HEADER TRANSFERASE 09-MAR-21 7EBB TITLE CRYSTAL STRUCTURE OF HUMAN PYRUVATE DEHYDROGENASE KINASE 4 IN COMPLEX TITLE 2 WITH COMPOUND 2 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 7EBB 1 REMARK REVDAT 1 04-AUG-21 7EBB 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 60326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2964 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 80.0200 - 5.2400 0.98 2812 145 0.2087 0.2097 REMARK 3 2 5.2400 - 4.1600 1.00 2800 136 0.1652 0.1664 REMARK 3 3 4.1600 - 3.6300 1.00 2782 135 0.1743 0.1990 REMARK 3 4 3.6300 - 3.3000 1.00 2765 136 0.1902 0.2099 REMARK 3 5 3.3000 - 3.0700 0.99 2761 138 0.2119 0.2316 REMARK 3 6 3.0700 - 2.8800 0.99 2724 163 0.2174 0.2280 REMARK 3 7 2.8800 - 2.7400 0.99 2776 131 0.1942 0.2498 REMARK 3 8 2.7400 - 2.6200 0.99 2714 147 0.2041 0.2468 REMARK 3 9 2.6200 - 2.5200 0.99 2768 131 0.2115 0.2561 REMARK 3 10 2.5200 - 2.4300 0.99 2729 137 0.1976 0.2571 REMARK 3 11 2.4300 - 2.3600 0.99 2713 131 0.1860 0.2276 REMARK 3 12 2.3600 - 2.2900 0.99 2732 156 0.1930 0.2075 REMARK 3 13 2.2900 - 2.2300 0.98 2682 154 0.1885 0.2346 REMARK 3 14 2.2300 - 2.1800 0.98 2733 121 0.1989 0.2185 REMARK 3 15 2.1700 - 2.1300 0.99 2725 138 0.1958 0.2415 REMARK 3 16 2.1300 - 2.0800 0.99 2667 172 0.1975 0.2473 REMARK 3 17 2.0800 - 2.0400 0.98 2689 138 0.2048 0.2357 REMARK 3 18 2.0400 - 2.0000 0.98 2716 128 0.2120 0.2657 REMARK 3 19 2.0000 - 1.9600 0.99 2706 137 0.2214 0.2615 REMARK 3 20 1.9600 - 1.9300 0.97 2686 142 0.2220 0.2528 REMARK 3 21 1.9300 - 1.9000 0.98 2682 148 0.2268 0.2470 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) : 0.188 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.745 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.10 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 5912 REMARK 3 ANGLE : 0.558 8044 REMARK 3 CHIRALITY : 0.043 894 REMARK 3 PLANARITY : 0.003 1030 REMARK 3 DIHEDRAL : 12.236 2191 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 22 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.6788 -12.8146 -0.5878 REMARK 3 T TENSOR REMARK 3 T11: 0.2788 T22: 0.2426 REMARK 3 T33: 0.2590 T12: 0.0355 REMARK 3 T13: 0.0577 T23: -0.0791 REMARK 3 L TENSOR REMARK 3 L11: 3.8168 L22: 1.8860 REMARK 3 L33: 4.0526 L12: 0.5312 REMARK 3 L13: 0.1422 L23: 2.0215 REMARK 3 S TENSOR REMARK 3 S11: -0.1958 S12: 0.2793 S13: -0.3557 REMARK 3 S21: -0.3411 S22: -0.1181 S23: 0.2211 REMARK 3 S31: 0.3823 S32: -0.0992 S33: 0.2716 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.5533 -11.1794 10.7817 REMARK 3 T TENSOR REMARK 3 T11: 0.1845 T22: 0.1962 REMARK 3 T33: 0.3005 T12: -0.0012 REMARK 3 T13: 0.0630 T23: -0.0511 REMARK 3 L TENSOR REMARK 3 L11: 2.3607 L22: 2.0388 REMARK 3 L33: 4.9275 L12: -0.0912 REMARK 3 L13: 0.0975 L23: -0.7097 REMARK 3 S TENSOR REMARK 3 S11: -0.0849 S12: 0.0036 S13: -0.3753 REMARK 3 S21: 0.0310 S22: -0.0367 S23: 0.2794 REMARK 3 S31: 0.1751 S32: -0.3960 S33: 0.0854 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 219 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.4456 15.3109 11.6554 REMARK 3 T TENSOR REMARK 3 T11: 0.2801 T22: 0.3548 REMARK 3 T33: 0.3319 T12: 0.1241 REMARK 3 T13: -0.0943 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 1.7752 L22: 2.0173 REMARK 3 L33: 3.3638 L12: 0.4113 REMARK 3 L13: 0.9738 L23: 0.6196 REMARK 3 S TENSOR REMARK 3 S11: -0.0772 S12: -0.1587 S13: 0.2407 REMARK 3 S21: -0.1484 S22: -0.0744 S23: 0.3017 REMARK 3 S31: -0.6482 S32: -0.5871 S33: 0.2475 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 220 THROUGH 244 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.8285 20.0377 7.8117 REMARK 3 T TENSOR REMARK 3 T11: 0.3839 T22: 0.2025 REMARK 3 T33: 0.2998 T12: 0.0446 REMARK 3 T13: -0.0587 T23: 0.0921 REMARK 3 L TENSOR REMARK 3 L11: 4.4068 L22: 3.0348 REMARK 3 L33: 1.1963 L12: 1.0969 REMARK 3 L13: 0.2336 L23: -0.5538 REMARK 3 S TENSOR REMARK 3 S11: -0.0434 S12: 0.3027 S13: 0.5353 REMARK 3 S21: -0.6169 