HEADER TRANSFERASE 26-JAN-05 2BIY TITLE STRUCTURE OF PDK1-S241A MUTANT KINASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 51-360 (KINASE DOMAIN); COMPND 5 SYNONYM: HPDK1; COMPND 6 EC: 2.7.1.37; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: T-LOOP MUTANT SER241ALA 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_TAXID: 7108; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS AGC KINASE, AC-HELIX, ATP-BINDING, PHOSPHORYLATION, PHOSPHOINOSITIDE KEYWDS 2 DEPENDENT PROTEIN KINASE, PI3-KINASE SIGNALLING, PIF-POCKET, PKA, KEYWDS 3 PKB, T-LOOP MUTANT, SERINE-THREONINE-PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.KOMANDER,G.S.KULAR,M.DEAK,D.R.ALESSI,D.M.F.VAN AALTEN REVDAT 6 13-DEC-23 2BIY 1 REMARK REVDAT 5 03-APR-19 2BIY 1 SOURCE REVDAT 4 19-DEC-18 2BIY 1 AUTHOR JRNL REMARK LINK REVDAT 3 24-FEB-09 2BIY 1 VERSN REVDAT 2 12-JUL-05 2BIY 1 JRNL REMARK REVDAT 1 23-FEB-05 2BIY 0 JRNL AUTH D.KOMANDER,G.KULAR,M.DEAK,D.R.ALESSI,D.M.VAN AALTEN JRNL TITL ROLE OF T-LOOP PHOSPHORYLATION IN PDK1 ACTIVATION, JRNL TITL 2 STABILITY, AND SUBSTRATE BINDING. JRNL REF J. BIOL. CHEM. V. 280 18797 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15741170 JRNL DOI 10.1074/JBC.M500977200 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 27210 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100 REMARK 3 FREE R VALUE TEST SET COUNT : 588 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1452 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2301 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.53000 REMARK 3 B22 (A**2) : 1.53000 REMARK 3 B33 (A**2) : -2.29000 REMARK 3 B12 (A**2) : 0.76000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.146 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2478 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2197 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3350 ; 1.512 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5130 ; 0.867 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 5.663 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2616 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 498 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 503 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2607 ; 0.252 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1416 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 157 ; 0.148 ; 0.200 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): 46 ; 0.758 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 73 ; 0.335 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.284 ; 0.200 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): 1440 ; 0.909 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2327 ; 1.676 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1038 ; 2.508 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1023 ; 4.033 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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. RESIDUES 51-71 ARE DISORDERED. UNIDENTIFIED ELECTRON REMARK 3 DENSITY NEAR THE T-LOOP. RESIDUES LACKING SIDE-CHAIN ELECTRON REMARK 3 DENSITY HAVE BEEN REFINED WITH OCCU=0.0 OR HAVE BEEN REFINED AS REMARK 3 ALA RESIDUES. REMARK 4 REMARK 4 2BIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1290022697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28782 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1H1W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 0.