PDB Short entry for 3NAY HEADER TRANSFERASE 02-JUN-10 3NAY TITLE PDK1 IN COMPLEX WITH INHIBITOR MP6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 66 TO 362; COMPND 5 SYNONYM: HPDK1; COMPND 6 EC: 2.7.11.1; 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 GENE: PDPK1, PDK1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS KINASE, SERINE/THREONINE PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.YAN,S.K.MUNSHI,T.ALLISON REVDAT 2 24-JAN-18 3NAY 1 JRNL REVDAT 1 24-NOV-10 3NAY 0 JRNL AUTH K.NAGASHIMA,S.D.SHUMWAY,S.SATHYANARAYANAN,A.CHEN,B.DOLINSKI, JRNL AUTH 2 Y.XU,H.KEILHACK,T.NGUYEN,M.WIZNEROWICZ,L.LI,B.A.LUTTERBACH, JRNL AUTH 3 C.PAWELETZ,T.ALLISON,Y.YAN,S.K.MUNSHI,A.KLIPPEL,M.KRAUS, JRNL AUTH 4 E.V.BOBKOVA,S.DESHMUKH,Z.XU,U.MUELLER,A.A.SZEWCZAK,B.-S.PAN, JRNL AUTH 5 V.RICHON,R.POLLOCK,P.BLUME-JENSEN,A.NORTHRUP,J.N.ANDERSEN JRNL TITL SELECTIVE INHIBITION OF PDK1 USING AN ALLOSTERIC KINASE JRNL TITL 2 INHIBITOR AND RNAI IMPAIRS CANCER CELL MIGRATION AND JRNL TITL 3 ANCHORAGE-INDEPENDENT GROWTH OF PRIMARY TUMOR LINES JRNL REF J.BIOL.CHEM. 2010 JRNL REFN ESSN 1083-351X REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 22984 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1181 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.47 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2679 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2977 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2537 REMARK 3 BIN R VALUE (WORKING SET) : 0.2972 REMARK 3 BIN FREE R VALUE : 0.3057 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 142 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 : 4544 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.28020 REMARK 3 B22 (A**2) : -5.28020 REMARK 3 B33 (A**2) : 10.56030 REMARK 3 B12 (A**2) : 0.00000 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) : 0.378 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.593 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4726 ; 2.000 ; NULL REMARK 3 BOND ANGLES : 6392 ; 2.000 ; NULL REMARK 3 TORSION ANGLES : 1628 ; 2.000 ; NULL REMARK 3 TRIGONAL CARBON PLANES : 120 ; 2.000 ; NULL REMARK 3 GENERAL PLANES : 678 ; 5.000 ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : 4726 ; 20.000 ; NULL REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : 6 ; 0.000 ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 590 ; 5.000 ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5361 ; 4.000 ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.15 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.62 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.97 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23041 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.83850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.83850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.50000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.83850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.83850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 133.50000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.83850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.83850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.50000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.83850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.83850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 133.50000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 89.