HEADER TRANSFERASE 01-DEC-07 2ZDY TITLE INHIBITOR-BOUND STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE DEHYDROGENASE KINASE ISOZYME 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 20-411; COMPND 5 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 4; COMPND 6 EC: 2.7.11.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PBLUEBAC4.5 KEYWDS PDK4, KINASE, ATP-BINDING, ADP, CARBOHYDRATE METABOLISM, GLUCOSE KEYWDS 2 METABOLISM, MITOCHONDRION, PHOSPHOPROTEIN, TRANSFERASE, TRANSIT KEYWDS 3 PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR M.KAWAMOTO,I.SHIROMIZU,M.KUKIMOTO-NIINO,A.TOKMAKOV,T.TERADA, AUTHOR 2 M.SHIROUZU,T.MATSUSUE,S.YOKOYAMA REVDAT 5 01-NOV-23 2ZDY 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 2ZDY 1 REMARK REVDAT 3 23-NOV-11 2ZDY 1 JRNL VERSN REVDAT 2 22-SEP-09 2ZDY 1 REMARK REVDAT 1 09-DEC-08 2ZDY 0 JRNL AUTH M.KUKIMOTO-NIINO,A.TOKMAKOV,T.TERADA,N.OHBAYASHI,T.FUJIMOTO, JRNL AUTH 2 S.GOMI,I.SHIROMIZU,M.KAWAMOTO,T.MATSUSUE,M.SHIROUZU, JRNL AUTH 3 S.YOKOYAMA JRNL TITL INHIBITOR-BOUND STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE JRNL TITL 2 KINASE 4. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 67 763 2011 JRNL REFN ISSN 0907-4449 JRNL PMID 21904029 JRNL DOI 10.1107/S090744491102405X REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2005 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) : 26.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 386058.450 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 28142 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1387 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 30399 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3893 REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 194 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5697 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82000 REMARK 3 B22 (A**2) : 4.24000 REMARK 3 B33 (A**2) : -3.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.17000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.16 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.650 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.410 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.360 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.080 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.030 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 38.74 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : ADP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : ADP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000027850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30416 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21400 REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 2E0A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7M AMMONIUM SULFATE, 2% PEG 400, REMARK 280 0.1M SODIUM HEPES, PH 7.1, 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 34.54500 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: 5410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 18 REMARK 465 GLU A 46 REMARK 465 ASN A 47 REMARK 465 ALA A 48 REMARK 465 ASP A 143 REMARK 465 ALA A 144 REMARK 465 CYS A 145 REMARK 465 VAL A 318 REMARK 465 MET A 319 REMARK 465 ASP A 320 REMARK 465 ASN A 321 REMARK 465 SER A 322 REMARK 465 ARG A 323 REMARK 465 ASN A 324 REMARK 465 ALA A 325 REMARK 465 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 ASP A 393 REMARK 465 ASP A 394 REMARK 465 TRP A 395 REMARK 465 CYS A 396 REMARK 465 ILE A 397 REMARK 465 PRO A 398 REMARK 465 SER A 399 REMARK 465 ARG A 400 REMARK 465 GLU A 401 REMARK 465 PRO A 402 REMARK 465 LYS A 403 REMARK 465 ASN A 404 REMARK 465 LEU A 405 REMARK 465 ALA A 406 REMARK 465 LYS A 407 REMARK 465 GLU A 408 REMARK 465 VAL A 409 REMARK 465 ALA A 410 REMARK 465 MET A 411 REMARK 465 GLY B 18 REMARK 465 PRO B 19 REMARK 465 VAL B 20 REMARK 465 ASP B 182 REMARK 465 SER B 183 REMARK 465 GLN B 184 REMARK 465 ALA B 314 REMARK 465 PRO B 315 REMARK 465 THR B 316 REMARK 465 PRO B 317 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 PRO B 326 REMARK 465 LEU B 327 REMARK 465 ALA B 328 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 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 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 SER A 221 162.56 174.90 REMARK 500 ASP A 236 -9.83 69.85 REMARK 500 ARG A 294 54.04 -114.33 REMARK 500 THR A 310 -8.71 77.99 REMARK 500 TYR A 356 -60.70 -140.37 REMARK 500 GLU B 46 -52.63 -123.26 REMARK 500 ALA B 48 72.94 37.77 REMARK 500 TYR B 218 -31.90 -146.78 REMARK 500 LYS B 233 -87.53 -56.51 REMARK 500 PRO B 235 7.95 -57.21 REMARK 500 ARG B 294 59.19 -108.59 REMARK 500 TYR B 356 -60.40 -143.05 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 O2B 90.2 REMARK 620 3 ADP A 501 O1A 89.9 71.0 REMARK 620 4 HOH A 676 O 147.7 62.4 66.