HEADER TRANSFERASE 14-APR-20 6YNR TITLE CRYSTAL STRUCTURE OF THE CAMP-DEPENDENT PROTEIN KINASE A IN COMPLEX TITLE 2 WITH 1,7-NAPHTHYRIDIN-8-AMINE (SOAKED) AND PKI (5-24) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PKA C-ALPHA; COMPND 5 EC: 2.7.11.11; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: PKI-ALPHA,CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, COMPND 11 MUSCLE/BRAIN ISOFORM; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRICETULUS GRISEUS; SOURCE 3 ORGANISM_COMMON: CHINESE HAMSTER; SOURCE 4 ORGANISM_TAXID: 10029; SOURCE 5 GENE: PRKACA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 12 ORGANISM_TAXID: 10090 KEYWDS PHOSPHOTRANSFERASE, SIGNALLING PATHWAYS, GLYCOGEN METABOLISM, KEYWDS 2 SERINE/THREONINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.OEBBEKE,A.HEINE,G.KLEBE REVDAT 4 24-JAN-24 6YNR 1 REMARK REVDAT 3 20-JAN-21 6YNR 1 JRNL REVDAT 2 21-OCT-20 6YNR 1 JRNL REVDAT 1 14-OCT-20 6YNR 0 JRNL AUTH B.WIENEN-SCHMIDT,M.OEBBEKE,K.NGO,A.HEINE,G.KLEBE JRNL TITL TWO METHODS, ONE GOAL: STRUCTURAL DIFFERENCES BETWEEN JRNL TITL 2 COCRYSTALLIZATION AND CRYSTAL SOAKING TO DISCOVER LIGAND JRNL TITL 3 BINDING POSES. JRNL REF CHEMMEDCHEM V. 16 292 2021 JRNL REFN ESSN 1860-7187 JRNL PMID 33029876 JRNL DOI 10.1002/CMDC.202000565 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 34586 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1730 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 43.5400 - 4.3400 0.99 2893 153 0.1850 0.1818 REMARK 3 2 4.3400 - 3.4500 0.99 2800 147 0.1688 0.2044 REMARK 3 3 3.4500 - 3.0100 0.99 2764 146 0.1909 0.2349 REMARK 3 4 3.0100 - 2.7400 0.99 2738 144 0.1965 0.2488 REMARK 3 5 2.7400 - 2.5400 1.00 2742 144 0.1948 0.2306 REMARK 3 6 2.5400 - 2.3900 1.00 2731 144 0.1797 0.2486 REMARK 3 7 2.3900 - 2.2700 1.00 2731 144 0.1769 0.2234 REMARK 3 8 2.2700 - 2.1700 0.99 2720 143 0.1873 0.2234 REMARK 3 9 2.1700 - 2.0900 0.99 2720 143 0.1846 0.2364 REMARK 3 10 2.0900 - 2.0200 0.99 2665 140 0.1994 0.2385 REMARK 3 11 2.0200 - 1.9500 1.00 2703 143 0.2148 0.2675 REMARK 3 12 1.9500 - 1.9000 0.97 2649 139 0.2592 0.2870 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.063 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.92 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 : 0.006 2974 REMARK 3 ANGLE : 0.727 4038 REMARK 3 CHIRALITY : 0.050 432 REMARK 3 PLANARITY : 0.005 531 REMARK 3 DIHEDRAL : 20.437 1071 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 54 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.8412 -9.3234 9.3332 REMARK 3 T TENSOR REMARK 3 T11: 0.1357 T22: 0.2494 REMARK 3 T33: 0.2287 T12: -0.0215 REMARK 3 T13: 0.0159 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 