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 52 REMARK 465 HIS A 53 REMARK 465 HIS A 54 REMARK 465 HIS A 55 REMARK 465 HIS A 56 REMARK 465 HIS A 57 REMARK 465 HIS A 58 REMARK 465 GLU A 59 REMARK 465 ASN A 60 REMARK 465 LEU A 61 REMARK 465 TYR A 62 REMARK 465 PHE A 63 REMARK 465 GLN A 64 REMARK 465 GLY 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 PRO A 72 REMARK 465 GLN A 73 REMARK 465 PRO A 74 REMARK 465 ARG A 75 REMARK 465 PRO A 232 REMARK 465 GLU A 233 REMARK 465 SER A 234 REMARK 465 LYS A 235 REMARK 465 GLN A 236 REMARK 465 ALA A 237 REMARK 465 ARG A 238 REMARK 465 ALA A 239 REMARK 465 MET B 52 REMARK 465 HIS B 53 REMARK 465 HIS B 54 REMARK 465 HIS B 55 REMARK 465 HIS B 56 REMARK 465 HIS B 57 REMARK 465 HIS B 58 REMARK 465 GLU B 59 REMARK 465 ASN B 60 REMARK 465 LEU B 61 REMARK 465 TYR B 62 REMARK 465 PHE B 63 REMARK 465 GLN B 64 REMARK 465 GLY B 65 REMARK 465 GLN B 66 REMARK 465 HIS B 67 REMARK 465 ALA B 68 REMARK 465 GLN B 69 REMARK 465 PRO B 70 REMARK 465 PRO B 71 REMARK 465 PRO B 72 REMARK 465 GLN B 73 REMARK 465 PRO B 74 REMARK 465 ARG B 75 REMARK 465 PRO B 232 REMARK 465 GLU B 233 REMARK 465 SER B 234 REMARK 465 LYS B 235 REMARK 465 GLN B 236 REMARK 465 ALA B 237 REMARK 465 ARG B 238 REMARK 465 ALA B 239 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 GLU B 303 CG CD OE1 OE2 REMARK 470 LYS B 304 CG CD CE NZ REMARK 470 GLU B 348 CG CD OE1 OE2 REMARK 470 LYS B 357 CG CD CE NZ 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 PHE A 93 13.94 -143.05 REMARK 500 SER A 105 8.53 80.14 REMARK 500 ASP A 138 86.12 -150.01 REMARK 500 ALA A 162 78.49 -108.64 REMARK 500 LYS A 163 -39.70 -39.44 REMARK 500 ARG A 204 -9.68 74.17 REMARK 500 ASP A 205 39.44 -146.56 REMARK 500 MET A 217 30.07 73.28 REMARK 500 ASP A 223 70.67 72.20 REMARK 500 SEP A 241 -138.94 72.35 REMARK 500 PHE A 305 126.66 -34.08 REMARK 500 GLU A 331 14.81 80.92 REMARK 500 SER A 344 -9.70 98.74 REMARK 500 ASP B 81 7.69 -62.97 REMARK 500 ASP B 138 81.31 -159.87 REMARK 500 ASP B 151 -166.16 -124.07 REMARK 500 ARG B 204 -13.79 76.39 REMARK 500 ASP B 205 46.80 -147.03 REMARK 500 ASP B 223 77.09 72.00 REMARK 500 SEP B 241 -96.29 -170.19 REMARK 500 PHE B 242 -119.99 -50.20 REMARK 500 VAL B 243 100.21 114.84 REMARK 500 LYS B 257 -16.13 60.71 REMARK 500 MET B 330 37.29 -141.85 REMARK 500 GLU B 331 17.34 52.75 REMARK 500 HIS B 339 133.77 -36.39 REMARK 500 PRO B 340 -37.43 -38.16 REMARK 500 GLU B 348 -75.55 -55.16 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 MP6 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MP6 B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NAX RELATED DB: PDB REMARK 900 PDK1 IN COMPLEX WITH INHIBITOR MP7 DBREF 3NAY A 66 362 UNP O15530 PDPK1_HUMAN 66 362 DBREF 3NAY B 66 362 UNP O15530 PDPK1_HUMAN 66 362 SEQADV 3NAY MET A 52 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS A 53 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS A 54 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS A 55 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS A 56 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS A 57 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS A 58 UNP O15530 EXPRESSION TAG SEQADV 3NAY GLU A 59 UNP O15530 EXPRESSION TAG SEQADV 3NAY ASN A 60 UNP O15530 EXPRESSION TAG SEQADV 3NAY LEU A 61 UNP O15530 EXPRESSION TAG SEQADV 3NAY TYR A 62 UNP O15530 EXPRESSION TAG SEQADV 3NAY PHE A 63 UNP O15530 EXPRESSION TAG SEQADV 3NAY GLN A 64 UNP O15530 EXPRESSION TAG SEQADV 3NAY GLY A 65 UNP O15530 EXPRESSION TAG SEQADV 3NAY MET B 52 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS B 53 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS B 54 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS B 55 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS B 56 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS B 57 UNP O15530 EXPRESSION TAG SEQADV 3NAY HIS B 58 UNP O15530 EXPRESSION TAG SEQADV 3NAY GLU B 59 UNP O15530 EXPRESSION TAG SEQADV 3NAY ASN B 60 UNP O15530 EXPRESSION TAG SEQADV 3NAY LEU B 61 UNP O15530 EXPRESSION TAG SEQADV 3NAY TYR B 62 UNP O15530 EXPRESSION TAG SEQADV 3NAY PHE B 63 UNP O15530 EXPRESSION TAG SEQADV 3NAY GLN B 64 UNP O15530 EXPRESSION TAG SEQADV 3NAY GLY B 65 UNP O15530 EXPRESSION TAG SEQRES 1 A 311 MET HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE GLN SEQRES 2 A 311 GLY GLN HIS ALA GLN PRO PRO PRO GLN PRO ARG LYS LYS SEQRES 3 A 311 ARG PRO GLU ASP PHE LYS PHE GLY LYS ILE LEU GLY GLU SEQRES 4 A 311 GLY SER PHE SER THR VAL VAL LEU ALA ARG GLU LEU ALA SEQRES 5 A 311 THR SER ARG GLU TYR ALA ILE LYS ILE LEU GLU LYS ARG SEQRES 6 A 311 HIS ILE ILE LYS GLU ASN LYS VAL PRO TYR VAL THR ARG SEQRES 7 A 311 GLU ARG ASP VAL MET SER ARG LEU ASP HIS PRO PHE PHE SEQRES 8 A 311 VAL LYS LEU TYR PHE THR PHE GLN ASP ASP GLU LYS LEU SEQRES 9 A 311 TYR PHE GLY LEU SER TYR ALA LYS ASN GLY GLU LEU LEU SEQRES 10 A 311 LYS TYR ILE ARG LYS ILE GLY SER PHE ASP GLU THR CYS SEQRES 11 A 311 THR ARG PHE TYR THR ALA GLU ILE VAL SER ALA LEU GLU SEQRES 12 A 311 TYR LEU HIS GLY LYS GLY ILE ILE HIS ARG ASP LEU LYS SEQRES 13 A 311 PRO GLU ASN ILE LEU LEU ASN GLU ASP MET HIS ILE GLN SEQRES 14 A 311 ILE THR ASP PHE GLY THR ALA LYS VAL LEU SER PRO GLU SEQRES 15 A 311 SER LYS GLN ALA ARG ALA ASN SEP PHE VAL GLY THR ALA SEQRES 16 A 311 GLN TYR VAL SER PRO GLU LEU LEU THR GLU LYS SER ALA SEQRES 17 A 311 CYS LYS SER SER ASP LEU TRP ALA LEU GLY CYS ILE ILE SEQRES 18 A 311 TYR GLN LEU VAL ALA GLY LEU PRO PRO PHE ARG ALA GLY SEQRES 19 A 311 ASN GLU TYR LEU ILE PHE GLN LYS ILE ILE LYS LEU GLU SEQRES 20 A 311 TYR ASP PHE PRO GLU LYS PHE PHE PRO LYS ALA ARG ASP SEQRES 21 A 311 LEU VAL GLU LYS LEU LEU VAL LEU ASP ALA THR LYS ARG SEQRES 22 A 311 LEU GLY CYS GLU GLU MET GLU GLY TYR GLY PRO LEU LYS SEQRES 23 A 311 ALA HIS PRO PHE PHE GLU SER VAL THR TRP GLU ASN LEU SEQRES 24 A 311 HIS GLN GLN THR PRO PRO LYS LEU THR ALA TYR LEU SEQRES 1 B 311 MET HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE GLN SEQRES 2 B 311 GLY GLN HIS ALA GLN PRO