HEADER TRANSFERASE 17-JUL-01 1JM6 TITLE PYRUVATE DEHYDROGENASE KINASE, ISOZYME 2, CONTAINING ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE DEHYDROGENASE KINASE, ISOZYME 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: [PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 2, COMPND 5 MITOCHONDRIAL, PDK P45; COMPND 6 EC: 2.7.1.99; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21[DE3]; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A (NOVAGEN) KEYWDS KINASE, MITOCHONDION, SERINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.N.STEUSSY,K.M.POPOV,M.M.BOWKER-KINLEY,R.B.SLOAN,R.A.HARRIS, AUTHOR 2 J.A.HAMILTON REVDAT 4 07-FEB-24 1JM6 1 REMARK LINK REVDAT 3 24-FEB-09 1JM6 1 VERSN REVDAT 2 01-APR-03 1JM6 1 JRNL REVDAT 1 24-OCT-01 1JM6 0 JRNL AUTH C.N.STEUSSY,K.M.POPOV,M.M.BOWKER-KINLEY,R.B.SLOAN JR., JRNL AUTH 2 R.A.HARRIS,J.A.HAMILTON JRNL TITL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE. NOVEL FOLDING JRNL TITL 2 PATTERN FOR A SERINE PROTEIN KINASE. JRNL REF J.BIOL.CHEM. V. 276 37443 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11483605 JRNL DOI 10.1074/JBC.M104285200 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.191 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.208 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1508 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 28853 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.184 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.200 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1375 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 26651 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5393 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 228 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 5677.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 22712 REMARK 3 NUMBER OF RESTRAINTS : 29468 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.316 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.019 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.104 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.076 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.139 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.044 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-99; 26-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 110; NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; NSLS REMARK 200 BEAMLINE : NULL; X12C REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.9803, 0.9802, 0.9300 REMARK 200 MONOCHROMATOR : GRAPHITE; SI 111 REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II; CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35685 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6K, IMIDAZOLE, ADP, MAGNESIUM REMARK 280 CHLORIDE, IODO-PROPIONIC ACID, PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, 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 54.93700 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 300 REMARK: BIOLOGICAL DIMER IS RECREATED USING A CRYSTALLOGRAPHICALLY REMARK 300 EQUIVALENT POSITION OF THE B SUBUNIT. THIS CAN BE ACHIEVED BY REMARK 300 APPLYING THE FOLLOWING TRANSLATION VECTOR TO THE B COORDINATES; REMARK 300 17.90 -109.87 -69.13 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: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 993 REMARK 465 ARG A 994 REMARK 465 TRP A 995 REMARK 465 PHE A 996 REMARK 465 ARG A 997 REMARK 465 ALA A 998 REMARK 465 LEU A 999 REMARK 465 LEU A 1000 REMARK 465 LYS A 1001 REMARK 465 ASN A 1002 REMARK 465 SER A 1033 