S22: 0.1346 S23: 0.0515 REMARK 3 S31: -0.5710 S32: -0.2310 S33: -0.1393 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 245 THROUGH 266 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.8969 11.6629 19.3788 REMARK 3 T TENSOR REMARK 3 T11: 0.1513 T22: 0.2883 REMARK 3 T33: 0.2668 T12: 0.0683 REMARK 3 T13: -0.0098 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 2.5393 L22: 7.6539 REMARK 3 L33: 6.1133 L12: 2.3192 REMARK 3 L13: 2.7433 L23: 6.6041 REMARK 3 S TENSOR REMARK 3 S11: -0.2528 S12: -0.3827 S13: 0.1372 REMARK 3 S21: 0.2747 S22: -0.2653 S23: 0.5713 REMARK 3 S31: 0.2980 S32: -0.5826 S33: 0.5396 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 267 THROUGH 299 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.9384 17.8938 19.9791 REMARK 3 T TENSOR REMARK 3 T11: 0.1723 T22: 0.2111 REMARK 3 T33: 0.1923 T12: 0.0568 REMARK 3 T13: -0.0417 T23: -0.0267 REMARK 3 L TENSOR REMARK 3 L11: 2.8344 L22: 3.9540 REMARK 3 L33: 2.1964 L12: 1.0067 REMARK 3 L13: 0.8580 L23: -0.6939 REMARK 3 S TENSOR REMARK 3 S11: -0.0853 S12: -0.2352 S13: 0.2970 REMARK 3 S21: 0.1954 S22: 0.0090 S23: 0.0760 REMARK 3 S31: -0.3679 S32: -0.1093 S33: 0.0225 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 300 THROUGH 344 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3746 0.4986 20.0940 REMARK 3 T TENSOR REMARK 3 T11: 0.2490 T22: 0.2965 REMARK 3 T33: 0.2279 T12: -0.0155 REMARK 3 T13: 0.0260 T23: 0.0471 REMARK 3 L TENSOR REMARK 3 L11: 2.7052 L22: 2.0744 REMARK 3 L33: 4.5776 L12: 1.5935 REMARK 3 L13: 3.5167 L23: 2.1081 REMARK 3 S TENSOR REMARK 3 S11: 0.3022 S12: -0.4524 S13: -0.0814 REMARK 3 S21: 0.2716 S22: -0.1570 S23: 0.1193 REMARK 3 S31: 0.1896 S32: -0.8107 S33: -0.1647 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 345 THROUGH 365 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6444 9.4933 17.8487 REMARK 3 T TENSOR REMARK 3 T11: 0.2237 T22: 0.1944 REMARK 3 T33: 0.2103 T12: 0.0243 REMARK 3 T13: -0.0134 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 2.5532 L22: 3.1051 REMARK 3 L33: 8.3042 L12: 2.1634 REMARK 3 L13: 3.6154 L23: 4.6004 REMARK 3 S TENSOR REMARK 3 S11: 0.0460 S12: -0.0615 S13: 0.0194 REMARK 3 S21: 0.0703 S22: -0.0173 S23: -0.0964 REMARK 3 S31: 0.1381 S32: 0.0086 S33: -0.0763 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 366 THROUGH 396 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4365 -10.6507 10.9840 REMARK 3 T TENSOR REMARK 3 T11: 0.3096 T22: 0.3762 REMARK 3 T33: 0.3480 T12: 0.0891 REMARK 3 T13: 0.0842 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.5564 L22: 0.7968 REMARK 3 L33: 1.6655 L12: 1.0950 REMARK 3 L13: 1.4487 L23: 1.0542 REMARK 3 S TENSOR REMARK 3 S11: -0.0087 S12: -0.1788 S13: -0.5445 REMARK 3 S21: 0.1370 S22: 0.1835 S23: -0.1394 REMARK 3 S31: 0.2608 S32: 0.1118 S33: -0.1409 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 20 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.3881 -8.3774 30.3929 REMARK 3 T TENSOR REMARK 3 T11: 0.1920 T22: 0.1366 REMARK 3 T33: 0.3170 T12: -0.0076 REMARK 3 T13: 0.0620 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 2.3608 L22: 2.2315 REMARK 3 L33: 2.3361 L12: -0.1190 REMARK 3 L13: 0.7323 L23: 0.7343 REMARK 3 S TENSOR REMARK 3 S11: 0.0081 S12: 0.0971 S13: -0.3146 REMARK 3 S21: -0.0531 S22: 0.0196 S23: -0.1712 REMARK 3 S31: 0.1009 S32: 0.1046 S33: -0.0148 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 181 THROUGH 386 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3695 11.2702 23.2237 REMARK 3 T TENSOR REMARK 3 T11: 0.1708 T22: 0.1634 REMARK 3 T33: 0.1780 T12: -0.0286 REMARK 3 T13: 0.0184 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 1.8055 L22: 1.5023 REMARK 3 L33: 1.3979 L12: -0.1657 REMARK 3 L13: 0.5789 L23: -0.5633 REMARK 3 S TENSOR REMARK 3 S11: -0.1078 S12: 0.1083 S13: 0.1304 REMARK 3 S21: -0.1425 S22: 0.0262 S23: -0.0821 REMARK 3 S31: -0.0720 S32: -0.0043 S33: 0.0875 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 7EBB 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_1300021102. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-13 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 : CLSI REMARK 200 BEAMLINE : 08ID-1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60356 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 80.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 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) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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 (%): 42.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 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 34.68000 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: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 VAL A 20 REMARK 465 PRO A 21 REMARK 465 SER A 45 REMARK 465 GLU A 46 REMARK 465 ASN A 47 REMARK 465 ALA A 48 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 ASN A 187 REMARK 465 PRO A 188 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 GLN A 387 REMARK 465 MET A 388 REMARK 465 SER A 389 REMARK 465 SER A 390 REMARK 465 GLU A 391 REMARK 465 ALA A 392 REMARK 465 ILE A 397 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 VAL B 318 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 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 23 CG CD OE1 OE2 REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 PHE A 330 CG CD1 CD2 CE1 CE2 CZ 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 ASN A 269 45.08 -92.54 REMARK 500 TYR A 356 -64.29 -136.17 REMARK 500 SER B 45 -95.22 -134.77 REMARK 500 CYS B 145 -3.82 -143.59 REMARK 500 ARG B 294 53.11 -117.05 REMARK 500 THR B 310 -9.61 83.34 REMARK 500 TYR B 356 -63.08 -136.76 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 ADP B 504 O3B 90.1 REMARK 620 3 ADP B 504 O2A 89.2 87.8 REMARK 620 4 SO4 B 505 O2 172.8 96.8 89.0 REMARK 620 N 1 2 3 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 THE SAME COMPOUND REMARK 900 RELATED ID: 7EAT 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 7EBB A 10 411 UNP Q16654 PDK4_HUMAN 10 411 DBREF 7EBB B 10 411 UNP Q16654 PDK4_HUMAN 10 411 SEQADV 7EBB GLY A 8 UNP Q16654 EXPRESSION TAG SEQADV 7EBB PRO A 9 UNP Q16654 EXPRESSION TAG SEQADV 7EBB GLY B 8 UNP Q16654 EXPRESSION TAG SEQADV 7EBB 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 42A A 502 11 HET SO4 A 503 5 HET SO4 B 501 5 HET SO4 B 502 5 HET MG B 503 1 HET ADP B 504 27 HET SO4 B 505 5 HETNAM SO4 SULFATE ION HETNAM 42A 1H-PYRROLO[2,3-B]PYRIDINE-3-CARBONITRILE HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 SO4 5(O4 S 2-) FORMUL 4 42A C8 H5 N3 FORMUL 8 MG MG 2+ FORMUL 9 ADP C10 H15 N5 O10 P2 FORMUL 11 HOH *294(H2 O) HELIX 1 AA1 ARG A 22 ARG A 29 1 8 HELIX 2 AA2 SER A 36 GLY A 44 1 9 HELIX 3 AA3 GLU A 50 ASP A 73 1 24 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 TYR A 386 1 8 HELIX 16 AB7 PRO B 21 SER B 28 1 8 HELIX 17 AB8 SER B 36 PHE B 43 1 8 HELIX 18 AB9 CYS B 49 ILE B 74 1 26 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 ASP B 109 HIS B 128 1 20 HELIX 22 AC4 ASN B 129 THR B 146 1 18 HELIX 23 AC5 ASN B 152 SER B 181 1 30 HELIX 24 AC6 VAL B 200 LEU B 220 1 21 HELIX 25 AC7 VAL B 244 GLN B 267 1 24 HELIX 26 AC8 PRO B 299 ARG B 301 5 3 HELIX 27 AC9 ILE B 302 PHE B 307 1 6 HELIX 28 AD1 TYR B 332 PHE B 344 1 13 HELIX 29 AD2 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 ASP A 293 -1 O SER A 292 N GLU A 277 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 280 N VAL B 230 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 2.16 LINK MG MG B 503 O3B ADP B 504 1555 1555 2.11 LINK MG MG B 503 O2A ADP B 504 1555 1555 1.95 LINK MG MG B 503 O2 SO4 B 505 1555 1555 2.09 CRYST1 70.624 69.360 81.283 90.00 100.12 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 0.014159 0.000000 0.002527 0.00000 SCALE2 0.000000 0.014418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012497 0.00000