HEADER TRANSFERASE 09-MAR-21 7EBG TITLE CRYSTAL STRUCTURE OF HUMAN PYRUVATE DEHYDROGENASE KINASE 4 IN COMPLEX TITLE 2 WITH COMPOUND 7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: [PYRUVATE DEHYDROGENASE (ACETYL-TRANSFERRING)] KINASE COMPND 3 ISOZYME 4, MITOCHONDRIAL; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 4; COMPND 6 EC: 2.7.11.2; COMPND 7 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: PDK4, PDHK4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PDHK, KINASE INHIBITORS, FRAGMENT SCREENING, PDK1, PDK2, PDK3, PDK4, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.ORITA,S.DOI,T.IWANAGA,T.ADACHI REVDAT 2 29-NOV-23 7EBG 1 REMARK REVDAT 1 04-AUG-21 7EBG 0 JRNL AUTH T.AKAKI,Y.BESSHO,T.ITO,S.FUJIOKA,M.UBUKATA,G.MORI, JRNL AUTH 2 K.YAMANAKA,T.ORITA,S.DOI,T.IWANAGA,K.IKEGASHIRA,Y.HANTANI, JRNL AUTH 3 I.NAKANISHI,T.ADACHI JRNL TITL FRAGMENT-BASED LEAD DISCOVERY TO IDENTIFY NOVEL INHIBITORS JRNL TITL 2 THAT TARGET THE ATP BINDING SITE OF PYRUVATE DEHYDROGENASE JRNL TITL 3 KINASES. JRNL REF BIOORG.MED.CHEM. V. 44 16283 2021 JRNL REFN ESSN 1464-3391 JRNL PMID 34274549 JRNL DOI 10.1016/J.BMC.2021.116283 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19RC3_4028 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 + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 51289 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 2388 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 68.6400 - 5.0100 0.97 2955 151 0.2034 0.2282 REMARK 3 2 5.0100 - 3.9800 0.98 2927 149 0.1754 0.1737 REMARK 3 3 3.9800 - 3.4800 0.98 2881 167 0.1789 0.2167 REMARK 3 4 3.4800 - 3.1600 0.99 2915 136 0.2027 0.2136 REMARK 3 5 3.1600 - 2.9300 0.98 2906 140 0.2139 0.2631 REMARK 3 6 2.9300 - 2.7600 0.98 2908 135 0.2115 0.2410 REMARK 3 7 2.7600 - 2.6200 0.98 2848 135 0.2087 0.2287 REMARK 3 8 2.6200 - 2.5100 0.97 2877 136 0.2225 0.2708 REMARK 3 9 2.5100 - 2.4100 0.97 2851 134 0.2097 0.2392 REMARK 3 10 2.4100 - 2.3300 0.97 2842 151 0.2092 0.2265 REMARK 3 11 2.3300 - 2.2500 0.98 2858 128 0.2146 0.2590 REMARK 3 12 2.2500 - 2.1900 0.98 2893 129 0.2073 0.2562 REMARK 3 13 2.1900 - 2.1300 0.97 2866 145 0.2202 0.2681 REMARK 3 14 2.1300 - 2.0800 0.97 2858 142 0.2206 0.2698 REMARK 3 15 2.0800 - 2.0300 0.97 2837 134 0.2248 0.3032 REMARK 3 16 2.0300 - 1.9900 0.97 2821 140 0.2369 0.2652 REMARK 3 17 1.9900 - 1.9500 0.97 2858 136 0.2426 0.2894 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) : 0.208 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.21 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 : 0.002 5761 REMARK 3 ANGLE : 0.513 7837 REMARK 3 CHIRALITY : 0.040 876 REMARK 3 PLANARITY : 0.003 999 REMARK 3 DIHEDRAL : 11.131 2119 