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULPHATE, 0.1 M TRIS REMARK 280 PH7.5, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 31.83333 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 15.91667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.91667 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 31.83333 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC 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 400 REMARK 400 COMPOUND REMARK 400 FUNCTION: PHOSPHORYLATES AND ACTIVATES PKB/AKT, PKA, REMARK 400 PKC-ZETA, P70S6K AND P90S6K/RSK. REMARK 400 ENGINEERED MUTATION IN CHAIN A SER 241 TO ALA 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 51 REMARK 465 ASP A 52 REMARK 465 GLY A 53 REMARK 465 THR A 54 REMARK 465 ALA A 55 REMARK 465 ALA A 56 REMARK 465 GLU A 57 REMARK 465 PRO A 58 REMARK 465 ARG A 59 REMARK 465 PRO A 60 REMARK 465 GLY A 61 REMARK 465 ALA A 62 REMARK 465 GLY A 63 REMARK 465 SER A 64 REMARK 465 LEU A 65 REMARK 465 GLN A 66 REMARK 465 HIS A 67 REMARK 465 ALA A 68 REMARK 465 GLN A 69 REMARK 465 PRO A 70 REMARK 465 PRO A 71 REMARK 465 ALA A 360 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 73 CG CD OE1 NE2 REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 ARG A 238 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 GLU A 343 CG CD OE1 OE2 REMARK 470 GLU A 348 CG CD OE1 OE2 REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 THR A 359 CA C O CB OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 S SO4 A 1367 O3 SO4 A 1367 4556 0.99 REMARK 500 O3 SO4 A 1367 O4 SO4 A 1367 4556 1.24 REMARK 500 O2 SO4 A 1367 O3 SO4 A 1367 4556 1.43 REMARK 500 O1 SO4 A 1367 O2 SO4 A 1367 4556 1.43 REMARK 500 S SO4 A 1367 O2 SO4 A 1367 4556 1.60 REMARK 500 O1 GOL A 1360 O1 GOL A 1362 1554 1.69 REMARK 500 OE1 GLU A 303 OE1 GLU A 303 5675 1.70 REMARK 500 O1 SO4 A 1367 O3 SO4 A 1367 4556 1.79 REMARK 500 S SO4 A 1367 O4 SO4 A 1367 4556 1.82 REMARK 500 S SO4 A 1367 O1 SO4 A 1367 4556 1.84 REMARK 500 O4 SO4 A 1367 O4 SO4 A 1367 4556 1.95 REMARK 500 O2 GOL A 1360 O2 GOL A 1362 1554 2.04 REMARK 500 NZ LYS A 144 O4 SO4 A 1367 4556 2.08 REMARK 500 O3 GOL A 1360 O3 GOL A 1362 1554 2.10 REMARK 500 C1 GOL A 1360 O1 GOL A 1362 1554 2.14 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 ASP A 138 CB - CG - OD2 ANGL. DEV. = 5.8 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 151 -157.83 -114.27 REMARK 500 ARG A 204 -11.09 78.44 REMARK 500 ASP A 205 41.93 -141.36 REMARK 500 ASP A 223 67.67 82.91 REMARK 500 ASN A 349 46.19 -144.66 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 SO4 A1366 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1368 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1369 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1370 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A1373 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1359 