HEADER TRANSFERASE/INHIBITOR 01-SEP-21 7VBV TITLE CRYSTAL STRUCTURE OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 IN COMPLEX TITLE 2 WITH COMPOUND 7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: [PYRUVATE DEHYDROGENASE (ACETYL-TRANSFERRING)] KINASE COMPND 3 ISOZYME 2, MITOCHONDRIAL; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 2,PDH KINASE 2,PDKII; 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: PDK2, PDHK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PDHK, KINASE INHIBITORS, FRAGMENT SCREENING, PDK1, PDK2, PDK3, PDK4, KEYWDS 2 TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.ORITA,S.DOI,T.IWANAGA,A.FUJISHIMA,T.ADACHI REVDAT 2 29-NOV-23 7VBV 1 REMARK REVDAT 1 16-FEB-22 7VBV 0 JRNL AUTH Y.BESSHO,T.AKAKI,Y.HARA,M.YAMAKAWA,S.OBIKA,G.MORI,M.UBUKATA, JRNL AUTH 2 K.YASUE,Y.NAKANE,Y.TERASAKO,T.ORITA,S.DOI,T.IWANAGA, JRNL AUTH 3 A.FUJISHIMA,T.ADACHI,H.UENO,T.MOTOMURA JRNL TITL STRUCTURE-BASED DRUG DESIGN OF NOVEL AND HIGHLY POTENT JRNL TITL 2 PYRUVATE DEHYDROGENASE KINASE INHIBITORS. JRNL REF BIOORG.MED.CHEM. V. 52 16514 2021 JRNL REFN ESSN 1464-3391 JRNL DOI 10.1016/J.BMC.2021.116514 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 55.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 54688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 2839 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 62.9500 - 6.0100 0.92 2574 137 0.1819 0.2287 REMARK 3 2 6.0000 - 4.7700 0.89 2496 125 0.1633 0.2170 REMARK 3 3 4.7700 - 4.1600 0.93 2621 144 0.1548 0.1750 REMARK 3 4 4.1600 - 3.7800 0.95 2677 124 0.1714 0.2314 REMARK 3 5 3.7800 - 3.5100 0.93 2604 150 0.1949 0.2256 REMARK 3 6 3.5100 - 3.3100 0.85 2394 153 0.2259 0.2511 REMARK 3 7 3.3100 - 3.1400 0.93 2604 152 0.2344 0.3140 REMARK 3 8 3.1400 - 3.0000 0.94 2640 140 0.2414 0.2265 REMARK 3 9 3.0000 - 2.8900 0.94 2658 132 0.2628 0.2545 REMARK 3 10 2.8900 - 2.7900 0.94 2613 148 0.2671 0.3242 REMARK 3 11 2.7900 - 2.7000 0.93 2625 147 0.2699 0.2708 REMARK 3 12 2.7000 - 2.6200 0.86 2434 142 0.2735 0.3356 REMARK 3 13 2.6200 - 2.5500 0.92 2538 159 0.2816 0.2956 REMARK 3 14 2.5500 - 2.4900 0.93 2634 142 0.2905 0.3007 REMARK 3 15 2.4900 - 2.4400 0.93 2616 152 0.2954 0.2783 REMARK 3 16 2.4400 - 2.3800 0.93 2609 154 0.2876 0.3082 REMARK 3 17 2.3800 - 2.3400 0.93 2598 160 0.3054 0.3228 REMARK 3 18 2.3400 - 2.2900 0.92 2628 150 0.3111 0.3045 REMARK 3 19 2.2900 - 2.2500 0.94 2628 126 0.3091 0.3662 REMARK 3 20 2.2500 - 2.2100 0.94 2664 96 0.3161 0.3173 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.924 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.13 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 : 0.004 5600 REMARK 3 ANGLE : 0.458 7571 REMARK 3 CHIRALITY : 0.039 832 REMARK 3 PLANARITY : 0.005 966 REMARK 3 DIHEDRAL : 10.595 2084 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 14 THROUGH 175 ) REMARK 3 ORIGIN FOR THE GROUP (A): 54.3697 46.3986 84.1837 REMARK 3 T TENSOR REMARK 3 T11: 0.7134 T22: 0.5648 REMARK 3 T33: 0.4617 T12: 0.0822 REMARK 3 T13: -0.2698 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 1.3604 L22: 1.9581 REMARK 3 L33: 1.8379 L12: -0.3770 REMARK 3 L13: -0.1880 L23: 0.3874 REMARK 3 S TENSOR REMARK 3 S11: -0.0956 S12: -0.2912 S13: 0.0344 REMARK 3 S21: 0.5588 S22: -0.0438 S23: -0.5059 REMARK 3 S31: -0.1000 S32: 