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 20 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.5762 -11.2211 5.8736 REMARK 3 T TENSOR REMARK 3 T11: 0.2050 T22: 0.2487 REMARK 3 T33: 0.2413 T12: -0.0108 REMARK 3 T13: 0.0044 T23: -0.0494 REMARK 3 L TENSOR REMARK 3 L11: 1.5902 L22: 1.8085 REMARK 3 L33: 4.3540 L12: 0.1251 REMARK 3 L13: -0.3390 L23: -0.6396 REMARK 3 S TENSOR REMARK 3 S11: -0.0229 S12: 0.0987 S13: -0.2082 REMARK 3 S21: -0.0834 S22: -0.1059 S23: 0.2079 REMARK 3 S31: 0.3385 S32: -0.2315 S33: 0.0957 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 397 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.5468 9.1094 13.7363 REMARK 3 T TENSOR REMARK 3 T11: 0.1685 T22: 0.2768 REMARK 3 T33: 0.2559 T12: 0.0546 REMARK 3 T13: -0.0343 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 2.4956 L22: 1.1558 REMARK 3 L33: 2.1523 L12: 0.4094 REMARK 3 L13: 0.6960 L23: 0.5261 REMARK 3 S TENSOR REMARK 3 S11: -0.1740 S12: -0.1736 S13: 0.3254 REMARK 3 S21: -0.0656 S22: -0.0733 S23: 0.1685 REMARK 3 S31: -0.1261 S32: -0.2227 S33: 0.1014 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 20 THROUGH 50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.7439 -12.1114 36.7654 REMARK 3 T TENSOR REMARK 3 T11: 0.2365 T22: 0.2167 REMARK 3 T33: 0.2693 T12: -0.0437 REMARK 3 T13: 0.0176 T23: 0.1104 REMARK 3 L TENSOR REMARK 3 L11: 3.0373 L22: 5.2567 REMARK 3 L33: 3.6780 L12: -1.4825 REMARK 3 L13: -0.4523 L23: 3.2055 REMARK 3 S TENSOR REMARK 3 S11: -0.0162 S12: -0.0134 S13: -0.4548 REMARK 3 S21: 0.6918 S22: -0.1535 S23: 0.1622 REMARK 3 S31: 0.6800 S32: -0.1264 S33: 0.1473 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 51 THROUGH 152 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.3318 -10.0811 28.4315 REMARK 3 T TENSOR REMARK 3 T11: 0.1722 T22: 0.1371 REMARK 3 T33: 0.3039 T12: 0.0201 REMARK 3 T13: 0.0227 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 3.3068 L22: 3.4498 REMARK 3 L33: 4.8918 L12: -0.0247 REMARK 3 L13: -0.3817 L23: 0.9032 REMARK 3 S TENSOR REMARK 3 S11: -0.1131 S12: 0.1417 S13: -0.2460 REMARK 3 S21: -0.0720 S22: 0.0751 S23: -0.1177 REMARK 3 S31: 0.0250 S32: 0.0602 S33: 0.0404 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 153 THROUGH 199 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4461 0.6779 32.4845 REMARK 3 T TENSOR REMARK 3 T11: 0.1346 T22: 0.1706 REMARK 3 T33: 0.2055 T12: -0.0206 REMARK 3 T13: 0.0295 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 1.8816 L22: 3.1195 REMARK 3 L33: 3.4277 L12: -1.0261 REMARK 3 L13: 0.1251 L23: 0.6970 REMARK 3 S TENSOR REMARK 3 S11: -0.0012 S12: -0.0184 S13: -0.0087 REMARK 3 S21: 0.0499 S22: 0.0220 S23: -0.1153 REMARK 3 S31: -0.0091 S32: 0.1460 