 7VDS SER A 1 UNP Q00535 EXPRESSION TAG SEQADV 7VDS SER B 1 UNP Q00535 EXPRESSION TAG SEQADV 7VDS MET C 99 UNP Q15078 INITIATING METHIONINE SEQADV 7VDS MET D 99 UNP Q15078 INITIATING METHIONINE SEQRES 1 A 292 SER GLN LYS TYR GLU LYS LEU GLU LYS ILE GLY GLU GLY SEQRES 2 A 292 THR TYR GLY THR VAL PHE LYS ALA LYS ASN ARG GLU THR SEQRES 3 A 292 HIS GLU ILE VAL ALA LEU LYS ARG VAL ARG LEU ASP ASP SEQRES 4 A 292 ASP ASP GLU GLY VAL PRO SER SER ALA LEU ARG GLU ILE SEQRES 5 A 292 CYS LEU LEU LYS GLU LEU LYS HIS LYS ASN ILE VAL ARG SEQRES 6 A 292 LEU HIS ASP VAL LEU HIS SER ASP LYS LYS LEU THR LEU SEQRES 7 A 292 VAL PHE GLU PHE CYS ASP GLN ASP LEU LYS LYS TYR PHE SEQRES 8 A 292 ASP SER CYS ASN GLY ASP LEU ASP PRO GLU ILE VAL LYS SEQRES 9 A 292 SER PHE LEU PHE GLN LEU LEU LYS GLY LEU GLY PHE CYS SEQRES 10 A 292 HIS SER ARG ASN VAL LEU HIS ARG ASP LEU LYS PRO GLN SEQRES 11 A 292 ASN LEU LEU ILE ASN ARG ASN GLY GLU LEU LYS LEU ALA SEQRES 12 A 292 ASP PHE GLY LEU ALA ARG ALA PHE GLY ILE PRO VAL ARG SEQRES 13 A 292 CYS TYR SER ALA GLU VAL VAL THR LEU TRP TYR ARG PRO SEQRES 14 A 292 PRO ASP VAL LEU PHE GLY ALA LYS LEU TYR SER THR SER SEQRES 15 A 292 ILE ASP MET TRP SER ALA GLY CYS ILE PHE ALA GLU LEU SEQRES 16 A 292 ALA ASN ALA GLY ARG PRO LEU PHE PRO GLY ASN ASP VAL SEQRES 17 A 292 ASP ASP GLN LEU LYS ARG ILE PHE ARG LEU LEU GLY THR SEQRES 18 A 292 PRO THR GLU GLU GLN TRP PRO SER MET THR LYS LEU PRO SEQRES 19 A 292 ASP TYR LYS PRO TYR PRO MET TYR PRO ALA THR THR SER SEQRES 20 A 292 LEU VAL ASN VAL VAL PRO LYS LEU ASN ALA THR GLY ARG SEQRES 21 A 292 ASP LEU LEU GLN ASN LEU LEU LYS CYS ASN PRO VAL GLN SEQRES 22 A 292 ARG ILE SER ALA GLU GLU ALA LEU GLN HIS PRO TYR PHE SEQRES 23 A 292 SER ASP PHE CYS PRO PRO SEQRES 1 B 292 SER GLN LYS TYR GLU LYS LEU GLU LYS ILE GLY GLU GLY SEQRES 2 B 292 THR TYR GLY THR VAL PHE LYS ALA LYS ASN ARG GLU THR SEQRES 3 B 292 HIS GLU ILE VAL ALA LEU LYS ARG VAL ARG LEU ASP ASP SEQRES 4 B 292 ASP ASP GLU GLY VAL PRO SER SER ALA LEU ARG GLU ILE SEQRES 5 B 292 CYS LEU LEU LYS GLU LEU LYS HIS LYS ASN ILE VAL ARG SEQRES 6 B 292 LEU HIS ASP VAL LEU HIS SER ASP LYS LYS LEU THR LEU SEQRES 7 B 292 VAL PHE GLU PHE CYS ASP GLN ASP LEU LYS LYS TYR PHE SEQRES 8 B 292 ASP SER CYS ASN GLY ASP LEU ASP PRO GLU ILE VAL LYS SEQRES 9 B 292 SER PHE LEU PHE GLN LEU LEU LYS