0.3522 S33: 0.0008 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND ((RESID 176 THROUGH 374 ) OR (RESID REMARK 3 5000)) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2622 45.1318 61.5720 REMARK 3 T TENSOR REMARK 3 T11: 0.3761 T22: 0.4774 REMARK 3 T33: 0.2925 T12: 0.0523 REMARK 3 T13: -0.0269 T23: -0.0302 REMARK 3 L TENSOR REMARK 3 L11: 3.2997 L22: 2.4468 REMARK 3 L33: 1.6077 L12: 0.9812 REMARK 3 L13: 0.2704 L23: 0.5923 REMARK 3 S TENSOR REMARK 3 S11: -0.1841 S12: 0.5969 S13: -0.1840 REMARK 3 S21: 0.1111 S22: 0.1186 S23: -0.2965 REMARK 3 S31: -0.0157 S32: 0.1930 S33: -0.0091 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 14 THROUGH 175 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5845 48.7412 84.5953 REMARK 3 T TENSOR REMARK 3 T11: 0.7706 T22: 0.5047 REMARK 3 T33: 0.5094 T12: 0.0993 REMARK 3 T13: 0.2633 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.2149 L22: 1.9044 REMARK 3 L33: 2.3527 L12: -0.7136 REMARK 3 L13: -0.5316 L23: -0.1787 REMARK 3 S TENSOR REMARK 3 S11: -0.2292 S12: -0.1890 S13: -0.1022 REMARK 3 S21: 0.5248 S22: 0.0589 S23: 0.4902 REMARK 3 S31: -0.0303 S32: -0.3171 S33: -0.0010 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND ((RESID 176 THROUGH 372 ) OR (RESID REMARK 3 5000)) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3273 50.1592 61.4467 REMARK 3 T TENSOR REMARK 3 T11: 0.4202 T22: 0.5476 REMARK 3 T33: 0.2886 T12: 0.0556 REMARK 3 T13: 0.0088 T23: 0.0288 REMARK 3 L TENSOR REMARK 3 L11: 3.5876 L22: 1.9179 REMARK 3 L33: 1.6549 L12: 0.6368 REMARK 3 L13: -0.3921 L23: -0.3994 REMARK 3 S TENSOR REMARK 3 S11: -0.0622 S12: 0.5173 S13: 0.2386 REMARK 3 S21: 0.2269 S22: 0.0209 S23: 0.3409 REMARK 3 S31: -0.0958 S32: -0.1591 S33: -0.0064 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 7VBV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300024409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-15 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU 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 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54702 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 94.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.65300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 7EBH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA ACETATE PH 5.5, 100 MM REMARK 280 MAGNESIUM CHLORIDE AND 8% (V/V) ISOPROPANOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,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 28.09600 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 56.19200 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: 29640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 SER A 179 REMARK 465 THR A 180 REMARK 465 ASN A 181 REMARK 465 PRO A 182 REMARK 465 ALA A 183 REMARK 465 HIS A 184 REMARK 465 PRO A 185 REMARK 465 THR A 310 REMARK 465 ALA A 311 REMARK 465 PRO A 312 REMARK 465 THR A 313 REMARK 465 PRO A 314 REMARK 465 GLN A 315 REMARK 465 PRO A 316 REMARK 465 GLY A 317 REMARK 465 THR A 318 REMARK 465 GLY A 319 REMARK 465 GLY A 320 REMARK 465 THR A 321 REMARK 465 PRO A 322 REMARK 465 LEU A 323 REMARK 465 ALA A 324 REMARK 465 GLY A 325 REMARK 465 PHE A 326 REMARK 465 ASN A 375 REMARK 465 LYS A 376 REMARK 465 SER A 377 REMARK 465 ALA A 378 REMARK 465 TRP A 379 REMARK 465 ARG A 380 REMARK 465 