PDB Short entry for 3D2R HEADER TRANSFERASE 08-MAY-08 3D2R TITLE CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 4 IN TITLE 2 COMPLEX WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: [PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 4; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 4; COMPND 5 EC: 2.7.11.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: PDK4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN-NUCLEOTIDE COMPLEX, HOMODIMER, GHKL SUPERFAMILY, KINASE, KEYWDS 2 CARBOHYDRATE METABOLISM, GLUCOSE METABOLISM, MITOCHONDRION, KEYWDS 3 PHOSPHOPROTEIN, TRANSFERASE, TRANSIT PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR M.KATO,R.M.WYNN,L.C.CHUANG,S.-C.TSO,J.LI,D.T.CHUANG REVDAT 6 30-AUG-23 3D2R 1 REMARK SEQADV SHEET LINK REVDAT 5 13-JUL-11 3D2R 1 VERSN REVDAT 4 24-FEB-09 3D2R 1 VERSN REVDAT 3 23-SEP-08 3D2R 1 JRNL REVDAT 2 19-AUG-08 3D2R 1 AUTHOR REVDAT 1 05-AUG-08 3D2R 0 JRNL AUTH R.M.WYNN,M.KATO,J.L.CHUANG,S.C.TSO,J.LI,D.T.CHUANG JRNL TITL PYRUVATE DEHYDROGENASE KINASE-4 STRUCTURES REVEAL A JRNL TITL 2 METASTABLE OPEN CONFORMATION FOSTERING ROBUST CORE-FREE JRNL TITL 3 BASAL ACTIVITY. JRNL REF J.BIOL.CHEM. V. 283 25305 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18658136 JRNL DOI 10.1074/JBC.M802249200 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 47925 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2564 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3392 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5756 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 287 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 34.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : 0.84000 REMARK 3 B33 (A**2) : -0.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.61000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.193 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.464 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5958 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8084 ; 1.817 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 706 ; 6.056 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 276 ;36.978 ;24.130 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1012 ;16.829 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;19.908 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 904 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4458 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3583 ; 1.059 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5833 ; 1.819 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2375 ; 3.062 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2251 ; 4.738 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 21 A 181 REMARK 3 ORIGIN FOR THE GROUP (A): -26.9380 -11.9830 7.1290 REMARK 3 T TENSOR REMARK 3 T11: -0.1106 T22: -0.0851 REMARK 3 T33: -0.0480 T12: -0.0132 REMARK 3 T13: 0.0302 T23: -0.0446 REMARK 3 L TENSOR REMARK 3 L11: 2.5719 L22: 1.9922 REMARK 3 L33: 4.6537 L12: -0.0897 REMARK 