HEADER TRANSFERASE 12-DEC-19 6LIL TITLE CRYSTAL STRUCTURE OF HUMAN PDK2 COMPLEXED WITH AN ALLOSTERIC INHIBITOR TITLE 2 COMPOUND 8C 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 2,PYRUVATE DEHYDROGENASE COMPND 6 KINASE ISOFORM 2,PDKII; COMPND 7 EC: 2.7.11.2; COMPND 8 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 MITOCHONDRIA, KINASE, INHIBITOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.KANG,J.KIM REVDAT 2 22-NOV-23 6LIL 1 REMARK REVDAT 1 30-SEP-20 6LIL 0 JRNL AUTH J.KANG,H.S.PAGIRE,D.KANG,Y.H.SONG,I.K.LEE,K.T.LEE,C.J.PARK, JRNL AUTH 2 J.H.AHN,J.KIM JRNL TITL STRUCTURAL BASIS FOR THE INHIBITION OF PDK2 BY NOVEL ATP- JRNL TITL 2 AND LIPOYL-BINDING SITE TARGETING COMPOUNDS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 527 778 2020 JRNL REFN ESSN 1090-2104 JRNL PMID 32444142 JRNL DOI 10.1016/J.BBRC.2020.04.102 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 59243 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2955 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4347 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 196 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5438 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 112 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.90000 REMARK 3 B22 (A**2) : -0.36000 REMARK 3 B33 (A**2) : 0.67000 REMARK 3 B12 (A**2) : -1.43000 REMARK 3 B13 (A**2) : 0.97000 REMARK 3 B23 (A**2) : -0.72000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.362 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5694 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5215 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7720 ; 1.528 ; 1.641 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12104 ; 1.351 ; 1.569 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 688 ; 6.481 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 277 ;30.306 ;22.455 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 944 ;14.966 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;20.787 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 732 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6280 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1176 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 16 373 B 16 373 11135 0.070 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6LIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300012699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62684 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 1.23100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4MP2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM CITRATE TRIBASIC PH 7.0, REMARK 280 20% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 4370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 MET A -24 REMARK 465 ALA A -23 REMARK 465 GLY A -22 REMARK 465 SER A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 GLY A -14 REMARK 465 MET A -13 REMARK 465 ALA A -12 REMARK 465 SER A -11 REMARK 465 MET A -10 REMARK 465 THR A -9 REMARK 465 GLY A -8 REMARK 465 GLY A -7 REMARK 465 GLN A -6 REMARK 465 GLN A -5 REMARK 465 MET A -4 REMARK 465 GLY A -3 REMARK 465 ARG A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 ASP A 1 REMARK 465 ASP A 2 REMARK 465 ASP A 3 REMARK 465 ASP A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 LEU A 7 REMARK 465 LEU A 8 REMARK 465 LYS A 9 REMARK 465 ASN A 10 REMARK 465 ALA A 11 REMARK 465 SER A 12 REMARK 465 LEU A 13 REMARK 465 ALA A 14 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 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 TYR A 374 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 MET B -24 REMARK 465 ALA B -23 REMARK 465 GLY B -22 REMARK 465 SER B -21 REMARK 465 HIS B -20 REMARK 465 HIS B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 GLY B -14 REMARK 465 MET B -13 REMARK 465 ALA B -12 REMARK 465 SER B -11 REMARK 465 MET B -10 REMARK 465 THR B -9 REMARK 465 GLY B -8 REMARK 465 GLY B -7 REMARK 465 GLN B -6 REMARK 465 GLN B -5 REMARK 465 MET B -4 REMARK 465 GLY B -3 REMARK 465 ARG B -2 REMARK 465 SER B -1 REMARK 465 GLY B 0 REMARK 465 ASP B 1 REMARK 465 ASP B 2 REMARK 465 ASP B 3 REMARK 465 ASP B 4 REMARK 465 LYS B 5 REMARK 465 ALA B 6 REMARK 465 LEU B 7 REMARK 465 LEU B 8 REMARK 465 LYS B 9 REMARK 465 ASN B 10 REMARK 