HIS A 381 REMARK 465 TYR A 382 REMARK 465 GLN A 383 REMARK 465 THR A 384 REMARK 465 ILE A 385 REMARK 465 GLN A 386 REMARK 465 GLU A 387 REMARK 465 ALA A 388 REMARK 465 GLY A 389 REMARK 465 ASP A 390 REMARK 465 TRP A 391 REMARK 465 CYS A 392 REMARK 465 VAL A 393 REMARK 465 PRO A 394 REMARK 465 SER A 395 REMARK 465 THR A 396 REMARK 465 GLU A 397 REMARK 465 PRO A 398 REMARK 465 LYS A 399 REMARK 465 ASN A 400 REMARK 465 THR A 401 REMARK 465 SER A 402 REMARK 465 THR A 403 REMARK 465 TYR A 404 REMARK 465 ARG A 405 REMARK 465 VAL A 406 REMARK 465 SER A 407 REMARK 465 PHE B 39 REMARK 465 GLY B 40 REMARK 465 SER B 41 REMARK 465 SER B 42 REMARK 465 ASN B 43 REMARK 465 ALA B 44 REMARK 465 SER B 179 REMARK 465 THR B 180 REMARK 465 ASN B 181 REMARK 465 PRO B 182 REMARK 465 ALA B 183 REMARK 465 HIS B 184 REMARK 465 PRO B 185 REMARK 465 THR B 313 REMARK 465 PRO B 314 REMARK 465 GLN B 315 REMARK 465 PRO B 316 REMARK 465 GLY B 317 REMARK 465 THR B 318 REMARK 465 GLY B 319 REMARK 465 GLY B 320 REMARK 465 THR B 321 REMARK 465 PRO B 322 REMARK 465 VAL B 373 REMARK 465 TYR B 374 REMARK 465 ASN B 375 REMARK 465 LYS B 376 REMARK 465 SER B 377 REMARK 465 ALA B 378 REMARK 465 TRP B 379 REMARK 465 ARG B 380 REMARK 465 HIS B 381 REMARK 465 TYR B 382 REMARK 465 GLN B 383 REMARK 465 THR B 384 REMARK 465 ILE B 385 REMARK 465 GLN B 386 REMARK 465 GLU B 387 REMARK 465 ALA B 388 REMARK 465 GLY B 389 REMARK 465 ASP B 390 REMARK 465 TRP B 391 REMARK 465 CYS B 392 REMARK 465 VAL B 393 REMARK 465 PRO B 394 REMARK 465 SER B 395 REMARK 465 THR B 396 REMARK 465 GLU B 397 REMARK 465 PRO B 398 REMARK 465 LYS B 399 REMARK 465 ASN B 400 REMARK 465 THR B 401 REMARK 465 SER B 402 REMARK 465 THR B 403 REMARK 465 TYR B 404 REMARK 465 ARG B 405 REMARK 465 VAL B 406 REMARK 465 SER B 407 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS B 18 O SER B 267 3565 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 125 46.87 -99.14 REMARK 500 ASP A 143 69.23 -116.08 REMARK 500 ASN A 194 51.02 -112.73 REMARK 500 LYS A 233 -4.15 70.09 REMARK 500 HIS A 264 30.96 -98.97 REMARK 500 PHE A 352 -75.45 -122.68 REMARK 500 ASP B 125 34.18 -90.14 REMARK 500 ASP B 143 77.80 -105.27 REMARK 500 ASN B 194 58.45 -113.68 REMARK 500 LYS B 233 -1.22 71.32 REMARK 500 GLU B 282 -31.41 -131.39 REMARK 500 ASP B 290 -169.28 -117.95 REMARK 500 ARG B 291 51.50 -143.84 REMARK 500 TYR B 328 -71.26 -71.79 REMARK 500 PHE B 352 -79.71 -124.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7VBU RELATED DB: PDB REMARK 900 RELATED ID: 7VBX RELATED DB: PDB DBREF 7VBV A 16 407 UNP Q15119 PDK2_HUMAN 16 407 DBREF 7VBV B 16 407 UNP Q15119 PDK2_HUMAN 16 407 SEQADV 7VBV GLY A 14 UNP Q15119 EXPRESSION TAG SEQADV 7VBV SER A 15 UNP Q15119 EXPRESSION TAG SEQADV 7VBV GLY B 14 UNP Q15119 EXPRESSION TAG SEQADV 7VBV SER B 15 UNP Q15119 EXPRESSION TAG SEQRES 1 A 394 GLY SER ALA PRO LYS TYR ILE GLU HIS PHE SER LYS PHE SEQRES 2 A 394 SER PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP PHE SEQRES 3 A 394 GLY SER SER ASN ALA CYS GLU LYS THR SER PHE THR PHE SEQRES 4 A 394 LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE MET SEQRES 5 A 394 LYS GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER THR SEQRES 6 A 394 PRO SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SER SEQRES 7 A 394 LEU LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO GLU SEQRES 8 A 394 ASP HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU VAL SEQRES 9 A 394 THR ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR MET SEQRES 10 A 394 ALA GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY ASP SEQRES 11 A 394 ASP PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU ASP SEQRES 12 A 394 ARG PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU ILE SEQRES 13 A 394 ASN GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN PRO SEQRES 14 A 394 ALA HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN CYS SEQRES 15 A 394 ASN VAL SER GLU VAL VAL LYS ASP ALA TYR ASP MET ALA SEQRES 16 A 394 LYS LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO ASP SEQRES 17 A 394 LEU GLU ILE GLN GLU ILE ASN ALA ALA ASN SER LYS GLN SEQRES 18 A 394 PRO ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR HIS SEQRES 19 A 394 MET LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR SEQRES 20 A 394 VAL GLU SER HIS GLU SER SER LEU ILE LEU PRO PRO ILE SEQRES 21 A 394 LYS VAL MET VAL ALA LEU GLY GLU GLU ASP LEU SER ILE SEQRES 22 A 394 LYS MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS SEQRES 23 A 394 ILE GLU ARG LEU PHE SER TYR MET TYR SER THR ALA PRO SEQRES 24 A 394 THR PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA GLY SEQRES 25 A 394 PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA LYS SEQRES 26 A 394 TYR PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU GLY SEQRES 27 A 394 PHE GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER SEQRES 28 A 394 THR ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SER SEQRES 29 A 394 ALA TRP ARG HIS TYR GLN THR ILE GLN GLU ALA GLY ASP SEQRES 30 A 394 TRP CYS VAL PRO SER THR GLU PRO LYS ASN THR SER THR SEQRES 31 A 394 TYR ARG VAL SER SEQRES 1 B 394 GLY SER ALA PRO LYS TYR ILE GLU HIS PHE SER LYS PHE SEQRES 2 B 394 SER PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP PHE SEQRES 3 B 394 GLY SER SER ASN ALA CYS GLU LYS THR SER PHE THR PHE SEQRES 4 B 394 LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE MET SEQRES 5 B 394 LYS GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER THR SEQRES 6 B 394 PRO SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SER SEQRES 7 B 394 LEU LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO GLU SEQRES 8 B 394 ASP HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU VAL SEQRES 9 B 394 THR ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR MET SEQRES 10 B 394 ALA GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY ASP SEQRES 11 B 394 ASP PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU ASP SEQRES 12 B 394 ARG PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU ILE SEQRES 13 B 394 ASN GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN PRO SEQRES 14 B 394 ALA HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN CYS SEQRES 15 B 394 ASN VAL SER GLU VAL VAL LYS ASP ALA TYR ASP MET ALA SEQRES 16 B 394 LYS LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO ASP SEQRES 17 B 394 LEU GLU ILE GLN GLU ILE ASN ALA ALA ASN SER LYS GLN SEQRES 18 B 394 PRO ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR HIS SEQRES 19 B 394 MET LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR SEQRES 20 B 394 VAL GLU