HEADER TRANSFERASE 08-JUN-05 2BU2 TITLE CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 CONTAINING TITLE 2 PHYSIOLOGICAL AND SYNTHETIC LIGANDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE DEHYDROGENSAE KINASE ISOENZYME 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 2; COMPND 5 EC: 2.7.1.99; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFASTBAC1 KEYWDS GHKL MOTIF REGULATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.R.KNOECHEL,A.D.TUCKER,C.M.ROBINSON,C.PHILLIPS,W.TAYLOR,P.J.BUNGAY, AUTHOR 2 S.A.KASTEN,T.E.ROCHE,D.G.BROWN REVDAT 5 13-DEC-23 2BU2 1 LINK REVDAT 4 03-APR-19 2BU2 1 REMARK REVDAT 3 27-MAR-19 2BU2 1 SOURCE REVDAT 2 24-FEB-09 2BU2 1 VERSN REVDAT 1 02-FEB-06 2BU2 0 JRNL AUTH T.R.KNOECHEL,A.D.TUCKER,C.M.ROBINSON,C.PHILLIPS,W.TAYLOR, JRNL AUTH 2 P.J.BUNGAY,S.A.KASTEN,T.E.ROCHE,D.G.BROWN JRNL TITL REGULATORY ROLES OF THE N-TERMINAL DOMAIN BASED ON CRYSTAL JRNL TITL 2 STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 JRNL TITL 3 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS. JRNL REF BIOCHEMISTRY V. 45 402 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16401071 JRNL DOI 10.1021/BI051402S REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 21888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1067 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2883 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.97600 REMARK 3 B22 (A**2) : -4.97600 REMARK 3 B33 (A**2) : 9.95300 REMARK 3 B12 (A**2) : -5.98000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.635 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 46.98 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : HET.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : ATP.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BU2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1290024411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9326 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21971 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.440 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.16 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.910 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNX REMARK 200 STARTING MODEL: PDB ENTRY 2BTZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES PH5.8-6, 10% ISOPROPANOL, REMARK 280 200MM CALCIUM ACETATE, 10MG/ML PROTEIN 4 DEGREES, PH 5.80, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 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 27.95167 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 55.90333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.95167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.90333 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 54.35150 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 94.13956 REMARK 350 BIOMT3 2 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 32 REMARK 465 SER A 33 REMARK 465 GLY A 170 REMARK 465 SER A 171 REMARK 465 THR A 172 REMARK 465 ASN A 173 REMARK 465 PRO A 174 REMARK 465 ALA A 175 REMARK 465 HIS A 176 REMARK 465 ALA A 303 REMARK 465 PRO A 304 REMARK 465 THR A 305 REMARK 465 PRO A 306 REMARK 465 GLN A 307 REMARK 465 PRO A 308 REMARK 465 GLY A 309 REMARK 465 THR A 310 REMARK 465 GLY A 311 REMARK 465 GLY A 312 REMARK 465 THR A 313 REMARK 465 PRO A 314 REMARK 465 PRO A 386 REMARK 465 SER A 387 REMARK 465 THR A 388 REMARK 465 GLU A 389 REMARK 465 PRO A 390 REMARK 465 LYS A 391 REMARK 465 ASN A 392 REMARK 465 THR A 393 REMARK 465 SER A 394 REMARK 465 THR A 395 REMARK 465 TYR A 396 REMARK 465 ARG A 397 REMARK 465 VAL A 398 REMARK 465 SER A 399 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 GLN A 378 CG CD OE1 NE2 REMARK 470 GLU A 379 CG CD OE1 OE2 REMARK 470 VAL A 385 CA C O CB CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 72 O HOH A 2004 1.82 REMARK 500 OE1 GLU A 128 O HOH A 2004 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A 319 N - CA - C ANGL. DEV. = 21.5 DEGREES REMARK 500 TYR A 320 N - CA - C ANGL. DEV. = -21.6 DEGREES 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 30 41.77 -70.63 REMARK 500 ASN A 35 48.70 102.52 REMARK 500 ALA A 36 30.98 -86.62 REMARK 500 CYS A 37 124.03 72.03 REMARK 500 SER A 72 -80.46 -53.69 REMARK 500 GLU A 89 -25.31 -34.54 REMARK 500 LYS A 93 -176.51 -59.79 REMARK 500 PRO A 95 -138.14 -62.60 REMARK 500 GLU A 96 -45.19 61.56 REMARK 500 HIS A 98 0.04 -54.88 REMARK 500 ASP A 135 78.83 -118.51 REMARK 500 LYS A 178 -61.40 -0.35 REMARK 500 ILE A 180 79.66 -109.31 REMARK 500 ALA A 210 139.58 -177.81 REMARK 500 SER A 224 -40.36 -22.01 REMARK 500 PHE A 318 -78.89 -86.12 REMARK 500 TYR A 320 40.60 90.50 REMARK 500 PHE A 344 -66.31 -140.93 REMARK 500 GLU A 379 97.14 -179.32 REMARK 500 ALA A 380 105.79 79.