S33: -0.0454 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 200 THROUGH 307 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9408 16.9874 21.6041 REMARK 3 T TENSOR REMARK 3 T11: 0.1521 T22: 0.1774 REMARK 3 T33: 0.2143 T12: 0.0129 REMARK 3 T13: -0.0113 T23: -0.0246 REMARK 3 L TENSOR REMARK 3 L11: 2.0126 L22: 1.3743 REMARK 3 L33: 4.3993 L12: 0.4220 REMARK 3 L13: 0.4103 L23: -0.9712 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: 0.1039 S13: 0.2208 REMARK 3 S21: -0.0081 S22: -0.0399 S23: 0.0187 REMARK 3 S31: -0.2210 S32: 0.1410 S33: 0.0596 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 308 THROUGH 386 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1439 1.5876 20.7001 REMARK 3 T TENSOR REMARK 3 T11: 0.2101 T22: 0.2674 REMARK 3 T33: 0.2357 T12: -0.0036 REMARK 3 T13: -0.0187 T23: -0.0436 REMARK 3 L TENSOR REMARK 3 L11: 2.0613 L22: 2.9024 REMARK 3 L33: 0.9963 L12: -0.9010 REMARK 3 L13: 0.7211 L23: -1.6727 REMARK 3 S TENSOR REMARK 3 S11: 0.1306 S12: 0.2666 S13: -0.1417 REMARK 3 S21: -0.3827 S22: -0.1507 S23: 0.0549 REMARK 3 S31: 0.1765 S32: 0.0027 S33: 0.0426 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 7EBG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021104. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51337 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 68.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2ZKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM KHPO4 PH 7.5, 1.7 M AMMONIUM REMARK 280 SULFATE AND 4% (V/V) PEG400, 5 MM ADP, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 33.72050 REMARK 290 SMTRY3 2 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: 4490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -89.0 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 8 REMARK 465 PRO A 9 REMARK 465 SER A 10 REMARK 465 ALA A 11 REMARK 465 GLY A 12 REMARK 465 SER A 13 REMARK 465 LEU A 14 REMARK 465 ASN A 15 REMARK 465 GLY A 16 REMARK 465 ALA A 17 REMARK 465 GLY A 18 REMARK 465 LEU A 19 REMARK 465 SER A 45 REMARK 465 GLU A 46 REMARK 465 ASN A 47 REMARK 465 ALA A 48 REMARK 465 CYS A 49 REMARK 465 ASP A 182 REMARK 465 SER A 183 REMARK 465 GLN A 184 REMARK 465 THR A 185 REMARK 465 GLY A 186 REMARK 465 GLU A 268 REMARK 465 ASN A 269 REMARK 465 GLN A 270 REMARK 465 PRO A 271 REMARK 465 SER A 272 REMARK 465 THR A 310 REMARK 465 TYR A 311 REMARK 465 SER A 312 REMARK 465 THR A 313 REMARK 465 ALA A 314 REMARK 465 PRO A 315 REMARK 465 THR A 316 REMARK 465 PRO A 317 REMARK 465 VAL A 318 REMARK 465 MET A 319 REMARK 465 ASP A 320 REMARK 465 ASN A 321 REMARK 465 SER A 322 REMARK 465 ARG A 323 REMARK 465 ASN A 324 REMARK 465 ALA A 325 REMARK 465 PRO A 326 REMARK 465 LEU A 327 