3 L13: 0.3443 L23: -0.2773 REMARK 3 S TENSOR REMARK 3 S11: -0.0690 S12: -0.0546 S13: -0.1942 REMARK 3 S21: -0.0165 S22: -0.0017 S23: 0.1631 REMARK 3 S31: 0.1578 S32: -0.3155 S33: 0.0706 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 189 A 386 REMARK 3 ORIGIN FOR THE GROUP (A): -16.1020 9.6840 16.0490 REMARK 3 T TENSOR REMARK 3 T11: -0.1426 T22: -0.0935 REMARK 3 T33: -0.1484 T12: 0.0481 REMARK 3 T13: -0.0307 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.1948 L22: 2.3152 REMARK 3 L33: 2.2940 L12: 0.5444 REMARK 3 L13: 0.1909 L23: 0.8304 REMARK 3 S TENSOR REMARK 3 S11: -0.0404 S12: -0.0476 S13: 0.0328 REMARK 3 S21: -0.0162 S22: 0.0381 S23: 0.1022 REMARK 3 S31: -0.0222 S32: -0.1372 S33: 0.0023 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 20 B 181 REMARK 3 ORIGIN FOR THE GROUP (A): 22.6980 -8.5930 30.8200 REMARK 3 T TENSOR REMARK 3 T11: -0.1609 T22: -0.1369 REMARK 3 T33: -0.0940 T12: -0.0001 REMARK 3 T13: 0.0145 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 3.0009 L22: 2.3426 REMARK 3 L33: 1.9050 L12: -0.4286 REMARK 3 L13: 0.9334 L23: -0.1858 REMARK 3 S TENSOR REMARK 3 S11: 0.0802 S12: 0.0918 S13: -0.1405 REMARK 3 S21: -0.0506 S22: 0.0461 S23: -0.0822 REMARK 3 S31: 0.1000 S32: 0.1980 S33: -0.1262 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 188 B 386 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0090 11.3450 22.5930 REMARK 3 T TENSOR REMARK 3 T11: -0.1385 T22: -0.1136 REMARK 3 T33: -0.1573 T12: -0.0249 REMARK 3 T13: 0.0049 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.2848 L22: 1.4557 REMARK 3 L33: 1.9486 L12: -0.1537 REMARK 3 L13: 0.7323 L23: -0.5539 REMARK 3 S TENSOR REMARK 3 S11: -0.0458 S12: 0.0964 S13: 0.0456 REMARK 3 S21: -0.1369 S22: 0.0098 S23: -0.0126 REMARK 3 S31: -0.1250 S32: 0.0423 S33: 0.0359 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3D2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047518. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50510 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.25500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2ZKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9M AMMONIUM SULFATE, 4% POLYETHYLENE REMARK 280 GLYCOL 400, 100 MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 34.68700 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: 6200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.7 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 ALA A 18 REMARK 465 SER A 19 REMARK 465 VAL A 20 REMARK 465 ALA A 48 REMARK 465 THR A 146 REMARK 465 VAL A 147 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 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 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 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 ALA B 18 REMARK 465 SER B 19 REMARK 465 ASP B 143 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 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 ILE B 397 CG1 CG2 CD1 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 ASP B 148 