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1360 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1361 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1362 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1363 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1364 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1365 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H1W RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 CATALYTIC DOMAIN REMARK 900 RELATED ID: 1OKY RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH STAUROSPORINE REMARK 900 RELATED ID: 1OKZ RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH UCN-01 REMARK 900 RELATED ID: 1UU3 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH LY333531 REMARK 900 RELATED ID: 1UU7 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-2 REMARK 900 RELATED ID: 1UU8 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1 REMARK 900 RELATED ID: 1UU9 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-3 REMARK 900 RELATED ID: 1UVR RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-8 REMARK 900 RELATED ID: 1W1D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND REMARK 900 TO INOSITOL (1, 3,4,5)-TETRAKISPHOSPHATE REMARK 900 RELATED ID: 1W1G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND REMARK 900 TO DIC4- PHOSPHATIDYLINOSITOL (3,4,5)-TRISPHOSPHATE REMARK 900 RELATED ID: 1W1H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 SER241ALA MUTANT DBREF 2BIY A 51 360 UNP O15530 PDPK_HUMAN 51 360 SEQADV 2BIY ALA A 241 UNP O15530 SER 241 ENGINEERED MUTATION SEQRES 1 A 310 MET ASP GLY THR ALA ALA GLU PRO ARG PRO GLY ALA GLY SEQRES 2 A 310 SER LEU GLN HIS ALA GLN PRO PRO PRO GLN PRO ARG LYS SEQRES 3 A 310 LYS ARG PRO GLU ASP PHE LYS PHE GLY LYS ILE LEU GLY SEQRES 4 A 310 GLU GLY SER PHE SER THR VAL VAL LEU ALA ARG GLU LEU SEQRES 5 A 310 ALA THR SER ARG GLU TYR ALA ILE LYS ILE LEU GLU LYS SEQRES 6 A 310 ARG HIS ILE ILE LYS GLU ASN LYS VAL PRO TYR VAL THR SEQRES 7 A 310 ARG GLU ARG ASP VAL MET SER ARG LEU ASP HIS PRO PHE SEQRES 8 A 310 PHE VAL LYS LEU TYR PHE THR PHE GLN ASP ASP GLU LYS SEQRES 9 A 310 LEU TYR PHE GLY LEU SER TYR ALA LYS ASN GLY GLU LEU SEQRES 10 A 310 LEU LYS TYR ILE ARG LYS ILE GLY SER PHE ASP GLU THR SEQRES 11 A 310 CYS THR ARG PHE TYR THR ALA GLU ILE VAL SER ALA LEU SEQRES 12 A 310 GLU TYR LEU HIS GLY LYS GLY ILE ILE HIS ARG ASP LEU SEQRES 13 A 310 LYS PRO GLU ASN ILE LEU LEU ASN GLU ASP MET HIS ILE SEQRES 14 A 310 GLN ILE THR ASP PHE GLY THR ALA LYS VAL LEU SER PRO SEQRES 15 A 310 GLU SER LYS GLN ALA ARG ALA ASN ALA PHE VAL GLY THR SEQRES 16 A 310 ALA GLN TYR VAL SER PRO GLU LEU LEU THR GLU LYS SER SEQRES 17 A 310 ALA CYS LYS SER SER ASP LEU TRP ALA LEU GLY CYS ILE SEQRES 18 A 310 ILE TYR GLN LEU VAL ALA GLY LEU PRO PRO PHE ARG ALA SEQRES 19 A 310 GLY ASN GLU TYR LEU ILE PHE GLN LYS ILE ILE LYS LEU SEQRES 20 A 310 GLU TYR ASP PHE PRO GLU LYS PHE PHE PRO LYS ALA ARG SEQRES 21 A 310 ASP LEU VAL GLU LYS LEU LEU VAL LEU ASP ALA THR LYS SEQRES 22 A 310 ARG LEU GLY CYS GLU GLU MET GLU GLY TYR GLY PRO LEU SEQRES 23 A 310 LYS ALA HIS PRO PHE PHE GLU SER VAL THR TRP