REMARK 465 ALA A 328 REMARK 465 GLY A 329 REMARK 465 PHE A 330 REMARK 465 SER A 389 REMARK 465 SER A 390 REMARK 465 GLU A 391 REMARK 465 ALA A 392 REMARK 465 ASP A 393 REMARK 465 PRO A 398 REMARK 465 SER A 399 REMARK 465 ARG A 400 REMARK 465 GLU A 401 REMARK 465 PRO A 402 REMARK 465 LYS A 403 REMARK 465 ASN A 404 REMARK 465 LEU A 405 REMARK 465 ALA A 406 REMARK 465 LYS A 407 REMARK 465 GLU A 408 REMARK 465 VAL A 409 REMARK 465 ALA A 410 REMARK 465 MET A 411 REMARK 465 GLY B 8 REMARK 465 PRO B 9 REMARK 465 SER B 10 REMARK 465 ALA B 11 REMARK 465 GLY B 12 REMARK 465 SER B 13 REMARK 465 LEU B 14 REMARK 465 ASN B 15 REMARK 465 GLY B 16 REMARK 465 ALA B 17 REMARK 465 GLY B 18 REMARK 465 LEU B 19 REMARK 465 GLU B 46 REMARK 465 ASN B 47 REMARK 465 ALA B 48 REMARK 465 CYS B 49 REMARK 465 ASP B 143 REMARK 465 ALA B 144 REMARK 465 CYS B 145 REMARK 465 THR B 146 REMARK 465 VAL B 147 REMARK 465 ASP B 148 REMARK 465 PRO B 149 REMARK 465 MET B 319 REMARK 465 ASP B 320 REMARK 465 ASN B 321 REMARK 465 SER B 322 REMARK 465 ARG B 323 REMARK 465 ASN B 324 REMARK 465 ALA B 325 REMARK 465 GLN B 387 REMARK 465 MET B 388 REMARK 465 SER B 389 REMARK 465 SER B 390 REMARK 465 GLU B 391 REMARK 465 ALA B 392 REMARK 465 ASP B 393 REMARK 465 ASP B 394 REMARK 465 TRP B 395 REMARK 465 CYS B 396 REMARK 465 ILE B 397 REMARK 465 PRO B 398 REMARK 465 SER B 399 REMARK 465 ARG B 400 REMARK 465 GLU B 401 REMARK 465 PRO B 402 REMARK 465 LYS B 403 REMARK 465 ASN B 404 REMARK 465 LEU B 405 REMARK 465 ALA B 406 REMARK 465 LYS B 407 REMARK 465 GLU B 408 REMARK 465 VAL B 409 REMARK 465 ALA B 410 REMARK 465 MET B 411 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 VAL A 20 CG1 CG2 REMARK 470 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 51 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 380 CG CD CE NZ REMARK 470 LYS A 384 CG CD CE NZ REMARK 470 MET A 388 CG SD CE REMARK 470 ASP A 394 CG OD1 OD2 REMARK 470 ILE A 397 CG1 CG2 CD1 REMARK 470 VAL B 20 CG1 CG2 REMARK 470 LYS B 142 CG CD CE NZ REMARK 470 VAL B 150 CG1 CG2 REMARK 470 GLN B 153 CG CD OE1 NE2 REMARK 470 VAL B 318 CG1 CG2 REMARK 470 LYS B 380 CG CD CE NZ REMARK 470 LYS B 384 CG CD CE NZ 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 SER A 221 141.60 -173.60 REMARK 500 SER A 221 141.61 -173.40 REMARK 500 PHE A 344 42.21 -105.23 REMARK 500 TYR A 356 -62.41 -132.80 REMARK 500 ASP B 109 97.52 -67.06 REMARK 500 ASN B 231 78.28 -104.63 REMARK 500 ARG B 294 54.59 -116.88 REMARK 500 THR B 310 -22.53 83.25 REMARK 500 PRO B 317 -178.10 -65.68 REMARK 500 TYR B 356 -65.44 -132.