465 ALA B 11 REMARK 465 SER B 12 REMARK 465 LEU B 13 REMARK 465 ALA B 14 REMARK 465 GLY B 15 REMARK 465 GLY B 178 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 PRO B 312 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 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 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 LYS A 18 CG CD CE NZ REMARK 470 TYR A 19 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 LYS A 47 CG CD CE NZ REMARK 470 LEU A 70 CG CD1 CD2 REMARK 470 ASP A 73 CG OD1 OD2 REMARK 470 ASP A 100 CG OD1 OD2 REMARK 470 ASP A 144 CG OD1 OD2 REMARK 470 VAL A 146 CG1 CG2 REMARK 470 GLN A 149 CG CD OE1 NE2 REMARK 470 ASN A 150 CG OD1 ND2 REMARK 470 HIS A 184 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 18 CG CD CE NZ REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 ASP B 100 CG OD1 OD2 REMARK 470 ASP B 144 CG OD1 OD2 REMARK 470 GLN B 149 CG CD OE1 NE2 REMARK 470 HIS B 184 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 214 CG CD CE NZ REMARK 470 LYS B 233 CG CD CE NZ REMARK 470 GLU B 301 CG CD OE1 OE2 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 ARG A 166 NE - CZ - NH1 ANGL. DEV. = -3.4 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 145 -114.55 -91.01 REMARK 500 ARG A 291 51.09 -110.39 REMARK 500 PRO B 145 -128.13 -86.84 REMARK 500 ARG B 291 52.53 -111.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FLC A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EGX A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FLC B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EGX B 404 DBREF 6LIL A 6 386 UNP Q15119 PDK2_HUMAN 6 386 DBREF 6LIL B 6 386 UNP Q15119 PDK2_HUMAN 6 386 SEQADV 6LIL MET A -24 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ALA A -23 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY A -22 UNP Q15119 EXPRESSION TAG SEQADV 6LIL SER A -21 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS A -20 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS A -19 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS A -18 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS A -17 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS A -16 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS A -15 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY A -14 UNP Q15119 EXPRESSION TAG SEQADV 6LIL MET A -13 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ALA A -12 UNP Q15119 EXPRESSION TAG SEQADV 6LIL SER A -11 UNP Q15119 EXPRESSION TAG SEQADV 6LIL MET A -10 UNP Q15119 EXPRESSION TAG SEQADV 6LIL THR A -9 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY A -8 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY A -7 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLN A -6 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLN A -5 UNP Q15119 EXPRESSION TAG SEQADV 6LIL MET A -4 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY A -3 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ARG A -2 UNP Q15119 EXPRESSION TAG SEQADV 6LIL SER A -1 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY A 0 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ASP A 1 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ASP A 2 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ASP A 3 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ASP A 4 UNP Q15119 EXPRESSION TAG SEQADV 6LIL LYS A 5 UNP Q15119 EXPRESSION TAG SEQADV 6LIL MET B -24 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ALA B -23 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY B -22 UNP Q15119 EXPRESSION TAG SEQADV 6LIL SER B -21 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS B -20 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS B -19 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS B -18 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS B -17 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS B -16 UNP Q15119 EXPRESSION TAG SEQADV 6LIL HIS B -15 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY B -14 UNP Q15119 EXPRESSION TAG SEQADV 6LIL MET B -13 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ALA B -12 UNP Q15119 EXPRESSION TAG SEQADV 6LIL SER B -11 UNP Q15119 EXPRESSION TAG SEQADV 6LIL MET B -10 UNP Q15119 EXPRESSION TAG SEQADV 6LIL THR B -9 