REMARK 465 SER A 1034 REMARK 465 ASN A 1035 REMARK 465 LYS A 1130 REMARK 465 ASP A 1131 REMARK 465 THR A 1132 REMARK 465 TYR A 1133 REMARK 465 GLY A 1134 REMARK 465 ASP A 1135 REMARK 465 GLY A 1170 REMARK 465 SER A 1171 REMARK 465 THR A 1172 REMARK 465 ASN A 1173 REMARK 465 PRO A 1174 REMARK 465 ALA A 1175 REMARK 465 HIS A 1176 REMARK 465 GLN A 1307 REMARK 465 PRO A 1308 REMARK 465 GLY A 1309 REMARK 465 THR A 1310 REMARK 465 GLY A 1311 REMARK 465 GLY A 1312 REMARK 465 THR A 1313 REMARK 465 PRO A 1314 REMARK 465 LEU A 1315 REMARK 465 ASN A 1367 REMARK 465 LYS A 1368 REMARK 465 SER A 1369 REMARK 465 ALA A 1370 REMARK 465 TRP A 1371 REMARK 465 ARG A 1372 REMARK 465 HIS A 1373 REMARK 465 TYR A 1374 REMARK 465 GLN A 1375 REMARK 465 THR A 1376 REMARK 465 ILE A 1377 REMARK 465 GLN A 1378 REMARK 465 GLU A 1379 REMARK 465 ALA A 1380 REMARK 465 GLY A 1381 REMARK 465 ASP A 1382 REMARK 465 TRP A 1383 REMARK 465 CYS A 1384 REMARK 465 VAL A 1385 REMARK 465 PRO A 1386 REMARK 465 SER A 1387 REMARK 465 THR A 1388 REMARK 465 GLU A 1389 REMARK 465 PRO A 1390 REMARK 465 LYS A 1391 REMARK 465 ASN A 1392 REMARK 465 THR A 1393 REMARK 465 SER A 1394 REMARK 465 THR A 1395 REMARK 465 TYR A 1396 REMARK 465 ARG A 1397 REMARK 465 VAL A 1398 REMARK 465 SER A 1399 REMARK 465 MET B 993 REMARK 465 ARG B 994 REMARK 465 TRP B 995 REMARK 465 PHE B 996 REMARK 465 ARG B 997 REMARK 465 ALA B 998 REMARK 465 LEU B 999 REMARK 465 LEU B 1000 REMARK 465 LYS B 1001 REMARK 465 SER B 1033 REMARK 465 SER B 1034 REMARK 465 ASN B 1035 REMARK 465 LYS B 1130 REMARK 465 ASP B 1131 REMARK 465 THR B 1132 REMARK 465 TYR B 1133 REMARK 465 GLY B 1134 REMARK 465 ASP B 1135 REMARK 465 ASP B 1136 REMARK 465 PRO B 1137 REMARK 465 VAL B 1138 REMARK 465 SER B 1139 REMARK 465 ASN B 1140 REMARK 465 GLY B 1170 REMARK 465 SER B 1171 REMARK 465 THR B 1172 REMARK 465 ASN B 1173 REMARK 465 PRO B 1174 REMARK 465 ALA B 1175 REMARK 465 HIS B 1176 REMARK 465 GLN B 1307 REMARK 465 PRO B 1308 REMARK 465 GLY B 1309 REMARK 465 THR B 1310 REMARK 465 GLY B 1311 REMARK 465 GLY B 1312 REMARK 465 THR B 1313 REMARK 465 TYR B 1366 REMARK 465 ASN B 1367 REMARK 465 LYS B 1368 REMARK 465 SER B 1369 REMARK 465 ALA B 1370 REMARK 465 TRP B 1371 REMARK 465 ARG B 1372 REMARK 465 HIS B 1373 REMARK 465 TYR B 1374 REMARK 465 GLN B 1375 REMARK 465 THR B 1376 REMARK 465 ILE B 1377 REMARK 465 GLN B 1378 REMARK 465 GLU B 1379 REMARK 465 ALA B 1380 REMARK 465 GLY B 1381 REMARK 465 ASP B 1382 REMARK 465 TRP B 1383 REMARK 465 CYS B 1384 REMARK 465 VAL B 1385 REMARK 465 PRO B 1386 REMARK 465 SER B 1387 REMARK 465 THR B 1388 REMARK 465 GLU B 1389 REMARK 465 PRO B 1390 REMARK 465 LYS B 1391 REMARK 465 ASN B 1392 REMARK 465 THR B 1393 REMARK 465 SER B 1394 REMARK 465 THR B 1395 REMARK 465 TYR B 1396 REMARK 465 ARG B 1397 REMARK 465 VAL B 1398 REMARK 465 SER B 1399 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A1090 C LEU A1091 N -0.197 REMARK 500 LYS A1178 C HIS A1179 N -0.176 REMARK 500 GLU A1215 CB GLU A1215 CG 0.135 REMARK 500 GLU B1215 CD GLU B1215 OE2 0.071 REMARK 500 PRO B1306 CA PRO B1306 C 0.147 REMARK 500 PRO B1306 C PRO B1306 O 0.120 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 A1007 C - N - CA ANGL. DEV. = -20.0 DEGREES REMARK 500 PHE A1090 CA - C - N ANGL. DEV. = 20.4 DEGREES REMARK 500 PHE A1090 O - C - N ANGL. DEV. = -20.0 DEGREES REMARK 500 LEU A1091 C - N - CA ANGL. DEV. = 18.6 DEGREES REMARK 500 GLU A1096 CA - C - N ANGL. DEV. = 13.5 DEGREES REMARK 500 PRO A1120 C - N - CD ANGL. DEV. = -13.0 DEGREES REMARK 500 PRO A1137 C - N - CD ANGL. DEV. = -13.8 