HEADER TRANSFERASE 08-JUN-05 2BU2
TITLE CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2 CONTAINING
TITLE 2 PHYSIOLOGICAL AND SYNTHETIC LIGANDS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PYRUVATE DEHYDROGENSAE KINASE ISOENZYME 2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 2;
COMPND 5 EC: 2.7.1.99;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7111;
SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFASTBAC1
KEYWDS GHKL MOTIF REGULATION, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.R.KNOECHEL,A.D.TUCKER,C.M.ROBINSON,C.PHILLIPS,W.TAYLOR,P.J.BUNGAY,
AUTHOR 2 S.A.KASTEN,T.E.ROCHE,D.G.BROWN
REVDAT 5 13-DEC-23 2BU2 1 LINK
REVDAT 4 03-APR-19 2BU2 1 REMARK
REVDAT 3 27-MAR-19 2BU2 1 SOURCE
REVDAT 2 24-FEB-09 2BU2 1 VERSN
REVDAT 1 02-FEB-06 2BU2 0
JRNL AUTH T.R.KNOECHEL,A.D.TUCKER,C.M.ROBINSON,C.PHILLIPS,W.TAYLOR,
JRNL AUTH 2 P.J.BUNGAY,S.A.KASTEN,T.E.ROCHE,D.G.BROWN
JRNL TITL REGULATORY ROLES OF THE N-TERMINAL DOMAIN BASED ON CRYSTAL
JRNL TITL 2 STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2
JRNL TITL 3 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS.
JRNL REF BIOCHEMISTRY V. 45 402 2006
JRNL REFN ISSN 0006-2960
JRNL PMID 16401071
JRNL DOI 10.1021/BI051402S
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNX
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS
REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA,
REMARK 3 : YIP,DZAKULA)
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 21888
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.238
REMARK 3 R VALUE (WORKING SET) : 0.238
REMARK 3 FREE R VALUE : 0.247
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 1067
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2883
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 59
REMARK 3 SOLVENT ATOMS : 91
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -4.97600
REMARK 3 B22 (A**2) : -4.97600
REMARK 3 B33 (A**2) : 9.95300
REMARK 3 B12 (A**2) : -5.98000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.635
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : 0.35
REMARK 3 BSOL : 46.98
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : HET.PAR
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : ION.PARAM
REMARK 3 PARAMETER FILE 5 : ATP.PAR
REMARK 3 PARAMETER FILE 6 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2BU2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-05.
REMARK 100 THE DEPOSITION ID IS D_1290024411.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 5.80
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9326
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21971
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 3.440
REMARK 200 R MERGE (I) : 0.05000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2
REMARK 200 DATA REDUNDANCY IN SHELL : 3.16
REMARK 200 R MERGE FOR SHELL (I) : 0.31000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.910
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNX
REMARK 200 STARTING MODEL: PDB ENTRY 2BTZ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES PH5.8-6, 10% ISOPROPANOL,
REMARK 280 200MM CALCIUM ACETATE, 10MG/ML PROTEIN 4 DEGREES, PH 5.80,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 -X,-Y,Z
REMARK 290 5555 Y,-X+Y,Z+1/3
REMARK 290 6555 X-Y,X,Z+2/3
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.95167
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.90333
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.95167
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.90333
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 54.35150
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 94.13956
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A 32
REMARK 465 SER A 33
REMARK 465 GLY A 170
REMARK 465 SER A 171
REMARK 465 THR A 172
REMARK 465 ASN A 173
REMARK 465 PRO A 174
REMARK 465 ALA A 175
REMARK 465 HIS A 176
REMARK 465 ALA A 303