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 258 OD1 REMARK 620 2 SO4 B 502 O2 170.7 REMARK 620 3 ADP B 504 O3B 87.6 97.9 REMARK 620 4 ADP B 504 O2A 91.1 95.6 97.4 REMARK 620 5 ADP B 504 O3A 124.8 64.4 56.5 58.9 REMARK 620 6 HOH B 604 O 85.8 87.7 169.2 91.2 134.2 REMARK 620 7 HOH B 628 O 79.4 93.4 87.0 169.4 130.7 83.5 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7EA0 RELATED DB: PDB REMARK 900 PDHK2 IN COMPLEX WITH A RELATED COMPOUND REMARK 900 RELATED ID: 7EAS RELATED DB: PDB REMARK 900 PDHK2 IN COMPLEX WITH A RELATED COMPOUND REMARK 900 RELATED ID: 7EAT RELATED DB: PDB REMARK 900 PDHK4 IN COMPLEX WITH A RELATED COMPOUND REMARK 900 RELATED ID: 7EBB RELATED DB: PDB REMARK 900 PDHK4 IN COMPLEX WITH A RELATED COMPOUND REMARK 900 RELATED ID: 7EBG RELATED DB: PDB REMARK 900 PDHK4 IN COMPLEX WITH A RELATED COMPOUND REMARK 900 RELATED ID: 7EBH RELATED DB: PDB REMARK 900 PDHK4 IN COMPLEX WITH A RELATED COMPOUND DBREF 7EBG A 10 411 UNP Q16654 PDK4_HUMAN 10 411 DBREF 7EBG B 10 411 UNP Q16654 PDK4_HUMAN 10 411 SEQADV 7EBG GLY A 8 UNP Q16654 EXPRESSION TAG SEQADV 7EBG PRO A 9 UNP Q16654 EXPRESSION TAG SEQADV 7EBG GLY B 8 UNP Q16654 EXPRESSION TAG SEQADV 7EBG PRO B 9 UNP Q16654 EXPRESSION TAG SEQRES 1 A 404 GLY PRO SER ALA GLY SER LEU ASN GLY ALA GLY LEU VAL SEQRES 2 A 404 PRO ARG GLU VAL GLU HIS PHE SER ARG TYR SER PRO SER SEQRES 3 A 404 PRO LEU SER MET LYS GLN LEU LEU ASP PHE GLY SER GLU SEQRES 4 A 404 ASN ALA CYS GLU ARG THR SER PHE ALA PHE LEU ARG GLN SEQRES 5 A 404 GLU LEU PRO VAL ARG LEU ALA ASN ILE LEU LYS GLU ILE SEQRES 6 A 404 ASP ILE LEU PRO THR GLN LEU VAL ASN THR SER SER VAL SEQRES 7 A 404 GLN LEU VAL LYS SER TRP TYR ILE GLN SER LEU MET ASP SEQRES 8 A 404 LEU VAL GLU PHE HIS GLU LYS SER PRO ASP ASP GLN LYS SEQRES 9 A 404 ALA LEU SER ASP PHE VAL ASP THR LEU ILE LYS VAL ARG SEQRES 10 A 404 ASN ARG HIS HIS ASN VAL VAL PRO THR MET ALA GLN GLY SEQRES 11 A 404 ILE ILE GLU TYR LYS ASP ALA CYS THR VAL ASP PRO VAL SEQRES 12 A 404 THR ASN GLN ASN LEU GLN TYR PHE LEU ASP ARG PHE TYR SEQRES 13 A 404 MET ASN ARG ILE SER THR ARG MET LEU MET ASN GLN HIS SEQRES 14 A 404 ILE LEU ILE PHE SER ASP SER GLN THR GLY ASN PRO SER SEQRES 15 A 404 HIS ILE GLY SER ILE ASP PRO ASN CYS ASP VAL VAL ALA SEQRES 16 A 404 VAL VAL GLN ASP ALA PHE GLU CYS SER ARG MET LEU CYS SEQRES 17 A 404 ASP GLN TYR TYR LEU SER SER PRO GLU LEU LYS LEU THR SEQRES 18 A 404 GLN VAL ASN GLY LYS PHE PRO ASP GLN PRO ILE HIS ILE SEQRES 19 A 404 VAL TYR VAL PRO SER HIS LEU HIS HIS MET LEU PHE GLU SEQRES 20 A 404 LEU PHE LYS ASN ALA MET ARG ALA THR VAL GLU HIS GLN SEQRES 21 A 404 GLU ASN GLN PRO SER LEU THR PRO ILE GLU VAL ILE VAL SEQRES 22 A 404 VAL LEU GLY LYS GLU ASP LEU THR ILE LYS ILE SER ASP SEQRES 23 A 404 ARG GLY GLY GLY VAL PRO LEU ARG ILE ILE ASP ARG LEU SEQRES 24 A 404 PHE SER TYR THR TYR SER THR