DEGREES REMARK 500 PRO A1137 N - CA - C ANGL. DEV. = 17.9 DEGREES REMARK 500 PRO A1137 CA - C - N ANGL. DEV. = -15.4 DEGREES REMARK 500 VAL A1138 C - N - CA ANGL. DEV. = 26.7 DEGREES REMARK 500 VAL A1138 N - CA - C ANGL. DEV. = 27.2 DEGREES REMARK 500 PRO A1306 C - N - CA ANGL. DEV. = 11.0 DEGREES REMARK 500 PRO A1306 C - N - CD ANGL. DEV. = -18.9 DEGREES REMARK 500 GLU B1059 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 ASN B1223 N - CA - CB ANGL. DEV. = 13.4 DEGREES REMARK 500 ASN B1223 N - CA - C ANGL. DEV. = -17.0 DEGREES REMARK 500 PRO B1227 C - N - CD ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG B1326 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 PRO B1364 C - N - CD ANGL. DEV. = -18.4 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 ALA A1006 -16.47 -148.51 REMARK 500 ASP A1092 -25.59 -141.75 REMARK 500 ASP A1094 99.12 -64.74 REMARK 500 PRO A1095 -9.17 -48.89 REMARK 500 PRO A1137 -172.69 -55.19 REMARK 500 VAL A1138 66.86 -59.33 REMARK 500 SER A1139 -52.05 -133.13 REMARK 500 ASN A1140 76.83 -107.01 REMARK 500 LYS A1178 61.12 -156.06 REMARK 500 ALA A1224 -19.35 -41.17 REMARK 500 THR A1225 22.24 -143.93 REMARK 500 ARG A1283 40.63 -106.87 REMARK 500 LEU A1295 -7.67 -44.46 REMARK 500 PRO A1304 99.87 -51.79 REMARK 500 THR A1305 158.67 -38.87 REMARK 500 GLN A1333 33.05 74.79 REMARK 500 PHE A1344 -71.32 -124.74 REMARK 500 PRO A1364 152.63 -47.61 REMARK 500 VAL A1365 127.45 -37.15 REMARK 500 LEU B1005 24.27 -74.82 REMARK 500 GLU B1128 70.92 -66.91 REMARK 500 MET B1199 -78.06 -53.97 REMARK 500 ALA B1200 -52.55 -27.63 REMARK 500 ARG B1283 47.76 -105.55 REMARK 500 PRO B1304 155.05 -40.67 REMARK 500 LEU B1315 -34.10 -155.19 REMARK 500 GLN B1333 37.06 78.91 REMARK 500 PHE B1344 -67.20 -120.72 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 A4601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A1247 OD1 REMARK 620 2 ADP A3500 O3B 82.4 REMARK 620 3 ADP A3500 O2A 66.7 85.7 REMARK 620 4 HOH A4602 O 88.1 161.6 104.9 REMARK 620 5 HOH A4603 O 76.9 86.9 143.5 75.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B4611 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B1247 OD1 REMARK 620 2 ADP B3510 O3B 89.9 REMARK 620 3 ADP B3510 O2A 72.1 85.7 REMARK 620 4 HOH B6003 O 79.5 161.7 104.9 REMARK 620 5 HOH B6004 O 72.1 87.0 143.5 75.6 REMARK 620 N 1 2 3 4 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 4601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 4611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 3500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 3510 DBREF 1JM6 A 993 1399 UNP Q64536 PDK2_RAT 1 407 DBREF 1JM6 B 993 1399 UNP Q64536 PDK2_RAT 1 407 SEQRES 1 A 407 MET ARG TRP PHE ARG ALA LEU LEU LYS ASN ALA SER LEU SEQRES 2 A 407 ALA GLY ALA PRO LYS TYR ILE GLU HIS PHE SER LYS PHE SEQRES 3 A 407 SER PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP PHE SEQRES 4 A 407 GLY SER SER ASN ALA CYS GLU LYS THR SER PHE THR PHE SEQRES 5 A 407 LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE MET SEQRES 6 A 407 LYS GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER THR SEQRES 7 A 407 PRO SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SER SEQRES 8 A 407 LEU LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO GLU SEQRES 9 A 407 ASP HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU VAL SEQRES 10 A 407 THR ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR MET SEQRES 11 A 407 ALA GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY ASP SEQRES 12 A 407 ASP PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU ASP SEQRES 13 A 407 ARG PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU ILE SEQRES 14 A 407 ASN GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN PRO SEQRES 15 A 407 ALA HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN CYS SEQRES 16 A 407 SER VAL SER ASP VAL VAL LYS ASP ALA TYR ASP MET ALA SEQRES 17 A 407 LYS LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO ASP SEQRES 18 A 407 LEU GLU ILE GLN GLU VAL ASN ALA THR ASN ALA THR GLN SEQRES 19 A 407 PRO ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR HIS SEQRES 20 A 407 MET LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR SEQRES 21 A 407 VAL GLU SER HIS GLU SER SER LEU THR LEU PRO PRO ILE SEQRES 22 A 407 LYS ILE MET VAL ALA LEU GLY GLU GLU ASP LEU SER ILE SEQRES 23 A 407 LYS MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS SEQRES 24 A 407 ILE GLU ARG LEU PHE SER TYR MET TYR SER THR ALA PRO SEQRES 25 A 407 THR PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA GLY SEQRES 26 A 407 PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA LYS SEQRES 27 A 407 TYR PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU GLY SEQRES 28 A 407 PHE GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER SEQRES 29 A 407 THR ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SER SEQRES 30 A 407 ALA TRP ARG HIS TYR GLN THR ILE GLN GLU ALA GLY ASP SEQRES 31 A 407 TRP CYS VAL PRO SER THR GLU PRO LYS ASN THR SER THR SEQRES 32 A 407 TYR ARG VAL SER SEQRES 1 B 407 MET ARG TRP PHE ARG ALA LEU LEU LYS ASN ALA SER LEU SEQRES 2 B 407 ALA GLY ALA PRO LYS TYR ILE GLU HIS PHE SER LYS PHE SEQRES 3 B 407 SER PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP PHE SEQRES 4 B 407 GLY SER SER ASN ALA CYS GLU LYS THR SER PHE THR PHE SEQRES 5 B 407 LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE MET SEQRES 6 B 407 LYS GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER THR SEQRES 7 B 407 PRO SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SER SEQRES 8 B 407 LEU LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO GLU SEQRES 9 B 407 ASP HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU VAL SEQRES 10 B 407 THR ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR MET SEQRES 11 B 407 ALA GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY ASP SEQRES 12 B 407 ASP PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU ASP SEQRES 13 B 407 ARG PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU ILE SEQRES 14 B 407 ASN GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN PRO SEQRES 15 B 407 ALA HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN CYS SEQRES 16 B 407 SER VAL SER ASP VAL VAL LYS ASP ALA TYR ASP MET ALA SEQRES 17 B 407 LYS LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO ASP SEQRES 18 B 407 LEU GLU ILE GLN GLU VAL ASN ALA THR ASN ALA THR GLN SEQRES 19 B 407 PRO ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR HIS SEQRES 20 B 407 MET LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR SEQRES 21 B 407 VAL GLU SER HIS GLU SER SER LEU THR LEU PRO PRO ILE SEQRES 22 B 407 LYS ILE MET VAL ALA LEU GLY GLU GLU ASP LEU SER ILE SEQRES 23 B 407 LYS MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS SEQRES 24 B 407 ILE GLU ARG LEU PHE SER TYR MET TYR SER THR ALA PRO SEQRES 25 B 407 THR PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA GLY SEQRES 26 B 407 PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA LYS SEQRES 27 B 407 TYR PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU GLY SEQRES 28 B 407 PHE GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER SEQRES 29 B 407 THR ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SER SEQRES 30 B 407 ALA TRP ARG HIS TYR GLN THR ILE GLN GLU ALA GLY ASP SEQRES 31 B 407 TRP CYS VAL PRO SER THR GLU PRO LYS ASN THR SER THR SEQRES 32 B 407 TYR ARG VAL SER HET MG A4601 1 HET ADP A3500 27 HET MG B4611 1 HET ADP B3510 27 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 MG 2(MG 2+) FORMUL 4 ADP 2(C10 H15 N5 O10 P2) FORMUL 7 HOH *228(H2 O) HELIX 1 1 GLY A 1007 SER A 1016 1 10 HELIX 2 2 SER A 1024 ASP A 1030 1 7 HELIX 3 3 CYS A 1037 ASN A 1061 1 25 HELIX 4 4 PRO A 1064 SER A 1069 1 6 HELIX 5 5 THR A 1070 GLU A 1089 1 20 HELIX 6 6 ASP A 1097 HIS A 1115 1 19 HELIX 7 7 ASP A 1117 GLU A 1128 1 12 HELIX 8 8 ASN A 1142 ASP A 1169 1 28 HELIX 9 9 VAL A 1189 MET A 1209 1 21 HELIX 10 10 VAL A 1233 HIS A 1256 1 24 HELIX 11 11 PRO A 1288 ILE A 1292 5 5 HELIX 12 12 GLU A 1293 SER A 1297 5 5 HELIX 13 13 TYR A 1320 PHE A 1332 1 13 HELIX 14 14 GLY B 1007 SER B 1016 1 10 HELIX 15 15 SER B 1024 ASP B 1030 1 7 HELIX 16 16 CYS B 1037 ASN B 1061 1 25 HELIX 17 17 PRO B 1064 SER B 1069 1 6 HELIX 18 18 THR B 1070 GLU B 1089 1 20 HELIX 19 19 PHE B 1090 LYS B 1093 5 4 HELIX 20 20 ASP B 1097 HIS B 1115 1 19 HELIX 21 21 ASP B 1117 GLU B 1128 1 12 HELIX 22 22 ASN B 1142 PHE B 1168 1 27 HELIX 23 23 VAL B 1189 LYS B 1206 1 18 HELIX 24 24 VAL B 1233 HIS B 1256 1 24 HELIX 25 25 PRO B 1288 ILE B 1292 5 5 HELIX 26 26 GLU B 1293 SER B 1297 5 5 HELIX 27 27 TYR B 1320 PHE B 1332 1 13 HELIX 28 28 LEU B 1355 SER B 1359 5 5 SHEET 1 A 2 ASP A1184 SER A1188 0 SHEET 2 A 2 HIS A1229 TYR A1232 -1 O MET A1230 N CYS A1187 SHEET 1 B 5 LEU A1214 ASN A1220 0 SHEET 2 B 5 ILE A1265 LEU A1271 1 O ILE A1265 N GLU A1215 SHEET 3 B 5 ASP A1275 ASP A1282 -1 O SER A1277 N ALA A1270 SHEET 4 B 5 GLY A1345 LYS A1353 -1 O THR A1346 N ASP A1282 SHEET 5 B 5 ASP A1335 MET A1341 -1 O ASP A1335 N TYR A1351 SHEET 1 C 2 ASP B1184 SER B1188 0 SHEET 2 C 2 HIS B1229 TYR B1232 -1 O MET B1230 N CYS B1187 SHEET 1 D 5 LEU B1214 ASN B1220 0 SHEET 2 D 5 ILE B1265 LEU B1271 1 O ILE B1265 N GLU B1215 SHEET 3 D 5 ASP B1275 ASP B1282 -1 O SER B1277 N ALA B1270 SHEET 4 D 5 GLY B1345 LYS B1353 -1 O THR B1346 N ASP B1282 SHEET 5 D 5 ASP B1335 MET B1341 -1 O ASP B1335 N TYR B1351 LINK OD1 ASN A1247 MG MG A4601 1555 1555 2.74 LINK O3B ADP A3500 MG MG A4601 1555 1555 2.21 LINK O2A ADP A3500 MG MG A4601 1555 1555 1.99 LINK MG MG A4601 O HOH A4602 1555 1555 2.04 LINK MG MG A4601 O HOH A4603 1555 1555 2.15 LINK OD1 ASN B1247 MG MG B4611 1555 1555 2.74 LINK O3B ADP B3510 MG MG B4611 1555 1555 2.21 LINK O2A ADP B3510 MG MG B4611 1555 1555 1.99 LINK MG MG B4611 O HOH B6003 1555 1555 2.04 LINK MG MG B4611 O HOH B6004 1555 1555 2.15 SITE 1 AC1 4 ASN A1247 ADP A3500 HOH A4602 HOH A4603 SITE 1 AC2 4 ASN B1247 ADP B3510 HOH B6003 HOH B6004 SITE 1 AC3 18 ASN A1247 ARG A1250 ALA A1251 ASP A1282 SITE 2 AC3 18 VAL A1287 LEU A1295 SER A1301 THR A1302 SITE 3 AC3 18 GLY A1317 PHE A1318 GLY A1319 GLY A1321 SITE 4 AC3 18 LEU A1322 THR A1346 MG A4601 HOH A4603 SITE 5 AC3 18 HOH A6050 HOH A6098 SITE 1 AC4 19 ASN B1247 ARG B1250 ALA B1251 ASP B1282 SITE 2 AC4 19 VAL B1287 LEU B1295 SER B1301 THR B1302 SITE 3 AC4 19 ALA B1316 GLY B1317 PHE B1318 GLY B1319 SITE 4 AC4 19 GLY B1321 LEU B1322 THR B1346 MG B4611 SITE 5 AC4 19 HOH B6004 HOH B6006 HOH B6060 CRYST1 71.421 109.874 71.414 90.00 104.52 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 0.014001 0.000000 0.003626 0.00000 SCALE2 0.000000 0.009101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014465 0.00000