0.4462 L22: 1.1075 REMARK 3 L33: 1.1723 L12: 0.4430 REMARK 3 L13: 0.2599 L23: -0.0787 REMARK 3 S TENSOR REMARK 3 S11: 0.0110 S12: 0.0085 S13: -0.0760 REMARK 3 S21: 0.1066 S22: 0.0107 S23: 0.1279 REMARK 3 S31: -0.0053 S32: -0.2431 S33: -0.0369 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 55 THROUGH 81 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.7067 -19.2095 -0.1826 REMARK 3 T TENSOR REMARK 3 T11: 0.1389 T22: 0.2170 REMARK 3 T33: 0.2019 T12: -0.0328 REMARK 3 T13: 0.0106 T23: -0.0216 REMARK 3 L TENSOR REMARK 3 L11: 0.6797 L22: 0.6250 REMARK 3 L33: 1.3174 L12: 0.0672 REMARK 3 L13: 0.3824 L23: -0.3620 REMARK 3 S TENSOR REMARK 3 S11: -0.1292 S12: 0.0837 S13: -0.1740 REMARK 3 S21: -0.1724 S22: 0.1326 S23: 0.0016 REMARK 3 S31: 0.1755 S32: -0.0532 S33: 0.0022 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 82 THROUGH 252 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.6540 -0.4491 2.9153 REMARK 3 T TENSOR REMARK 3 T11: 0.1628 T22: 0.1690 REMARK 3 T33: 0.1571 T12: -0.0077 REMARK 3 T13: -0.0052 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 0.6228 L22: 1.1861 REMARK 3 L33: 1.6740 L12: 0.1564 REMARK 3 L13: -0.1489 L23: -0.8966 REMARK 3 S TENSOR REMARK 3 S11: 0.0001 S12: 0.0289 S13: 0.0142 REMARK 3 S21: 0.0373 S22: -0.0207 S23: 0.0052 REMARK 3 S31: -0.1813 S32: 0.0474 S33: 0.0136 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 253 THROUGH 350 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.8328 3.4741 0.1774 REMARK 3 T TENSOR REMARK 3 T11: 0.1775 T22: 0.2055 REMARK 3 T33: 0.1671 T12: 0.0175 REMARK 3 T13: 0.0080 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.8094 L22: 1.3205 REMARK 3 L33: 1.8092 L12: 0.2966 REMARK 3 L13: -0.0388 L23: -0.3080 REMARK 3 S TENSOR REMARK 3 S11: -0.0156 S12: 0.0583 S13: 0.0865 REMARK 3 S21: -0.0296 S22: 0.0279 S23: 0.0687 REMARK 3 S31: -0.3653 S32: -0.1010 S33: -0.0208 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 5 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.9200 8.1334 -16.1240 REMARK 3 T TENSOR REMARK 3 T11: 0.2022 T22: 0.2621 REMARK 3 T33: 0.1776 T12: -0.0313 REMARK 3 T13: -0.0202 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 1.7709 L22: 6.5416 REMARK 3 L33: 1.4979 L12: 0.4825 REMARK 3 L13: -1.3778 L23: -0.9374 REMARK 3 S TENSOR REMARK 3 S11: 0.0319 S12: 0.1292 S13: 0.0158 REMARK 3 S21: -0.1259 S22: -0.2712 S23: 0.1769 REMARK 3 S31: -0.0248 S32: -0.1517 S33: 0.2235 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 12 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.2640 -2.8429 -6.5844 REMARK 3 T TENSOR REMARK 3 T11: 0.2118 T22: 0.2719 REMARK 3 T33: 0.2309 T12: -0.0132 REMARK 3 T13: 0.0082 T23: 