CB - CG - OD1 ANGL. DEV. = -7.7 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 PRO A 32 151.84 -48.84 REMARK 500 LEU A 220 -3.57 72.11 REMARK 500 ASP A 236 -6.60 79.16 REMARK 500 ARG A 294 53.86 -114.06 REMARK 500 THR A 310 -19.27 78.85 REMARK 500 TYR A 356 -63.81 -132.69 REMARK 500 CYS B 145 0.57 -46.03 REMARK 500 THR B 146 -21.08 74.30 REMARK 500 ASP B 236 -2.78 65.91 REMARK 500 ARG B 294 56.45 -117.56 REMARK 500 THR B 310 -18.13 80.65 REMARK 500 TYR B 356 -60.67 -136.04 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 A 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 258 OD1 REMARK 620 2 ADP A 501 O3B 96.1 REMARK 620 3 ADP A 501 O1A 92.2 87.6 REMARK 620 4 HOH A 508 O 85.5 175.0 97.0 REMARK 620 5 HOH A 516 O 175.2 85.3 92.4 92.7 REMARK 620 6 HOH A 534 O 84.0 86.2 172.4 89.3 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 258 OD1 REMARK 620 2 ADP B 501 O3B 95.0 REMARK 620 3 ADP B 501 O1A 89.3 86.5 REMARK 620 4 HOH B 513 O 85.1 179.5 93.1 REMARK 620 5 HOH B 525 O 178.4 85.8 89.4 94.1 REMARK 620 6 HOH B 527 O 86.3 89.8 174.0 90.6 95.1 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 A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZKJ RELATED DB: PDB REMARK 900 CRYSTALLIZED IN PHOSPHATE BUFFER DBREF 3D2R A 20 411 UNP Q16654 PDK4_HUMAN 20 411 DBREF 3D2R B 20 411 UNP Q16654 PDK4_HUMAN 20 411 SEQADV 3D2R ALA A 18 UNP Q16654 EXPRESSION TAG SEQADV 3D2R SER A 19 UNP Q16654 EXPRESSION TAG SEQADV 3D2R ALA B 18 UNP Q16654 EXPRESSION TAG SEQADV 3D2R SER B 19 UNP Q16654 EXPRESSION TAG SEQRES 1 A 394 ALA SER VAL PRO ARG GLU VAL GLU HIS PHE SER ARG TYR SEQRES 2 A 394 SER PRO SER PRO LEU SER MET LYS GLN LEU LEU ASP PHE SEQRES 3 A 394 GLY SER GLU ASN ALA CYS GLU ARG THR SER PHE ALA PHE SEQRES 4 A 394 LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE LEU SEQRES 5 A 394 LYS GLU ILE ASP ILE LEU PRO THR GLN LEU VAL ASN THR SEQRES 6 A 394 SER SER VAL GLN LEU VAL LYS SER TRP TYR ILE GLN SER SEQRES 7 A 394 LEU MET ASP LEU VAL GLU PHE HIS GLU LYS SER PRO ASP SEQRES 8 A 394 ASP GLN LYS ALA LEU SER ASP PHE VAL ASP THR LEU ILE SEQRES 9 A 394 LYS VAL ARG ASN ARG HIS HIS ASN VAL VAL PRO THR MET SEQRES 10 A 394 ALA GLN GLY ILE ILE GLU TYR LYS ASP ALA CYS THR VAL SEQRES 11 A 394 ASP PRO VAL THR ASN GLN ASN LEU GLN TYR PHE LEU ASP SEQRES 12 A 394 ARG PHE TYR MET ASN ARG ILE SER THR ARG MET LEU MET SEQRES 13 A 394 ASN GLN HIS ILE LEU ILE PHE SER ASP SER GLN THR GLY SEQRES 14 A 394 ASN PRO SER HIS ILE GLY SER ILE ASP PRO ASN CYS ASP SEQRES 15 A 394 VAL VAL ALA VAL VAL GLN ASP ALA PHE GLU CYS SER ARG SEQRES 16 A 394 MET LEU CYS ASP GLN TYR TYR LEU SER SER PRO GLU LEU SEQRES 17 A 394 LYS LEU THR GLN VAL ASN GLY LYS PHE PRO ASP GLN PRO SEQRES 18 A 394 ILE HIS ILE VAL TYR VAL PRO SER HIS LEU HIS HIS MET SEQRES 19 A 394 LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR VAL SEQRES 20 A 394 GLU HIS GLN GLU ASN GLN PRO SER LEU THR PRO ILE GLU SEQRES 21 A 394 VAL ILE VAL VAL LEU GLY LYS GLU ASP LEU THR ILE LYS SEQRES 22 A 394 ILE SER ASP