GLU ASN SEQRES 24 A 310 LEU HIS GLN GLN THR PRO PRO LYS LEU THR ALA HET GOL A1359 6 HET GOL A1360 6 HET GOL A1361 6 HET GOL A1362 6 HET GOL A1363 6 HET GOL A1364 6 HET GOL A1365 6 HET SO4 A1366 5 HET SO4 A1367 5 HET SO4 A1368 5 HET SO4 A1369 5 HET SO4 A1370 5 HET SO4 A1371 5 HET SO4 A1372 5 HET ATP A1373 31 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 7(C3 H8 O3) FORMUL 9 SO4 7(O4 S 2-) FORMUL 16 ATP C10 H16 N5 O13 P3 FORMUL 17 HOH *166(H2 O) HELIX 1 1 ARG A 78 GLU A 80 5 3 HELIX 2 2 LYS A 115 GLU A 121 1 7 HELIX 3 3 LYS A 123 LEU A 137 1 15 HELIX 4 4 LEU A 167 GLY A 175 1 9 HELIX 5 5 ASP A 178 LYS A 199 1 22 HELIX 6 6 THR A 245 VAL A 249 5 5 HELIX 7 7 SER A 250 GLU A 256 1 7 HELIX 8 8 LYS A 261 GLY A 278 1 18 HELIX 9 9 ASN A 286 LYS A 296 1 11 HELIX 10 10 PHE A 306 LEU A 317 1 12 HELIX 11 11 ASP A 320 ARG A 324 5 5 HELIX 12 12 CYS A 327 GLU A 331 5 5 HELIX 13 13 GLY A 332 ALA A 338 1 7 HELIX 14 14 HIS A 339 GLU A 343 5 5 HELIX 15 15 ASN A 349 GLN A 353 5 5 SHEET 1 AA 5 PHE A 82 GLU A 90 0 SHEET 2 AA 5 THR A 95 GLU A 101 -1 O VAL A 96 N LEU A 88 SHEET 3 AA 5 GLU A 107 GLU A 114 -1 O TYR A 108 N ALA A 99 SHEET 4 AA 5 LYS A 154 LEU A 159 -1 O LEU A 155 N LEU A 113 SHEET 5 AA 5 LEU A 145 GLN A 150 -1 N TYR A 146 O GLY A 158 SHEET 1 AB 3 GLY A 165 GLU A 166 0 SHEET 2 AB 3 ILE A 211 LEU A 213 -1 N LEU A 213 O GLY A 165 SHEET 3 AB 3 ILE A 219 ILE A 221 -1 O GLN A 220 N LEU A 212 SHEET 1 AC 2 ILE A 201 ILE A 202 0 SHEET 2 AC 2 LYS A 228 VAL A 229 -1 O LYS A 228 N ILE A 202 SHEET 1 AD 2 GLN A 236 ARG A 238 0 SHEET 2 AD 2 SER A 258 CYS A 260 -1 O ALA A 259 N ALA A 237 SITE 1 AC1 5 LYS A 83 VAL A 345 THR A 346 TRP A 347 SITE 2 AC1 5 GLU A 348 SITE 1 AC2 2 LYS A 144 TYR A 146 SITE 1 AC3 3 ARG A 75 ARG A 136 LYS A 199 SITE 1 AC4 5 LYS A 76 ARG A 131 THR A 148 PHE A 149 SITE 2 AC4 5 GLN A 150 SITE 1 AC5 4 ARG A 106 PRO A 140 HIS A 351 GOL A1359 SITE 1 AC6 6 TYR A 146 SER A 160 GLN A 220 GOL A1359 SITE 2 AC6 6 HOH A2051 HOH A2161 SITE 1 AC7 2 ARG A 310 HOH A2162 SITE 1 AC8 18 GLY A 89 GLY A 91 SER A 92 SER A 94 SITE 2 AC8 18 VAL A 96 ALA A 109 LYS A 111 SER A 160 SITE 3 AC8 18 ALA A 162 GLU A 166 LEU A 212 GOL A1361 SITE 4 AC8 18 HOH A2084 HOH A2160 HOH A2163 HOH A2164 SITE 5 AC8 18 HOH A2165 HOH A2166 SITE 1 AC9 7 ARG A 106 GLU A 107 SER A 160 TYR A 161 SITE 2 AC9 7 SO4 A1370 SO4 A1371 HOH A2051 SITE 1 BC1 9 PHE A 84 GLU A 194 TYR A 333 GLY A 334 SITE 2 BC1 9 LYS A 337 GOL A1362 HOH A2141 HOH A2158 SITE 3 BC1 9 HOH A2159 SITE 1 BC2 7 PHE A 93 SER A 94 LYS A 111 GLU A 130 SITE 2 BC2 7 ATP A1373 HOH A2160 HOH A2164 SITE 1 BC3 8 PHE A 82 LYS A 83 PHE A 84 GLU A 194 SITE 2 BC3 8 LYS A 337 GOL A1360 HOH A2004 HOH A2009 SITE 1 BC4 6 PRO A 79 PHE A 84 LYS A 154 TYR A 156 SITE 2 BC4 6 GLU A 331 GLY A 332 SITE 1 BC5 2 PRO A 307 LYS A 308 SITE 1 BC6 9 ALA A 103 THR A 104 HIS A 139 SER A 191 SITE 2 BC6 9 TRP A 347 GLU A 348 ASN A 349 LEU A 350 SITE 3 BC6 9 HIS A 351 CRYST1 121.827 121.827 47.750 90.00 90.00 120.00 P 32 2 1 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 0.008208 0.004739 0.000000 0.00000 SCALE2 0.000000 0.009478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020942 0.00000