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 258 OD1 REMARK 620 2 ADP B1501 O3B 80.0 REMARK 620 3 ADP B1501 O1A 82.6 64.4 REMARK 620 N 1 2 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 B1500 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 B1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZDX RELATED DB: PDB DBREF 2ZDY A 20 411 UNP Q16654 PDK4_HUMAN 20 411 DBREF 2ZDY B 20 411 UNP Q16654 PDK4_HUMAN 20 411 SEQADV 2ZDY GLY A 18 UNP Q16654 EXPRESSION TAG SEQADV 2ZDY PRO A 19 UNP Q16654 EXPRESSION TAG SEQADV 2ZDY GLY B 18 UNP Q16654 EXPRESSION TAG SEQADV 2ZDY PRO B 19 UNP Q16654 EXPRESSION TAG SEQRES 1 A 394 GLY PRO 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 GLY PRO 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 EPE A 600 15 HET MG B1500 1 HET ADP B1501 27 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 MG 2(MG 2+) FORMUL 4 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 8 HOH *180(H2 O) HELIX 1 1 PRO A 21 SER A 28 1 8 HELIX 2 2 SER A 36 PHE A 43 1 8 HELIX 3 3 CYS A 49 ILE A 74 1 26 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 ASP A 109 HIS A 127 1 19 HELIX 7 7 ASN A 129 LYS A 142 1 14 HELIX 8 8 ASN A 152 SER A 181 1 30 HELIX 9 9 VAL A 200 LEU A 220 1 21 HELIX 10 10 VAL A 244 GLN A 267 1 24 HELIX 11 11 PRO A 299 ARG A 301 5 3 HELIX 12 12 ILE A 302 PHE A 307 1 6 HELIX 13 13 TYR A 332 PHE A 344 1 13 HELIX 14 14 LEU A 367 SER A 371 5 5 HELIX 15 15 ASN A 379 TYR A 386 1 8 HELIX 16 16 PRO B 21 SER B 28 1 8 HELIX 17 17 SER B 36 PHE B 43 1 8 HELIX 18 18 CYS B 49 ASP B 73 1 25 HELIX 19 19 PRO B 76 ASN B 81 1 6 HELIX 20 20 THR B 82 GLU B 101 1 20 HELIX 21 21 PHE B 102 GLU B 104 5 3 HELIX 22 22 ASP B 109 HIS B 127 1 19 HELIX 23 23 ASN B 129 CYS B 145 1 17 HELIX 24 24 ASP B 148 SER B 181 1 34 HELIX 25 25 VAL B 200 LEU B 220 1 21 HELIX 26 26 VAL B 244 GLN B 267 1 24 HELIX 27 27 ILE B 302 PHE B 307 1 6 HELIX 28 28 TYR B 332 PHE B 344 1 13 HELIX 29 29 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 SER A 292 -1 O SER A 292 N GLU A 277 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 2 ASP B 195 ASP B 199 0 SHEET 2 C 2 HIS B 240 TYR B 243 -1 O TYR B 243 N ASP B 195 SHEET 1 D 5 LEU B 225 ASN B 231 0 SHEET 2 D 5 ILE B 276 LEU B 282 1 O VAL B 280 N VAL B 230 SHEET 3 D 5 ASP B 286 ASP B 293 -1 O SER B 292 N GLU B 277 SHEET 4 D 5 GLY B 357 LYS B 365 -1 O ALA B 360 N ILE B 291 SHEET 5 D 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 2.38 LINK MG MG A 500 O2B ADP A 501 1555 1555 2.48 LINK MG MG A 500 O1A ADP A 501 1555 1555 2.59 LINK MG MG A 500 O HOH A 676 1555 1555 2.79 LINK OD1 ASN B 258 MG MG B1500 1555 1555 2.62 LINK MG MG B1500 O3B ADP B1501 1555 1555 2.49 LINK MG MG B1500 O1A ADP B1501 1555 1555 2.66 SITE 1 AC1 4 GLU A 254 ASN A 258 ADP A 501 HOH A 676 SITE 1 AC2 3 GLU B 254 ASN B 258 ADP B1501 SITE 1 AC3 19 ASN A 258 ARG A 261 ALA A 262 ASP A 293 SITE 2 AC3 19 VAL A 298 LEU A 306 SER A 312 THR A 313 SITE 3 AC3 19 ALA A 328 GLY A 329 PHE A 330 GLY A 331 SITE 4 AC3 19 GLY A 333 LEU A 334 THR A 358 MG A 500 SITE 5 AC3 19 HOH A 602 HOH A 604 HOH A 676 SITE 1 AC4 17 ASN B 258 ARG B 261 ALA B 262 ASP B 293 SITE 2 AC4 17 VAL B 298 LEU B 306 SER B 312 THR B 313 SITE 3 AC4 17 GLY B 329 PHE B 330 GLY B 331 GLY B 333 SITE 4 AC4 17 LEU B 334 THR B 358 MG B1500 HOH B1503 SITE 5 AC4 17 HOH B1510 SITE 1 AC5 5 ASP A 160 ARG A 338 LYS A 342 LYS A 374 SITE 2 AC5 5 TRP B 395 CRYST1 70.713 69.090 81.492 90.00 99.66 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 0.014142 0.000000 0.002408 0.00000 SCALE2 0.000000 0.014474 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012448 0.00000