0.0229 REMARK 3 L TENSOR REMARK 3 L11: 1.8061 L22: 2.6120 REMARK 3 L33: 2.3726 L12: 0.9422 REMARK 3 L13: -1.2494 L23: -1.0657 REMARK 3 S TENSOR REMARK 3 S11: -0.3810 S12: -0.0416 S13: -0.3298 REMARK 3 S21: -0.1139 S22: 0.0770 S23: -0.3294 REMARK 3 S31: 0.2044 S32: 0.2120 S33: 0.2075 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 6YNR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107951. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34597 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.898 REMARK 200 RESOLUTION RANGE LOW (A) : 43.542 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49600 REMARK 200 FOR SHELL : 3.020 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: 6F14 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 MM PKA, 100 MM MBT (MES/BIS-TRIS REMARK 280 PUFFER PH 6.9), 1 MM DTT, 0.1 MM EDTA, 75 MM LICL, 0.2 MM MEGA8, REMARK 280 0.5 MM PKI AND 18-23% (V/V) METHANOL. SOAKING IN BUFFER REMARK 280 DESCRIBED ABOVE WITH 10% (V/V) 1,7-NAPHTHYDRIN-8-AMINE IN DMSO REMARK 280 (1M STOCK) AND 30% (V/V) MPD, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 36.20300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.11250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.13200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.11250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.20300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.13200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLY A 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 GLY A 9 REMARK 465 ASP B 24 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 11 CD OE1 OE2 REMARK 470 GLN A 12 OE1 NE2 REMARK 470 GLU A 17 CG CD OE1 OE2 REMARK 470 LYS A 21 CD CE NZ REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 LYS A 28 CE NZ REMARK 470 PHE A 54 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 61 CE NZ REMARK 470 LYS A 63 CE NZ REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 78 NZ REMARK 470 LYS A 81 CD CE NZ REMARK 470 LYS A 83 CE NZ REMARK 470 LYS A 105 CD CE NZ REMARK 470 HIS A 142 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 176 OE1 NE2 REMARK 470 ARG A 194 CZ NH1 NH2 REMARK 470 LYS A 213 CD CE NZ REMARK 470 LYS A 217 NZ REMARK 470 GLN A 242 OE1 NE2 REMARK 470 ILE A 244 CG1 CD1 REMARK 470 GLN A 245 CG CD OE1 NE2 REMARK 470 LYS A 254 CG CD CE NZ REMARK 470 LYS A 279 CG CD CE NZ REMARK 470 LYS A 285 CG CD CE NZ REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 PHE A 318 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 319 CG CD CE NZ REMARK 470 GLU A 331 CG CD OE1 OE2 REMARK 470 GLU A 333 CG CD OE1 OE2 REMARK 470 GLU A 334 CG CD OE1 OE2 REMARK 470 ILE A 335 CG1 CD1 REMARK 470 ILE A 339 CG1 CG2 CD1 REMARK 470 LYS A 345 CD CE NZ REMARK 470 ILE B 22 CG1 CD1 REMARK 470 HIS B 23 CG ND1 CD2 CE1 NE2 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 166 43.02 -145.70 REMARK 500 ASP A 184 91.48 59.21 REMARK 500 ASN A 216 -154.09 -139.93 REMARK 500 LEU A 273 48.83 -87.