REMARK 465 PRO A 304
REMARK 465 THR A 305
REMARK 465 PRO A 306
REMARK 465 GLN A 307
REMARK 465 PRO A 308
REMARK 465 GLY A 309
REMARK 465 THR A 310
REMARK 465 GLY A 311
REMARK 465 GLY A 312
REMARK 465 THR A 313
REMARK 465 PRO A 314
REMARK 465 PRO A 386
REMARK 465 SER A 387
REMARK 465 THR A 388
REMARK 465 GLU A 389
REMARK 465 PRO A 390
REMARK 465 LYS A 391
REMARK 465 ASN A 392
REMARK 465 THR A 393
REMARK 465 SER A 394
REMARK 465 THR A 395
REMARK 465 TYR A 396
REMARK 465 ARG A 397
REMARK 465 VAL A 398
REMARK 465 SER A 399
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLN A 378 CG CD OE1 NE2
REMARK 470 GLU A 379 CG CD OE1 OE2
REMARK 470 VAL A 385 CA C O CB CG1 CG2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OG SER A 72 O HOH A 2004 1.82
REMARK 500 OE1 GLU A 128 O HOH A 2004 1.97
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 GLY A 319 N - CA - C ANGL. DEV. = 21.5 DEGREES
REMARK 500 TYR A 320 N - CA - C ANGL. DEV. = -21.6 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ASP A 30 41.77 -70.63
REMARK 500 ASN A 35 48.70 102.52
REMARK 500 ALA A 36 30.98 -86.62
REMARK 500 CYS A 37 124.03 72.03
REMARK 500 SER A 72 -80.46 -53.69
REMARK 500 GLU A 89 -25.31 -34.54
REMARK 500 LYS A 93 -176.51 -59.79
REMARK 500 PRO A 95 -138.14 -62.60
REMARK 500 GLU A 96 -45.19 61.56
REMARK 500 HIS A 98 0.04 -54.88
REMARK 500 ASP A 135 78.83 -118.51
REMARK 500 LYS A 178 -61.40 -0.35
REMARK 500 ILE A 180 79.66 -109.31
REMARK 500 ALA A 210 139.58 -177.81
REMARK 500 SER A 224 -40.36 -22.01
REMARK 500 PHE A 318 -78.89 -86.12
REMARK 500 TYR A 320 40.60 90.50
REMARK 500 PHE A 344 -66.31 -140.93
REMARK 500 GLU A 379 97.14 -179.32
REMARK 500 ALA A 380 105.79 79.54
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 TYR A 11 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A1388 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 247 OD1
REMARK 620 2 ATP A1386 O2G 163.6
REMARK 620 3 ATP A1386 O1A 85.6 81.8
REMARK 620 4 ATP A1386 O2B 84.0 84.8 86.7
REMARK 620 5 HOH A2040 O 96.4 95.2 95.6 177.7
REMARK 620 6 HOH A2087 O 86.4 104.9 170.2 86.9 90.9
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1388
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A1386
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TF1 A1387
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2BTZ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2
REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS
REMARK 900 RELATED ID: 2BU5 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2
REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS
REMARK 900 RELATED ID: 2BU6 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2
REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS
REMARK 900 RELATED ID: 2BU7 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2
REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS
REMARK 900 RELATED ID: 2BU8 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 2
REMARK 900 CONTAINING PHYSIOLOGICAL AND SYNTHETIC LIGANDS
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 N -TERMINAL GS CLONING ARTEFACT
DBREF 2BU2 A 6 7 PDB 2BU2 2BU2 6 7
DBREF 2BU2 A 8 399 UNP Q15119 PDK2_HUMAN 16 407
SEQRES 1 A 394 GLY SER ALA PRO LYS TYR ILE GLU HIS PHE SER LYS PHE
SEQRES 2 A 394 SER PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP PHE
SEQRES 3 A 394 GLY SER SER ASN ALA CYS GLU LYS THR SER PHE THR PHE
SEQRES 4 A 394 LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE MET
SEQRES 5 A 394 LYS GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER THR
SEQRES 6 A 394 PRO SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SER
SEQRES 7 A 394 LEU LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO GLU
SEQRES 8 A 394 ASP HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU VAL
SEQRES 9 A 394 THR ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR MET
SEQRES 10 A 394 ALA GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY ASP