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY B -8 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY B -7 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLN B -6 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLN B -5 UNP Q15119 EXPRESSION TAG SEQADV 6LIL MET B -4 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY B -3 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ARG B -2 UNP Q15119 EXPRESSION TAG SEQADV 6LIL SER B -1 UNP Q15119 EXPRESSION TAG SEQADV 6LIL GLY B 0 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ASP B 1 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ASP B 2 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ASP B 3 UNP Q15119 EXPRESSION TAG SEQADV 6LIL ASP B 4 UNP Q15119 EXPRESSION TAG SEQADV 6LIL LYS B 5 UNP Q15119 EXPRESSION TAG SEQRES 1 A 411 MET ALA GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 A 411 SER MET THR GLY GLY GLN GLN MET GLY ARG SER GLY ASP SEQRES 3 A 411 ASP ASP ASP LYS ALA LEU LEU LYS ASN ALA SER LEU ALA SEQRES 4 A 411 GLY ALA PRO LYS TYR ILE GLU HIS PHE SER LYS PHE SER SEQRES 5 A 411 PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP PHE GLY SEQRES 6 A 411 SER SER ASN ALA CYS GLU LYS THR SER PHE THR PHE LEU SEQRES 7 A 411 ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE MET LYS SEQRES 8 A 411 GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER THR PRO SEQRES 9 A 411 SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SER LEU SEQRES 10 A 411 LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO GLU ASP SEQRES 11 A 411 HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU VAL THR SEQRES 12 A 411 ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR MET ALA SEQRES 13 A 411 GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY ASP ASP SEQRES 14 A 411 PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU ASP ARG SEQRES 15 A 411 PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU ILE ASN SEQRES 16 A 411 GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN PRO ALA SEQRES 17 A 411 HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN CYS ASN SEQRES 18 A 411 VAL SER GLU VAL VAL LYS ASP ALA TYR ASP MET ALA LYS SEQRES 19 A 411 LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO ASP LEU SEQRES 20 A 411 GLU ILE GLN GLU ILE ASN ALA ALA ASN SER LYS GLN PRO SEQRES 21 A 411 ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR HIS MET SEQRES 22 A 411 LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR VAL SEQRES 23 A 411 GLU SER HIS GLU SER SER LEU ILE LEU PRO PRO ILE LYS SEQRES 24 A 411 VAL MET VAL ALA LEU GLY GLU GLU ASP LEU SER ILE LYS SEQRES 25 A 411 MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS ILE SEQRES 26 A 411 GLU ARG LEU PHE SER TYR MET TYR SER THR ALA PRO THR SEQRES 27 A 411 PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA GLY PHE SEQRES 28 A 411 GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA LYS TYR SEQRES 29 A 411 PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU GLY PHE SEQRES 30 A 411 GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER THR SEQRES 31 A 411 ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SER ALA SEQRES 32 A 411 TRP ARG HIS TYR GLN THR ILE GLN SEQRES 1 B 411 MET ALA GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 B 411 SER MET THR GLY GLY GLN GLN MET GLY ARG SER GLY ASP SEQRES 3 B 411 ASP ASP ASP LYS ALA LEU LEU LYS ASN ALA SER LEU ALA SEQRES 4 B 411 GLY ALA PRO LYS TYR ILE GLU HIS PHE SER LYS PHE SER SEQRES 5 B 411 PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP PHE GLY SEQRES 6 B 411 SER SER ASN ALA CYS GLU LYS THR SER PHE THR PHE LEU SEQRES 7 B 411 ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE MET LYS SEQRES 8 B 411 GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER THR PRO SEQRES 9 B 411 SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SER LEU SEQRES 10 B 411 LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO GLU ASP SEQRES 11 B 411 HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU VAL THR SEQRES 12 B 411 ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR MET ALA SEQRES 13 B 411 GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY ASP ASP SEQRES 14 B 411 PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU ASP ARG SEQRES 15 B 411 PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU ILE ASN SEQRES 16 B 411 GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN PRO ALA SEQRES 17 B 411 HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN CYS ASN SEQRES 18 B 411 VAL SER GLU VAL VAL LYS ASP ALA TYR ASP MET ALA LYS SEQRES 19 B 411 LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO ASP LEU SEQRES 20 B 411 GLU ILE GLN GLU ILE ASN ALA ALA ASN SER LYS GLN PRO SEQRES 21 B 411 ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR HIS MET SEQRES 22 B 411 LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR VAL SEQRES 23 B 411 GLU SER HIS GLU SER SER LEU ILE LEU PRO PRO ILE LYS SEQRES 24 B 411 VAL MET VAL ALA LEU GLY GLU GLU ASP LEU SER ILE LYS SEQRES 25 B 411 MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS ILE SEQRES 26 B 411 GLU ARG LEU PHE SER TYR MET TYR SER THR ALA PRO THR SEQRES 27 B 411 PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA GLY PHE SEQRES 28 B 411 GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA LYS TYR SEQRES 29 B 411 PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU GLY PHE SEQRES 30 B 411 GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER THR SEQRES 31 B 411 ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SER ALA SEQRES 32 B 411 TRP ARG HIS TYR GLN THR ILE GLN HET FLC A 401 13 HET PEG A 402 7 HET GOL A 403 6 HET SO4 A 404 5 HET EGX A 405 27 HET FLC B 401 13 HET PEG B 402 7 HET PEG B 403 7 HET EGX B 404 27 HETNAM FLC CITRATE ANION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM EGX 1-(1-PIPERIDIN-4-YLPYRAZOL-4-YL)ANTHRACENE-9,10-DIONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FLC 2(C6 H5 O7 3-) FORMUL 4 PEG 3(C4 H10 O3) FORMUL 5 GOL C3 H8 O3 FORMUL 6 SO4 O4 S 2- FORMUL 7 EGX 2(C22 H19 N3 O2) FORMUL 12 HOH *246(H2 O) HELIX 1 AA1 GLY A 15 LYS A 25 1 11 HELIX 2 AA2 SER A 32 GLY A 40 1 9 HELIX 3 AA3 CYS A 45 LEU A 70 1 26 HELIX 4 AA4 PRO A 72 SER A 77 1 6 HELIX 5 AA5 THR A 78 GLU A 97 1 20 HELIX 6 AA6 ASP A 105 HIS A 123 1 19 HELIX 7 AA7 ASP A 125 GLY A 142 1 18 HELIX 8 AA8 SER A 147 ASP A 177 1 31 HELIX 9 AA9 VAL A 197 MET A 217 1 21 HELIX 10 AB1 VAL A 241 SER A 263 1 23 HELIX 11 AB2 PRO A 296 ARG A 298 5 3 HELIX 12 AB3 LYS A 299 PHE A 304 1 6 HELIX 13 AB4 TYR A 328 PHE A 340 1 13 HELIX 14 AB5 LEU A 363 SER A 367 5 5 HELIX 15 AB6 PRO B 17 LYS B 25 1 9 HELIX 16 AB7 SER B 32 GLY B 40 1 9 HELIX 17 AB8 CYS B 45 LEU B 70 1 26 HELIX 18 AB9 PRO B 72 SER B 77 1 6 HELIX 19 AC1 THR B 78 GLU B 97 1 20 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 SER B 147 ASP B 177 1 31 HELIX 23 AC5 VAL B 197 MET B 217 1 21 HELIX 24 AC6 VAL B 241 SER B 263 1 23 HELIX 25 AC7 PRO B 296 ARG B 298 5 3 HELIX 26 AC8 LYS B 299 PHE B 304 1 6 HELIX 27 AC9 TYR B 328 PHE B 340 1 13 HELIX 28 AD1 LEU B 363 SER B 367 5 5 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 ASP A 290 -1 O SER A 285 N ALA A 278 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 PHE A 347 O ASP A 355 SHEET 1 AA3 2 ASP B 192 ASN B 196 0 SHEET 2 AA3 2 HIS B 237 TYR B 240 -1 O TYR B 240 N ASP B 192 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 275 N GLU B 223 SHEET 3 AA4 5 ASP B 283 ASP B 290 -1 O SER B 289 N LYS B 274 SHEET 4 AA4 5 GLY B 353 LYS B 361 -1 O ALA B 356 N MET B 288 SHEET 5 AA4 5 ASP B 343 MET B 349 -1 N MET B 349 O GLY B 353 SITE 1 AC1 8 VAL A 127 ARG A 162 ARG A 166 HIS A 247 SITE 2 AC1 8 TYR A 336 HOH A 526 HOH A 549 HOH A 563 SITE 1 AC2 4 ARG A 258 LEU A 303 THR A 310 HOH A 556 SITE 1 AC3 3 ASP A 203 PRO A 242 TYR A 246 SITE 1 AC4 1 ARG A 370 SITE 1 AC5 11 LEU A 31 GLN A 35 PHE A 36 PHE A 39 SITE 2 AC5 11 THR A 48 SER A 49 PHE A 52 TYR A 215 SITE 3 AC5 11 TYR A 216 GLU A 262 GLU A 265 SITE 1 AC6 9 VAL B 127 ARG B 162 ARG B 166 HIS B 247 SITE 2 AC6 9 TYR B 336 HOH B 536 HOH B 538 HOH B 564 SITE 3 AC6 9 HOH B 567 SITE 1 AC7 9 ASN B 255 ARG B 258 THR B 310 GLY B 327 SITE 2 AC7 9 GLY B 329 LEU B 330 HOH B 570 HOH B 576 SITE 3 AC7 9 HOH B 605 SITE 1 AC8 1 ASP B 203 SITE 1 AC9 10 LEU B 31 GLN B 35 PHE B 36 PHE B 39 SITE 2 AC9 10 PHE B 52 TYR B 215 TYR B 216 GLU B 262 SITE 3 AC9 10 GLU B 265 HOH B 542 CRYST1 52.778 52.839 92.145 88.20 78.00 60.93 P 1 2 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 0.018947 -0.010535 -0.004901 0.00000 SCALE2 0.000000 0.021654 0.001770 0.00000 SCALE3 0.000000 0.000000 0.011132 0.00000