ARG GLY GLY GLY VAL PRO LEU ARG ILE ILE SEQRES 23 A 394 ASP ARG LEU PHE SER TYR THR TYR SER THR ALA PRO THR SEQRES 24 A 394 PRO VAL MET ASP ASN SER ARG ASN ALA 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 ASN LEU TYR SER LEU SER GLY SEQRES 27 A 394 TYR GLY THR ASP ALA ILE ILE TYR LEU LYS ALA LEU SER SEQRES 28 A 394 SER GLU SER ILE GLU LYS LEU PRO VAL PHE ASN LYS SER SEQRES 29 A 394 ALA PHE LYS HIS TYR GLN MET SER SER GLU ALA ASP ASP SEQRES 30 A 394 TRP CYS ILE PRO SER ARG GLU PRO LYS ASN LEU ALA LYS SEQRES 31 A 394 GLU VAL ALA MET SEQRES 1 B 394 ALA SER VAL PRO ARG GLU VAL GLU HIS PHE SER ARG TYR SEQRES 2 B 394 SER PRO SER PRO LEU SER MET LYS GLN LEU LEU ASP PHE SEQRES 3 B 394 GLY SER GLU ASN ALA CYS GLU ARG THR SER PHE ALA PHE SEQRES 4 B 394 LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE LEU SEQRES 5 B 394 LYS GLU ILE ASP ILE LEU PRO THR GLN LEU VAL ASN THR SEQRES 6 B 394 SER SER VAL GLN LEU VAL LYS SER TRP TYR ILE GLN SER SEQRES 7 B 394 LEU MET ASP LEU VAL GLU PHE HIS GLU LYS SER PRO ASP SEQRES 8 B 394 ASP GLN LYS ALA LEU SER ASP PHE VAL ASP THR LEU ILE SEQRES 9 B 394 LYS VAL ARG ASN ARG HIS HIS ASN VAL VAL PRO THR MET SEQRES 10 B 394 ALA GLN GLY ILE ILE GLU TYR LYS ASP ALA CYS THR VAL SEQRES 11 B 394 ASP PRO VAL THR ASN GLN ASN LEU GLN TYR PHE LEU ASP SEQRES 12 B 394 ARG PHE TYR MET ASN ARG ILE SER THR ARG MET LEU MET SEQRES 13 B 394 ASN GLN HIS ILE LEU ILE PHE SER ASP SER GLN THR GLY SEQRES 14 B 394 ASN PRO SER HIS ILE GLY SER ILE ASP PRO ASN CYS ASP SEQRES 15 B 394 VAL VAL ALA VAL VAL GLN ASP ALA PHE GLU CYS SER ARG SEQRES 16 B 394 MET LEU CYS ASP GLN TYR TYR LEU SER SER PRO GLU LEU SEQRES 17 B 394 LYS LEU THR GLN VAL ASN GLY LYS PHE PRO ASP GLN PRO SEQRES 18 B 394 ILE HIS ILE VAL TYR VAL PRO SER HIS LEU HIS HIS MET SEQRES 19 B 394 LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR VAL SEQRES 20 B 394 GLU HIS GLN GLU ASN GLN PRO SER LEU THR PRO ILE GLU SEQRES 21 B 394 VAL ILE VAL VAL LEU GLY LYS GLU ASP LEU THR ILE LYS SEQRES 22 B 394 ILE SER ASP ARG GLY GLY GLY VAL PRO LEU ARG ILE ILE SEQRES 23 B 394 ASP ARG LEU PHE SER TYR THR TYR SER THR ALA PRO THR SEQRES 24 B 394 PRO VAL MET ASP ASN SER ARG ASN ALA 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 ASN LEU TYR SER LEU SER GLY SEQRES 27 B 394 TYR GLY THR ASP ALA ILE ILE TYR LEU LYS ALA LEU SER SEQRES 28 B 394 SER GLU SER ILE GLU LYS LEU PRO VAL PHE ASN LYS SER SEQRES 29 B 394 ALA PHE LYS HIS TYR GLN MET SER SER GLU ALA ASP ASP SEQRES 30 B 394 TRP CYS ILE PRO SER ARG GLU PRO LYS ASN LEU ALA LYS SEQRES 31 B 394 GLU VAL ALA MET HET MG A 500 1 HET ADP A 501 27 HET GOL A 502 6 HET MG B 500 1 HET ADP B 501 27 HET GOL B 502 6 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG 2(MG 2+) FORMUL 4 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 9 HOH *287(H2 O) HELIX 1 1 PRO A 21 ARG A 29 1 9 HELIX 2 2 SER A 36 PHE A 43 1 8 HELIX 3 3 CYS A 49 ASP A 73 1 25 HELIX 4 4 PRO A 76 ASN A 81 1 6 HELIX 5 5 THR A 82 GLU A 101 1 20 HELIX 6 6 PHE A 102 LYS A 105 5 4 HELIX 