SER HIS GLU SER SER LEU ILE LEU PRO PRO ILE SEQRES 21 B 394 LYS VAL MET VAL ALA LEU GLY GLU GLU ASP LEU SER ILE SEQRES 22 B 394 LYS MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS SEQRES 23 B 394 ILE GLU ARG LEU PHE SER TYR MET TYR SER THR ALA PRO SEQRES 24 B 394 THR PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA GLY SEQRES 25 B 394 PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA LYS SEQRES 26 B 394 TYR PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU GLY SEQRES 27 B 394 PHE GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER SEQRES 28 B 394 THR ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SER SEQRES 29 B 394 ALA TRP ARG HIS TYR GLN THR ILE GLN GLU ALA GLY ASP SEQRES 30 B 394 TRP CYS VAL PRO SER THR GLU PRO LYS ASN THR SER THR SEQRES 31 B 394 TYR ARG VAL SER HET ACT A 501 4 HET ACT A 502 4 HET ACT A 503 4 HET DMS A 504 4 HET DMS A 505 4 HET 67V A 506 21 HET CL B 501 1 HET ACT B 502 4 HET ACT B 503 4 HET DMS B 504 4 HET DMS B 505 4 HET 67V B 506 21 HETNAM ACT ACETATE ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM 67V METHYL 8-CYCLOPROPYL-2-METHYL-9H-PYRIDO[2,3-B]INDOLE-3- HETNAM 2 67V CARBOXYLATE HETNAM CL CHLORIDE ION FORMUL 3 ACT 5(C2 H3 O2 1-) FORMUL 6 DMS 4(C2 H6 O S) FORMUL 8 67V 2(C17 H16 N2 O2) FORMUL 9 CL CL 1- FORMUL 15 HOH *82(H2 O) HELIX 1 AA1 SER A 15 PHE A 26 1 12 HELIX 2 AA2 SER A 32 GLY A 40 1 9 HELIX 3 AA3 SER A 41 ALA A 44 5 4 HELIX 4 AA4 CYS A 45 LEU A 70 1 26 HELIX 5 AA5 PRO A 72 SER A 77 1 6 HELIX 6 AA6 THR A 78 GLU A 97 1 20 HELIX 7 AA7 ASP A 105 HIS A 123 1 19 HELIX 8 AA8 ASP A 125 GLY A 142 1 18 HELIX 9 AA9 ASP A 144 PHE A 176 1 33 HELIX 10 AB1 VAL A 197 TYR A 216 1 20 HELIX 11 AB2 VAL A 241 HIS A 264 1 24 HELIX 12 AB3 PRO A 296 SER A 305 1 10 HELIX 13 AB4 TYR A 328 TYR A 339 1 12 HELIX 14 AB5 SER B 15 PHE B 26 1 12 HELIX 15 AB6 SER B 32 ASP B 38 1 7 HELIX 16 AB7 GLU B 46 LEU B 70 1 25 HELIX 17 AB8 PRO B 72 SER B 77 1 6 HELIX 18 AB9 THR B 78 GLU B 97 1 20 HELIX 19 AC1 PHE B 98 ASP B 100 5 3 HELIX 20 AC2 ASP B 105 HIS B 123 1 19 HELIX 21 AC3 ASP B 125 GLY B 142 1 18 HELIX 22 AC4 ASP B 144 PHE B 176 1 33 HELIX 23 AC5 VAL B 197 MET B 217 1 21 HELIX 24 AC6 VAL B 241 HIS B 264 1 24 HELIX 25 AC7 LYS B 299 SER B 305 1 7 HELIX 26 AC8 SER B 305 THR B 310 1 6 HELIX 27 AC9 GLY B 329 TYR B 339 1 11 SHEET 1 AA1 2 ASP A 192 ASN A 196 0 SHEET 2 AA1 2 HIS A 237 TYR A 240 -1 O TYR A 240 N ASP A 192 SHEET 1 AA2 5 LEU A 222 ASN A 228 0 SHEET 2 AA2 5 ILE A 273 LEU A 279 1 O VAL A 275 N GLU A 223 SHEET 3 AA2 5 ASP A 283 SER A 289 -1 O SER A 289 N LYS A 274 SHEET 4 AA2 5 GLY A 353 LYS A 361 -1 O ALA A 356 N MET A 288 SHEET 5 AA2 5 ASP A 343 MET A 349 -1 N ASP A 343 O TYR A 359 SHEET 1 AA3 2 ASP B 192 ASN B 196 0 SHEET 2 AA3 2 HIS B 237 TYR B 240 -1 O MET B 238 N CYS B 195 SHEET 1 AA4 5 LEU B 222 ASN B 228 0 SHEET 2 AA4 5 ILE B 273 LEU B 279 1 O VAL B 277 N ILE B 227 SHEET 3 AA4 5 ASP B 283 SER B 289 -1 O SER B 289 N LYS B 274 SHEET 4 AA4 5 GLY B 353 LYS B 361 -1 O LEU B 360 N LEU B 284 SHEET 5 AA4 5 ASP B 343 MET B 349 -1 N PHE B 347 O ASP B 355 CRYST1 109.300 109.300 84.288 90.00 90.00 120.00 P 31 6 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 0.009149 0.005282 0.000000 0.00000 SCALE2 0.000000 0.010565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011864 0.00000