GLY LEU GLY PHE CYS SEQRES 10 B 292 HIS SER ARG ASN VAL LEU HIS ARG ASP LEU LYS PRO GLN SEQRES 11 B 292 ASN LEU LEU ILE ASN ARG ASN GLY GLU LEU LYS LEU ALA SEQRES 12 B 292 ASP PHE GLY LEU ALA ARG ALA PHE GLY ILE PRO VAL ARG SEQRES 13 B 292 CYS TYR SER ALA GLU VAL VAL THR LEU TRP TYR ARG PRO SEQRES 14 B 292 PRO ASP VAL LEU PHE GLY ALA LYS LEU TYR SER THR SER SEQRES 15 B 292 ILE ASP MET TRP SER ALA GLY CYS ILE PHE ALA GLU LEU SEQRES 16 B 292 ALA ASN ALA GLY ARG PRO LEU PHE PRO GLY ASN ASP VAL SEQRES 17 B 292 ASP ASP GLN LEU LYS ARG ILE PHE ARG LEU LEU GLY THR SEQRES 18 B 292 PRO THR GLU GLU GLN TRP PRO SER MET THR LYS LEU PRO SEQRES 19 B 292 ASP TYR LYS PRO TYR PRO MET TYR PRO ALA THR THR SER SEQRES 20 B 292 LEU VAL ASN VAL VAL PRO LYS LEU ASN ALA THR GLY ARG SEQRES 21 B 292 ASP LEU LEU GLN ASN LEU LEU LYS CYS ASN PRO VAL GLN SEQRES 22 B 292 ARG ILE SER ALA GLU GLU ALA LEU GLN HIS PRO TYR PHE SEQRES 23 B 292 SER ASP PHE CYS PRO PRO SEQRES 1 C 209 MET GLN PRO PRO PRO ALA GLN PRO PRO ALA PRO PRO ALA SEQRES 2 C 209 SER GLN LEU SER GLY SER GLN THR GLY GLY SER SER SER SEQRES 3 C 209 VAL LYS LYS ALA PRO HIS PRO ALA VAL THR SER ALA GLY SEQRES 4 C 209 THR PRO LYS ARG VAL ILE VAL GLN ALA SER THR SER GLU SEQRES 5 C 209 LEU LEU ARG CYS LEU GLY GLU PHE LEU CYS ARG ARG CYS SEQRES 6 C 209 TYR ARG LEU LYS HIS LEU SER PRO THR ASP PRO VAL LEU SEQRES 7 C 209 TRP LEU ARG SER VAL ASP ARG SER LEU LEU LEU GLN GLY SEQRES 8 C 209 TRP GLN ASP GLN GLY PHE ILE THR PRO ALA ASN VAL VAL SEQRES 9 C 209 PHE LEU TYR MET LEU CYS ARG ASP VAL ILE SER SER GLU SEQRES 10 C 209 VAL GLY SER ASP HIS GLU LEU GLN ALA VAL LEU LEU THR SEQRES 11 C 209 CYS LEU TYR LEU SER TYR SER TYR MET GLY ASN GLU ILE SEQRES 12 C 209 SER TYR PRO LEU LYS PRO PHE LEU VAL GLU SER CYS LYS SEQRES 13 C 209 GLU ALA PHE TRP ASP ARG CYS LEU SER VAL ILE ASN LEU SEQRES 14 C 209 MET SER SER LYS MET LEU GLN ILE ASN ALA ASP PRO HIS SEQRES 15 C 209 TYR PHE THR GLN VAL PHE SER ASP LEU LYS ASN GLU SER SEQRES 16 C 209 GLY GLN GLU ASP LYS LYS ARG LEU LEU LEU GLY LEU ASP SEQRES 17 C 209 ARG SEQRES 1 D 209 MET GLN PRO PRO PRO ALA GLN PRO PRO ALA PRO PRO ALA SEQRES 2 D 209 SER GLN LEU SER GLY SER GLN THR GLY GLY SER SER SER SEQRES 3 D 209 VAL LYS LYS ALA PRO HIS PRO ALA VAL THR SER ALA GLY SEQRES 4 D 209 THR PRO LYS ARG VAL ILE VAL GLN ALA SER THR