7 7 ASP A 109 HIS A 128 1 20 HELIX 8 8 ASN A 129 CYS A 145 1 17 HELIX 9 9 ASP A 148 SER A 181 1 34 HELIX 10 10 VAL A 200 LEU A 220 1 21 HELIX 11 11 VAL A 244 GLN A 267 1 24 HELIX 12 12 PRO A 299 ARG A 301 5 3 HELIX 13 13 ILE A 302 PHE A 307 1 6 HELIX 14 14 TYR A 332 PHE A 344 1 13 HELIX 15 15 ASN A 379 TYR A 386 1 8 HELIX 16 16 PRO B 21 ARG B 29 1 9 HELIX 17 17 SER B 36 GLY B 44 1 9 HELIX 18 18 GLU B 46 ALA B 48 5 3 HELIX 19 19 CYS B 49 ILE B 74 1 26 HELIX 20 20 PRO B 76 ASN B 81 1 6 HELIX 21 21 THR B 82 GLU B 101 1 20 HELIX 22 22 PHE B 102 LYS B 105 5 4 HELIX 23 23 ASP B 109 HIS B 127 1 19 HELIX 24 24 ASN B 129 LYS B 142 1 14 HELIX 25 25 ASN B 152 SER B 181 1 30 HELIX 26 26 VAL B 200 LEU B 220 1 21 HELIX 27 27 VAL B 244 GLN B 267 1 24 HELIX 28 28 PRO B 299 ILE B 303 5 5 HELIX 29 29 ASP B 304 SER B 308 5 5 HELIX 30 30 TYR B 332 PHE B 344 1 13 HELIX 31 31 ASN B 379 TYR B 386 1 8 SHEET 1 A 2 ASP A 195 ASP A 199 0 SHEET 2 A 2 HIS A 240 TYR A 243 -1 O TYR A 243 N ASP A 195 SHEET 1 B 5 LEU A 225 ASN A 231 0 SHEET 2 B 5 ILE A 276 LEU A 282 1 O VAL A 278 N LYS A 226 SHEET 3 B 5 ASP A 286 ASP A 293 -1 O THR A 288 N VAL A 281 SHEET 4 B 5 GLY A 357 LYS A 365 -1 O ALA A 360 N ILE A 291 SHEET 5 B 5 ASP A 347 LEU A 353 -1 N TYR A 351 O ASP A 359 SHEET 1 C 1 LEU A 375 PRO A 376 0 SHEET 1 D 2 ASP B 195 ASP B 199 0 SHEET 2 D 2 HIS B 240 TYR B 243 -1 O TYR B 243 N ASP B 195 SHEET 1 E 5 LEU B 225 ASN B 231 0 SHEET 2 E 5 ILE B 276 LEU B 282 1 O VAL B 278 N LYS B 226 SHEET 3 E 5 ASP B 286 ASP B 293 -1 O SER B 292 N GLU B 277 SHEET 4 E 5 GLY B 357 LYS B 365 -1 O ALA B 360 N ILE B 291 SHEET 5 E 5 ASP B 347 LEU B 353 -1 N LEU B 353 O GLY B 357 LINK OD1 ASN A 258 MG MG A 500 1555 1555 2.14 LINK MG MG A 500 O3B ADP A 501 1555 1555 2.18 LINK MG MG A 500 O1A ADP A 501 1555 1555 2.00 LINK MG MG A 500 O HOH A 508 1555 1555 2.10 LINK MG MG A 500 O HOH A 516 1555 1555 2.21 LINK MG MG A 500 O HOH A 534 1555 1555 2.26 LINK OD1 ASN B 258 MG MG B 500 1555 1555 2.14 LINK MG MG B 500 O3B ADP B 501 1555 1555 2.09 LINK MG MG B 500 O1A ADP B 501 1555 1555 2.04 LINK MG MG B 500 O HOH B 513 1555 1555 2.16 LINK MG MG B 500 O HOH B 525 1555 1555 1.97 LINK MG MG B 500 O HOH B 527 1555 1555 2.06 SITE 1 AC1 1 ASN A 258 SITE 1 AC2 1 ASN B 258 SITE 1 AC3 15 ASN A 258 ARG A 261 ALA A 262 ASP A 293 SITE 2 AC3 15 LEU A 306 TYR A 311 SER A 312 THR A 313 SITE 3 AC3 15 ALA A 328 GLY A 329 PHE A 330 GLY A 331 SITE 4 AC3 15 GLY A 333 LEU A 334 THR A 358 SITE 1 AC4 15 ASN B 258 ARG B 261 ALA B 262 ASP B 293 SITE 2 AC4 15 LEU B 306 TYR B 311 SER B 312 THR B 313 SITE 3 AC4 15 ALA B 328 GLY B 329 PHE B 330 GLY B 331 SITE 4 AC4 15 GLY B 333 LEU B 334 THR B 358 SITE 1 AC5 4 ASP A 160 LYS A 342 LYS A 374 TRP B 395 SITE 1 AC6 5 TRP A 395 ASP B 160 LEU B 339 LYS B 342 SITE 2 AC6 5 LYS B 374 CRYST1 70.595 69.374 82.328 90.00 99.26 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 0.014165 0.000000 0.002310 0.00000 SCALE2 0.000000 0.014415 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012307 0.00000