ALA PRO THR PRO VAL MET SEQRES 25 A 404 ASP ASN SER ARG ASN ALA PRO LEU ALA GLY PHE GLY TYR SEQRES 26 A 404 GLY LEU PRO ILE SER ARG LEU TYR ALA LYS TYR PHE GLN SEQRES 27 A 404 GLY ASP LEU ASN LEU TYR SER LEU SER GLY TYR GLY THR SEQRES 28 A 404 ASP ALA ILE ILE TYR LEU LYS ALA LEU SER SER GLU SER SEQRES 29 A 404 ILE GLU LYS LEU PRO VAL PHE ASN LYS SER ALA PHE LYS SEQRES 30 A 404 HIS TYR GLN MET SER SER GLU ALA ASP ASP TRP CYS ILE SEQRES 31 A 404 PRO SER ARG GLU PRO LYS ASN LEU ALA LYS GLU VAL ALA SEQRES 32 A 404 MET SEQRES 1 B 404 GLY PRO SER ALA GLY SER LEU ASN GLY ALA GLY LEU VAL SEQRES 2 B 404 PRO ARG GLU VAL GLU HIS PHE SER ARG TYR SER PRO SER SEQRES 3 B 404 PRO LEU SER MET LYS GLN LEU LEU ASP PHE GLY SER GLU SEQRES 4 B 404 ASN ALA CYS GLU ARG THR SER PHE ALA PHE LEU ARG GLN SEQRES 5 B 404 GLU LEU PRO VAL ARG LEU ALA ASN ILE LEU LYS GLU ILE SEQRES 6 B 404 ASP ILE LEU PRO THR GLN LEU VAL ASN THR SER SER VAL SEQRES 7 B 404 GLN LEU VAL LYS SER TRP TYR ILE GLN SER LEU MET ASP SEQRES 8 B 404 LEU VAL GLU PHE HIS GLU LYS SER PRO ASP ASP GLN LYS SEQRES 9 B 404 ALA LEU SER ASP PHE VAL ASP THR LEU ILE LYS VAL ARG SEQRES 10 B 404 ASN ARG HIS HIS ASN VAL VAL PRO THR MET ALA GLN GLY SEQRES 11 B 404 ILE ILE GLU TYR LYS ASP ALA CYS THR VAL ASP PRO VAL SEQRES 12 B 404 THR ASN GLN ASN LEU GLN TYR PHE LEU ASP ARG PHE TYR SEQRES 13 B 404 MET ASN ARG ILE SER THR ARG MET LEU MET ASN GLN HIS SEQRES 14 B 404 ILE LEU ILE PHE SER ASP SER GLN THR GLY ASN PRO SER SEQRES 15 B 404 HIS ILE GLY SER ILE ASP PRO ASN CYS ASP VAL VAL ALA SEQRES 16 B 404 VAL VAL GLN ASP ALA PHE GLU CYS SER ARG MET LEU CYS SEQRES 17 B 404 ASP GLN TYR TYR LEU SER SER PRO GLU LEU LYS LEU THR SEQRES 18 B 404 GLN VAL ASN GLY LYS PHE PRO ASP GLN PRO ILE HIS ILE SEQRES 19 B 404 VAL TYR VAL PRO SER HIS LEU HIS HIS MET LEU PHE GLU SEQRES 20 B 404 LEU PHE LYS ASN ALA MET ARG ALA THR VAL GLU HIS GLN SEQRES 21 B 404 GLU ASN GLN PRO SER LEU THR PRO ILE GLU VAL ILE VAL SEQRES 22 B 404 VAL LEU GLY LYS GLU ASP LEU THR ILE LYS ILE SER ASP SEQRES 23 B 404 ARG GLY GLY GLY VAL PRO LEU ARG ILE ILE ASP ARG LEU SEQRES 24 B 404 PHE SER TYR THR TYR SER THR ALA PRO THR PRO VAL MET SEQRES 25 B 404 ASP ASN SER ARG ASN ALA PRO LEU ALA GLY PHE GLY TYR SEQRES 26 B 404 GLY LEU PRO ILE SER ARG LEU TYR ALA LYS TYR PHE GLN SEQRES 27 B 404 GLY ASP LEU ASN LEU TYR SER LEU SER GLY TYR GLY THR SEQRES 28 B 404 ASP ALA ILE ILE TYR LEU LYS ALA LEU SER SER GLU SER SEQRES 29 B 404 ILE GLU LYS LEU PRO VAL PHE ASN LYS SER ALA PHE LYS SEQRES 30 B 404 HIS TYR GLN MET SER SER GLU ALA ASP ASP TRP CYS ILE SEQRES 31 B 404 PRO SER ARG GLU PRO LYS ASN LEU ALA LYS GLU VAL ALA SEQRES 32 B 404 MET HET SO4 A 501 5 HET J0L A 502 14 HET SO4 B 