SER GLU SEQRES 5 D 209 LEU LEU ARG CYS LEU GLY GLU PHE LEU CYS ARG ARG CYS SEQRES 6 D 209 TYR ARG LEU LYS HIS LEU SER PRO THR ASP PRO VAL LEU SEQRES 7 D 209 TRP LEU ARG SER VAL ASP ARG SER LEU LEU LEU GLN GLY SEQRES 8 D 209 TRP GLN ASP GLN GLY PHE ILE THR PRO ALA ASN VAL VAL SEQRES 9 D 209 PHE LEU TYR MET LEU CYS ARG ASP VAL ILE SER SER GLU SEQRES 10 D 209 VAL GLY SER ASP HIS GLU LEU GLN ALA VAL LEU LEU THR SEQRES 11 D 209 CYS LEU TYR LEU SER TYR SER TYR MET GLY ASN GLU ILE SEQRES 12 D 209 SER TYR PRO LEU LYS PRO PHE LEU VAL GLU SER CYS LYS SEQRES 13 D 209 GLU ALA PHE TRP ASP ARG CYS LEU SER VAL ILE ASN LEU SEQRES 14 D 209 MET SER SER LYS MET LEU GLN ILE ASN ALA ASP PRO HIS SEQRES 15 D 209 TYR PHE THR GLN VAL PHE SER ASP LEU LYS ASN GLU SER SEQRES 16 D 209 GLY GLN GLU ASP LYS LYS ARG LEU LEU LEU GLY LEU ASP SEQRES 17 D 209 ARG HET 61U A 301 36 HET GOL A 302 6 HET GOL A 303 6 HET GOL A 304 6 HET GOL A 305 6 HET GOL A 306 6 HET GOL A 307 6 HET GOL A 308 6 HET EDO A 309 4 HET EDO A 310 4 HET EDO A 311 4 HET EDO A 312 4 HET EDO A 313 4 HET EDO A 314 4 HET EDO A 315 4 HET EDO A 316 4 HET EDO A 317 4 HET CL A 318 1 HET CL A 319 1 HET CL A 320 1 HET CL A 321 1 HET CL A 322 1 HET CL A 323 1 HET CL A 324 1 HET CL A 325 1 HET CL A 326 1 HET CL A 327 1 HET EDO B 301 4 HET EDO B 302 4 HET EDO B 303 4 HET GOL C 401 6 HET EDO C 402 4 HET EDO C 403 4 HET EDO C 404 4 HET EDO C 405 4 HET EDO C 406 4 HET EDO C 407 4 HET EDO C 408 4 HET EDO C 409 4 HET CL C 410 1 HET CL C 411 1 HET CL C 412 1 HET CL C 413 1 HET CL C 414 1 HET CL C 415 1 HET CL C 416 1 HET CL C 417 1 HET CL C 418 1 HETNAM 61U 5-FLUORANYL-4-[[2-[(1R)-1-(1-METHYLPIPERIDIN-4-YL)-1- HETNAM 2 61U OXIDANYL-ETHYL]-1,6-NAPHTHYRIDIN-7-YL]AMINO]-2- HETNAM 3 61U MORPHOLIN-4-YL-BENZENECARBONITRILE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 61U C27 H31 F N6 O2 FORMUL 6 GOL 8(C3 H8 O3) FORMUL 13 EDO 20(C2 H6 O2) FORMUL 22 CL 19(CL 1-) FORMUL 53 HOH *69(H2 O) HELIX 1 AA1 GLY A 43 LYS A 56 1 14 HELIX 2 AA2 LEU A 87 CYS A 94 1 8 HELIX 3 AA3 ASP A 99 ARG A 120 1 22 HELIX 4 AA4 LYS A 128 GLN A 130 5 3 HELIX 5 AA5 THR A 164 ARG A 168 5 5 HELIX 6 AA6 PRO A 169 PHE A 174 1 6 HELIX 7 AA7 THR A 181 ALA A 196 1 16 HELIX 8 AA8 ASP A 207 GLY A 220 1 14 HELIX 9 AA9 SER A 229 LEU A 233 5 5 HELIX 10 AB1 ASN A 256 LEU A 267 1 12 HELIX 