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 11 0.07 SIDE CHAIN 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 A1388 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 247 OD1 REMARK 620 2 ATP A1386 O2G 163.6 REMARK 620 3 ATP A1386 O1A 85.6 81.8 REMARK 620 4 ATP A1386 O2B 84.0 84.8 86.7 REMARK 620 5 HOH A2040 O 96.4 95.2 95.6 177.7 REMARK 620 6 HOH A2087 O 86.4 104.9 170.2 86.9 90.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1388 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A1386 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TF1 A1387 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BTZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS REMARK 900 RELATED ID: 2BU5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS REMARK 900 RELATED ID: 2BU6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS REMARK 900 RELATED ID: 2BU7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS REMARK 900 RELATED ID: 2BU8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS REMARK 999 REMARK 999 SEQUENCE REMARK 999 N -TERMINAL GS CLONING ARTEFACT DBREF 2BU2 A 6 7 PDB 2BU2 2BU2 6 7 DBREF 2BU2 A 8 399 UNP Q15119 PDK2_HUMAN 16 407 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 HET ATP A1386 31 HET TF1 A1387 27 HET MG A1388 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM TF1 4-({(2R,5S)-2,5-DIMETHYL-4-[(2R)-3,3,3-TRIFLUORO-2- HETNAM 2 TF1 HYDROXY-2-METHYLPROPANOYL]PIPERAZIN-1-YL}CARBONYL) HETNAM 3 TF1 BENZONITRILE HETNAM MG MAGNESIUM ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 TF1 C18 H20 F3 N3 O3 FORMUL 4 MG MG 2+ FORMUL 5 HOH *91(H2 O) HELIX 1 1 SER A 7 SER A 16 1 10 HELIX 2 2 SER A 24 ASP A 30 1 7 HELIX 3 3 GLU A 38 LEU A 62 1 25 HELIX 4 4 PRO A 64 SER A 69 1 6 HELIX 5 5 THR A 70 GLU A 89 1 20 HELIX 6 6 LEU A 101 HIS A 115 1 15 HELIX 7 7 ASP A 117 TYR A 133 1 17 HELIX 8 8 ASP A 136 PHE A 168 1 33 HELIX 9 9 VAL A 189 MET A 209 1 21 HELIX 10 10 VAL A 233 SER A 255 1 23 HELIX 11 11 PRO A 288 GLU A 293 1 6 HELIX 12 12 ARG A 294 SER A 297 5 4 HELIX 13 13 TYR A 320 PHE A 332 1 13 HELIX 14 14 ASN A 367 ARG A 372 1 6 HELIX 15 15 HIS A 373 GLN A 375 5 3 SHEET 1 AA 2 ASP A 184 ASN A 188 0 SHEET 2 AA 2 HIS A 229 TYR A 232 -1 O MET A 230 N CYS A 187 SHEET 1 AB 5 LEU A 214 ASN A 220 0 SHEET 2 AB 5 ILE A 265 LEU A 271 1 O ILE A 265 N GLU A 215 SHEET 3 AB 5 ASP A 275 GLY A 285 -1 O SER A 277 N ALA A 270 SHEET 4 AB 5 PHE A 344 LYS A 353 -1 O PHE A 344 N GLY A 285 SHEET 5 AB 5 ASP A 335 MET A 341 -1 O ASP A 335 N TYR A 351 LINK OD1 ASN A 247 MG MG A1388 1555 1555 2.30 LINK O2G ATP A1386 MG MG A1388 1555 1555 2.00 LINK O1A ATP A1386 MG MG A1388 1555 1555 2.30 LINK O2B ATP A1386 MG MG A1388 1555 1555 2.21 LINK MG MG A1388 O HOH A2040 1555 1555 1.98 LINK MG MG A1388 O HOH A2087 1555 1555 2.00 SITE 1 AC1 4 ASN A 247 ATP A1386 HOH A2040 HOH A2087 SITE 1 AC2 26 GLU A 243 ASN A 247 ARG A 250 ALA A 251 SITE 2 AC2 26 ASP A 282 VAL A 287 LEU A 295 LEU A 315 SITE 3 AC2 26 ALA A 316 GLY A 317 PHE A 318 GLY A 319 SITE 4 AC2 26 TYR A 320 GLY A 321 LEU A 322 PRO A 323 SITE 5 AC2 26 THR A 346 MG A1388 HOH A2040 HOH A2057 SITE 6 AC2 26 HOH A2084 HOH A2085 HOH A2086 HOH A2087 SITE 7 AC2 26 HOH A2088 HOH A2090 SITE 1 AC3 10 LEU A 23 GLN A 27 PHE A 28 PHE A 31 SITE 2 AC3 10 SER A 41 PHE A 44 LEU A 45 LEU A 160 SITE 3 AC3 10 GLN A 163 HOH A2091 CRYST1 108.703 108.703 83.855 90.00 90.00 120.00 P 64 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 0.009199 0.005311 0.000000 0.00000 SCALE2 0.000000 0.010623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011925 0.00000