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue O72 A 403 DBREF 6YNR A 0 350 UNP P25321 KAPCA_CRIGR 1 351 DBREF 6YNR B 5 24 UNP P63248 IPKA_MOUSE 6 25 SEQADV 6YNR GLY A -2 UNP P25321 EXPRESSION TAG SEQADV 6YNR HIS A -1 UNP P25321 EXPRESSION TAG SEQRES 1 A 353 GLY HIS MET GLY ASN ALA ALA ALA ALA LYS LYS GLY SEP SEQRES 2 A 353 GLU GLN GLU SER VAL LYS GLU PHE LEU ALA LYS ALA LYS SEQRES 3 A 353 GLU GLU PHE LEU LYS LYS TRP GLU SER PRO SER GLN ASN SEQRES 4 A 353 THR ALA GLN LEU ASP HIS PHE ASP ARG ILE LYS THR LEU SEQRES 5 A 353 GLY THR GLY SER PHE GLY ARG VAL MET LEU VAL LYS HIS SEQRES 6 A 353 LYS GLU THR GLY ASN HIS TYR ALA MET LYS ILE LEU ASP SEQRES 7 A 353 LYS GLN LYS VAL VAL LYS LEU LYS GLN ILE GLU HIS THR SEQRES 8 A 353 LEU ASN GLU LYS ARG ILE LEU GLN ALA VAL ASN PHE PRO SEQRES 9 A 353 PHE LEU VAL LYS LEU GLU PHE SER PHE LYS ASP ASN SER SEQRES 10 A 353 ASN LEU TYR MET VAL MET GLU TYR VAL PRO GLY GLY GLU SEQRES 11 A 353 MET PHE SER HIS LEU ARG ARG ILE GLY ARG PHE SER GLU SEQRES 12 A 353 PRO HIS ALA ARG PHE TYR ALA ALA GLN ILE VAL LEU THR SEQRES 13 A 353 PHE GLU TYR LEU HIS SER LEU ASP LEU ILE TYR ARG ASP SEQRES 14 A 353 LEU LYS PRO GLU ASN LEU LEU ILE ASP GLN GLN GLY TYR SEQRES 15 A 353 ILE GLN VAL THR ASP PHE GLY PHE ALA LYS ARG VAL LYS SEQRES 16 A 353 GLY ARG THR TRP TPO LEU CYS GLY THR PRO GLU TYR LEU SEQRES 17 A 353 ALA PRO GLU ILE ILE LEU SER LYS GLY TYR ASN LYS ALA SEQRES 18 A 353 VAL ASP TRP TRP ALA LEU GLY VAL LEU ILE TYR GLU MET SEQRES 19 A 353 ALA ALA GLY TYR PRO PRO PHE PHE ALA ASP GLN PRO ILE SEQRES 20 A 353 GLN ILE TYR GLU LYS ILE VAL SER GLY LYS VAL ARG PHE SEQRES 21 A 353 PRO SER HIS PHE SER SER ASP LEU LYS ASP LEU LEU ARG SEQRES 22 A 353 ASN LEU LEU GLN VAL ASP LEU THR LYS ARG PHE GLY ASN SEQRES 23 A 353 LEU LYS ASN GLY VAL ASN ASP ILE LYS ASN HIS LYS TRP SEQRES 24 A 353 PHE ALA THR THR ASP TRP ILE ALA ILE TYR GLN ARG LYS SEQRES 25 A 353 VAL GLU ALA PRO PHE ILE PRO LYS PHE LYS GLY PRO GLY SEQRES 26 A 353 ASP THR SER ASN PHE ASP ASP TYR GLU GLU GLU GLU ILE SEQRES 27 A 353 ARG VAL SEP ILE ASN GLU LYS CYS GLY LYS GLU PHE THR SEQRES 28 A 353 GLU PHE SEQRES 1 B 20 THR THR TYR ALA ASP PHE ILE ALA SER GLY ARG THR GLY SEQRES 2 B 20 ARG ARG ASN ALA ILE HIS ASP MODRES 6YNR SEP A 10 SER MODIFIED RESIDUE MODRES 6YNR TPO A 197 THR MODIFIED RESIDUE MODRES 6YNR SEP A 338 SER MODIFIED RESIDUE HET SEP A 10 10 HET TPO A 197 11 