11 AB2 ASN A 270 ARG A 274 5 5 HELIX 12 AB3 SER A 276 GLN A 282 1 7 HELIX 13 AB4 HIS A 283 SER A 287 5 5 HELIX 14 AB5 GLY B 43 LYS B 56 1 14 HELIX 15 AB6 LEU B 87 CYS B 94 1 8 HELIX 16 AB7 ASP B 99 ARG B 120 1 22 HELIX 17 AB8 LYS B 128 GLN B 130 5 3 HELIX 18 AB9 THR B 164 ARG B 168 5 5 HELIX 19 AC1 PRO B 169 PHE B 174 1 6 HELIX 20 AC2 THR B 181 ALA B 196 1 16 HELIX 21 AC3 ASP B 207 GLY B 220 1 14 HELIX 22 AC4 SER B 229 LEU B 233 5 5 HELIX 23 AC5 ASN B 256 LEU B 267 1 12 HELIX 24 AC6 ASN B 270 ARG B 274 5 5 HELIX 25 AC7 SER B 276 GLN B 282 1 7 HELIX 26 AC8 HIS B 283 SER B 287 5 5 HELIX 27 AC9 SER C 147 CYS C 163 1 17 HELIX 28 AD1 THR C 172 GLN C 188 1 17 HELIX 29 AD2 THR C 197 ILE C 212 1 16 HELIX 30 AD3 SER C 218 GLY C 238 1 21 HELIX 31 AD4 CYS C 253 ASP C 278 1 26 HELIX 32 AD5 ASP C 278 ASN C 291 1 14 HELIX 33 AD6 THR D 148 CYS D 163 1 16 HELIX 34 AD7 PRO D 171 GLN D 188 1 18 HELIX 35 AD8 THR D 197 ILE D 212 1 16 HELIX 36 AD9 SER D 218 GLY D 238 1 21 HELIX 37 AE1 CYS D 253 ASP D 278 1 26 HELIX 38 AE2 ASP D 278 ASN D 291 1 14 SHEET 1 AA1 5 TYR A 4 GLU A 12 0 SHEET 2 AA1 5 THR A 17 ASN A 23 -1 O LYS A 20 N GLU A 8 SHEET 3 AA1 5 ILE A 29 ARG A 36 -1 O ARG A 34 N THR A 17 SHEET 4 AA1 5 LYS A 75 GLU A 81 -1 O LEU A 76 N VAL A 35 SHEET 5 AA1 5 LEU A 66 SER A 72 -1 N HIS A 67 O VAL A 79 SHEET 1 AA2 3 GLN A 85 ASP A 86 0 SHEET 2 AA2 3 LEU A 132 ILE A 134 -1 O ILE A 134 N GLN A 85 SHEET 3 AA2 3 LEU A 140 LEU A 142 -1 O LYS A 141 N LEU A 133 SHEET 1 AA3 2 VAL A 122 LEU A 123 0 SHEET 2 AA3 2 ARG A 149 ALA A 150 -1 O ARG A 149 N LEU A 123 SHEET 1 AA4 5 TYR B 4 LYS B 6 0 SHEET 2 AA4 5 THR B 17 ASN B 23 -1 O LYS B 22 N GLU B 5 SHEET 3 AA4 5 ILE B 29 VAL B 35 -1 O ARG B 34 N THR B 17 SHEET 4 AA4 5 LYS B 75 GLU B 81 -1 O LEU B 76 N VAL B 35 SHEET 5 AA4 5 LEU B 66 SER B 72 -1 N HIS B 67 O VAL B 79 SHEET 1 AA5 3 GLN B 85 ASP B 86 0 SHEET 2 AA5 3 LEU B 132 ILE B 134 -1 O ILE B 134 N GLN B 85 SHEET 3 AA5 3 LEU B 140 LEU B 142 -1 O LYS B 141 N LEU B 133 SHEET 1 AA6 2 VAL B 122 LEU B 123 0 SHEET 2 AA6 2 ARG B 149 ALA B 150 -1 O ARG B 149 N LEU B 123 CRYST1 118.060 118.060 153.690 90.00 90.00 120.00 P 32 2 1 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 0.008470 0.004890 0.000000 0.00000 SCALE2 0.000000 0.009781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006507 0.00000