501 5 HET SO4 B 502 5 HET MG B 503 1 HET ADP B 504 27 HETNAM SO4 SULFATE ION HETNAM J0L 3,3-DIMETHYL-7-(METHYLAMINO)-1H-INDOL-2-ONE HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 J0L C11 H14 N2 O FORMUL 7 MG MG 2+ FORMUL 8 ADP C10 H15 N5 O10 P2 FORMUL 9 HOH *174(H2 O) HELIX 1 AA1 PRO A 21 ARG A 29 1 9 HELIX 2 AA2 SER A 36 ASP A 42 1 7 HELIX 3 AA3 ARG A 51 ASP A 73 1 23 HELIX 4 AA4 PRO A 76 ASN A 81 1 6 HELIX 5 AA5 THR A 82 GLU A 101 1 20 HELIX 6 AA6 PHE A 102 LYS A 105 5 4 HELIX 7 AA7 ASP A 109 HIS A 127 1 19 HELIX 8 AA8 ASN A 129 CYS A 145 1 17 HELIX 9 AA9 ASP A 148 SER A 181 1 34 HELIX 10 AB1 VAL A 200 LEU A 220 1 21 HELIX 11 AB2 VAL A 244 GLN A 267 1 24 HELIX 12 AB3 PRO A 299 ASP A 304 1 6 HELIX 13 AB4 ARG A 305 SER A 308 5 4 HELIX 14 AB5 TYR A 332 PHE A 344 1 13 HELIX 15 AB6 ASN A 379 MET A 388 1 10 HELIX 16 AB7 PRO B 21 ARG B 29 1 9 HELIX 17 AB8 SER B 36 PHE B 43 1 8 HELIX 18 AB9 ARG B 51 LEU B 75 1 25 HELIX 19 AC1 PRO B 76 ASN B 81 1 6 HELIX 20 AC2 THR B 82 GLU B 101 1 20 HELIX 21 AC3 PHE B 102 LYS B 105 5 4 HELIX 22 AC4 ASP B 109 HIS B 128 1 20 HELIX 23 AC5 ASN B 129 LYS B 142 1 14 HELIX 24 AC6 ASN B 152 SER B 181 1 30 HELIX 25 AC7 VAL B 200 LEU B 220 1 21 HELIX 26 AC8 VAL B 244 GLN B 267 1 24 HELIX 27 AC9 PRO B 299 ARG B 301 5 3 HELIX 28 AD1 ILE B 302 PHE B 307 1 6 HELIX 29 AD2 TYR B 332 PHE B 344 1 13 HELIX 30 AD3 ASN B 379 TYR B 386 1 8 SHEET 1 AA1 2 ASP A 195 ASP A 199 0 SHEET 2 AA1 2 HIS A 240 TYR A 243 -1 O TYR A 243 N ASP A 195 SHEET 1 AA2 5 LEU A 225 ASN A 231 0 SHEET 2 AA2 5 ILE A 276 LEU A 282 1 O VAL A 280 N VAL A 230 SHEET 3 AA2 5 ASP A 286 SER A 292 -1 O THR A 288 N VAL A 281 SHEET 4 AA2 5 GLY A 357 LYS A 365 -1 O ALA A 360 N ILE A 291 SHEET 5 AA2 5 ASP A 347 LEU A 353 -1 N LEU A 353 O GLY A 357 SHEET 1 AA3 2 ASP B 195 ASP B 199 0 SHEET 2 AA3 2 HIS B 240 TYR B 243 -1 O TYR B 243 N ASP B 195 SHEET 1 AA4 5 LEU B 225 ASN B 231 0 SHEET 2 AA4 5 ILE B 276 LEU B 282 1 O VAL B 278 N THR B 228 SHEET 3 AA4 5 ASP B 286 ASP B 293 -1 O SER B 292 N GLU B 277 SHEET 4 AA4 5 GLY B 357 LYS B 365 -1 O ALA B 360 N ILE B 291 SHEET 5 AA4 5 ASP B 347 LEU B 353 -1 N LEU B 353 O GLY B 357 LINK OD1 ASN B 258 MG MG B 503 1555 1555 2.26 LINK O2 SO4 B 502 MG MG B 503 1555 1555 2.00 LINK MG MG B 503 O3B ADP B 504 1555 1555 1.98 LINK MG MG B 503 O2A ADP B 504 1555 1555 1.92 LINK MG MG B 503 O3A ADP B 504 1555 1555 2.90 LINK MG MG B 503 O HOH B 604 1555 1555 2.12 LINK MG MG B 503 O HOH B 628 1555 1555 2.28 CRYST1 69.965 67.441 78.605 90.00 101.19 90.00 P 1 21 1 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 0.014293 0.000000 0.002826 0.00000 SCALE2 0.000000 0.014828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012968 0.00000