HET SEP A 338 10 HET MPD A 401 8 HET DMS A 402 4 HET O72 A 403 11 HETNAM SEP PHOSPHOSERINE HETNAM TPO PHOSPHOTHREONINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM O72 1,7-NAPHTHYRIDIN-8-AMINE HETSYN SEP PHOSPHONOSERINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 1 TPO C4 H10 N O6 P FORMUL 3 MPD C6 H14 O2 FORMUL 4 DMS C2 H6 O S FORMUL 5 O72 C8 H7 N3 FORMUL 6 HOH *216(H2 O) HELIX 1 AA1 SEP A 10 SER A 32 1 23 HELIX 2 AA2 GLN A 39 ASP A 41 5 3 HELIX 3 AA3 LYS A 76 LEU A 82 1 7 HELIX 4 AA4 GLN A 84 GLN A 96 1 13 HELIX 5 AA5 GLU A 127 GLY A 136 1 10 HELIX 6 AA6 SER A 139 LEU A 160 1 22 HELIX 7 AA7 LYS A 168 GLU A 170 5 3 HELIX 8 AA8 THR A 201 LEU A 205 5 5 HELIX 9 AA9 ALA A 206 LEU A 211 1 6 HELIX 10 AB1 LYS A 217 GLY A 234 1 18 HELIX 11 AB2 GLN A 242 GLY A 253 1 12 HELIX 12 AB3 SER A 262 LEU A 273 1 12 HELIX 13 AB4 ASP A 276 ARG A 280 5 5 HELIX 14 AB5 VAL A 288 ASN A 293 1 6 HELIX 15 AB6 HIS A 294 ALA A 298 5 5 HELIX 16 AB7 ASP A 301 GLN A 307 1 7 HELIX 17 AB8 THR B 6 SER B 13 1 8 SHEET 1 AA1 5 PHE A 43 THR A 51 0 SHEET 2 AA1 5 GLY A 55 HIS A 62 -1 O LEU A 59 N LYS A 47 SHEET 3 AA1 5 HIS A 68 ASP A 75 -1 O ILE A 73 N ARG A 56 SHEET 4 AA1 5 ASN A 115 GLU A 121 -1 O MET A 118 N LYS A 72 SHEET 5 AA1 5 LEU A 106 LYS A 111 -1 N PHE A 108 O VAL A 119 SHEET 1 AA2 2 LEU A 162 ILE A 163 0 SHEET 2 AA2 2 LYS A 189 ARG A 190 -1 O LYS A 189 N ILE A 163 SHEET 1 AA3 2 LEU A 172 ILE A 174 0 SHEET 2 AA3 2 ILE A 180 VAL A 182 -1 O GLN A 181 N LEU A 173 LINK C SEP A 10 N GLU A 11 1555 1555 1.33 LINK C TRP A 196 N TPO A 197 1555 1555 1.33 LINK C TPO A 197 N LEU A 198 1555 1555 1.33 LINK C VAL A 337 N SEP A 338 1555 1555 1.33 LINK C SEP A 338 N ILE A 339 1555 1555 1.33 SITE 1 AC1 4 SER A 130 ARG A 134 PHE A 327 ASP A 328 SITE 1 AC2 4 ASN A 36 ALA A 38 GLN A 39 HIS A 42 SITE 1 AC3 8 ALA A 70 VAL A 104 GLU A 121 TYR A 122 SITE 2 AC3 8 VAL A 123 LEU A 173 THR A 183 PHE A 327 CRYST1 72.406 74.264 80.225 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 0.013811 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013465 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012465 0.00000 HETATM 1 N SEP A 10 -43.920 20.294 14.645 1.00 31.36 N HETATM 2 CA SEP A 10 -44.881 19.192 14.667 1.00 34.62 C HETATM 3 CB SEP A 10 -46.267 19.672 14.223 1.00 39.26 C HETATM 4 OG SEP A 10 -46.227 20.099 12.870 1.00 51.23 O HETATM 5 C SEP A 10 -44.438 18.025 13.782 1.00 25.34 C HETATM 6 O SEP A 10 -44.627 16.862 14.149 1.00 24.48 O HETATM 7 P SEP A 10 -47.667 20.066 12.130 1.00 54.06 P HETATM 8 O1P SEP A 10 -47.456 20.660 10.648 1.00 58.81 O HETATM 9 O2P SEP A 10 -48.722 20.962 12.966 1.00 49.24 O HETATM 10 O3P SEP A 10 -48.207 18.552 12.030 1.00 51.30 O