SEQRES 11 A 394 ASP PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU ASP
SEQRES 12 A 394 ARG PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU ILE
SEQRES 13 A 394 ASN GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN PRO
SEQRES 14 A 394 ALA HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN CYS
SEQRES 15 A 394 ASN VAL SER GLU VAL VAL LYS ASP ALA TYR ASP MET ALA
SEQRES 16 A 394 LYS LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO ASP
SEQRES 17 A 394 LEU GLU ILE GLN GLU ILE ASN ALA ALA ASN SER LYS GLN
SEQRES 18 A 394 PRO ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR HIS
SEQRES 19 A 394 MET LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR
SEQRES 20 A 394 VAL GLU SER HIS GLU SER SER LEU ILE LEU PRO PRO ILE
SEQRES 21 A 394 LYS VAL MET VAL ALA LEU GLY GLU GLU ASP LEU SER ILE
SEQRES 22 A 394 LYS MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS
SEQRES 23 A 394 ILE GLU ARG LEU PHE SER TYR MET TYR SER THR ALA PRO
SEQRES 24 A 394 THR PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA GLY
SEQRES 25 A 394 PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA LYS
SEQRES 26 A 394 TYR PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU GLY
SEQRES 27 A 394 PHE GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER
SEQRES 28 A 394 THR ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SER
SEQRES 29 A 394 ALA TRP ARG HIS TYR GLN THR ILE GLN GLU ALA GLY ASP
SEQRES 30 A 394 TRP CYS VAL PRO SER THR GLU PRO LYS ASN THR SER THR
SEQRES 31 A 394 TYR ARG VAL SER
HET ATP A1386 31
HET TF1 A1387 27
HET MG A1388 1
HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE
HETNAM TF1 4-({(2R,5S)-2,5-DIMETHYL-4-[(2R)-3,3,3-TRIFLUORO-2-
HETNAM 2 TF1 HYDROXY-2-METHYLPROPANOYL]PIPERAZIN-1-YL}CARBONYL)
HETNAM 3 TF1 BENZONITRILE
HETNAM MG MAGNESIUM ION
FORMUL 2 ATP C10 H16 N5 O13 P3
FORMUL 3 TF1 C18 H20 F3 N3 O3
FORMUL 4 MG MG 2+
FORMUL 5 HOH *91(H2 O)
HELIX 1 1 SER A 7 SER A 16 1 10
HELIX 2 2 SER A 24 ASP A 30 1 7
HELIX 3 3 GLU A 38 LEU A 62 1 25
HELIX 4 4 PRO A 64 SER A 69 1 6
HELIX 5 5 THR A 70 GLU A 89 1 20
HELIX 6 6 LEU A 101 HIS A 115 1 15
HELIX 7 7 ASP A 117 TYR A 133 1 17
HELIX 8 8 ASP A 136 PHE A 168 1 33
HELIX 9 9 VAL A 189 MET A 209 1 21
HELIX 10 10 VAL A 233 SER A 255 1 23
HELIX 11 11 PRO A 288 GLU A 293 1 6
HELIX 12 12 ARG A 294 SER A 297 5 4
HELIX 13 13 TYR A 320 PHE A 332 1 13
HELIX 14 14 ASN A 367 ARG A 372 1 6
HELIX 15 15 HIS A 373 GLN A 375 5 3
SHEET 1 AA 2 ASP A 184 ASN A 188 0
SHEET 2 AA 2 HIS A 229 TYR A 232 -1 O MET A 230 N CYS A 187
SHEET 1 AB 5 LEU A 214 ASN A 220 0
SHEET 2 AB 5 ILE A 265 LEU A 271 1 O ILE A 265 N GLU A 215
SHEET 3 AB 5 ASP A 275 GLY A 285 -1 O SER A 277 N ALA A 270
SHEET 4 AB 5 PHE A 344 LYS A 353 -1 O PHE A 344 N GLY A 285
SHEET 5 AB 5 ASP A 335 MET A 341 -1 O ASP A 335 N TYR A 351
LINK OD1 ASN A 247 MG MG A1388 1555 1555 2.30
LINK O2G ATP A1386 MG MG A1388 1555 1555 2.00
LINK O1A ATP A1386 MG MG A1388 1555 1555 2.30
LINK O2B ATP A1386 MG MG A1388 1555 1555 2.21
LINK MG MG A1388 O HOH A2040 1555 1555 1.98
LINK MG MG A1388 O HOH A2087 1555 1555 2.00
SITE 1 AC1 4 ASN A 247 ATP A1386 HOH A2040 HOH A2087
SITE 1 AC2 26 GLU A 243 ASN A 247 ARG A 250 ALA A 251
SITE 2 AC2 26 ASP A 282 VAL A 287 LEU A 295 LEU A 315
SITE 3 AC2 26 ALA A 316 GLY A 317 PHE A 318 GLY A 319
SITE 4 AC2 26 TYR A 320 GLY A 321 LEU A 322 PRO A 323
SITE 5 AC2 26 THR A 346 MG A1388 HOH A2040 HOH A2057
SITE 6 AC2 26 HOH A2084 HOH A2085 HOH A2086 HOH A2087
SITE 7 AC2 26 HOH A2088 HOH A2090
SITE 1 AC3 10 LEU A 23 GLN A 27 PHE A 28 PHE A 31
SITE 2 AC3 10 SER A 41 PHE A 44 LEU A 45 LEU A 160
SITE 3 AC3 10 GLN A 163 HOH A2091
CRYST1 108.703 108.703 83.855 90.00 90.00 120.00 P 64 6
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.009199 0.005311 0.000000 0.00000
SCALE2 0.000000 0.010623 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011925 0.00000