PRO PRO GLN PRO ARG LYS LYS SEQRES 3 B 311 ARG PRO GLU ASP PHE LYS PHE GLY LYS ILE LEU GLY GLU SEQRES 4 B 311 GLY SER PHE SER THR VAL VAL LEU ALA ARG GLU LEU ALA SEQRES 5 B 311 THR SER ARG GLU TYR ALA ILE LYS ILE LEU GLU LYS ARG SEQRES 6 B 311 HIS ILE ILE LYS GLU ASN LYS VAL PRO TYR VAL THR ARG SEQRES 7 B 311 GLU ARG ASP VAL MET SER ARG LEU ASP HIS PRO PHE PHE SEQRES 8 B 311 VAL LYS LEU TYR PHE THR PHE GLN ASP ASP GLU LYS LEU SEQRES 9 B 311 TYR PHE GLY LEU SER TYR ALA LYS ASN GLY GLU LEU LEU SEQRES 10 B 311 LYS TYR ILE ARG LYS ILE GLY SER PHE ASP GLU THR CYS SEQRES 11 B 311 THR ARG PHE TYR THR ALA GLU ILE VAL SER ALA LEU GLU SEQRES 12 B 311 TYR LEU HIS GLY LYS GLY ILE ILE HIS ARG ASP LEU LYS SEQRES 13 B 311 PRO GLU ASN ILE LEU LEU ASN GLU ASP MET HIS ILE GLN SEQRES 14 B 311 ILE THR ASP PHE GLY THR ALA LYS VAL LEU SER PRO GLU SEQRES 15 B 311 SER LYS GLN ALA ARG ALA ASN SEP PHE VAL GLY THR ALA SEQRES 16 B 311 GLN TYR VAL SER PRO GLU LEU LEU THR GLU LYS SER ALA SEQRES 17 B 311 CYS LYS SER SER ASP LEU TRP ALA LEU GLY CYS ILE ILE SEQRES 18 B 311 TYR GLN LEU VAL ALA GLY LEU PRO PRO PHE ARG ALA GLY SEQRES 19 B 311 ASN GLU TYR LEU ILE PHE GLN LYS ILE ILE LYS LEU GLU SEQRES 20 B 311 TYR ASP PHE PRO GLU LYS PHE PHE PRO LYS ALA ARG ASP SEQRES 21 B 311 LEU VAL GLU LYS LEU LEU VAL LEU ASP ALA THR LYS ARG SEQRES 22 B 311 LEU GLY CYS GLU GLU MET GLU GLY TYR GLY PRO LEU LYS SEQRES 23 B 311 ALA HIS PRO PHE PHE GLU SER VAL THR TRP GLU ASN LEU SEQRES 24 B 311 HIS GLN GLN THR PRO PRO LYS LEU THR ALA TYR LEU MODRES 3NAY SEP A 241 SER PHOSPHOSERINE MODRES 3NAY SEP B 241 SER PHOSPHOSERINE HET SEP A 241 10 HET SEP B 241 10 HET MP6 A 1 32 HET MP6 B 2 32 HETNAM SEP PHOSPHOSERINE HETNAM MP6 4-(2-CYCLOPROPYLETHYLIDENE)-9-(1H-PYRAZOL-4-YL)-6- HETNAM 2 MP6 {[(1R)-1,2,2-TRIMETHYLPROPYL]AMINO}BENZO[C][1, HETNAM 3 MP6 6]NAPHTHYRIDIN-1(4H)-ONE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 3 MP6 2(C26 H29 N5 O) FORMUL 5 HOH *149(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 GLU A 166 GLY A 175 1 10 HELIX 5 5 ASP A 178 GLY A 198 1 21 HELIX 6 6 LYS A 207 GLU A 209 5 3 HELIX 7 7 THR A 245 VAL A 249 5 5 HELIX 8 8 SER A 250 GLU A 256 1 7 HELIX 9 9 CYS A 260 GLY A 278 1 19 HELIX 10 10 ASN A 286 LYS A 296 1 11 HELIX 11 11 PHE A 306 LEU A 317 1 12 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 HELIX 16 16 ARG B 78 GLU B 80 5 3 HELIX 17 17 LYS B 115 GLU B 121 1 7 HELIX 18 18 LYS B 123 LEU B 137 1 15 HELIX 19 19 GLU B 166 GLY B 175 1 10 HELIX 20 20 ASP B 178 LYS B 199 1 22 HELIX 21 21 THR B 245 VAL B 249 5 5 HELIX 22 22 SER B 250 GLU B 256 1 7 HELIX 23 23 CYS B 260 GLY B 278 1 19 HELIX 24 24 ASN B 286 LEU B 297 1 12 HELIX 25 25 PHE B 306 LEU B 317 1 12 HELIX 26 26 CYS B 327 GLU B 331 5 5 HELIX 27 27 GLY B 332 HIS B 339 1 8 HELIX 28 28 PRO B 340 GLU B 343 5 4 HELIX 29 29 ASN B 349 GLN B 353 5 5 SHEET 1 A 5 PHE A 82 GLU A 90 0 SHEET 2 A 5 THR A 95 GLU A 101 -1 O LEU A 98 N GLY A 85 SHEET 3 A 5 GLU A 107 GLU A 114 -1 O ILE A 112 N THR A 95 SHEET 4 A 5 LYS A 154 LEU A 159 -1 O LEU A 159 N ALA A 109 SHEET 5 A 5 LEU A 145 GLN A 150 -1 N TYR A 146 O GLY A 158 SHEET 1 B 2 ILE A 201 ILE A 202 0 SHEET 2 B 2 LYS A 228 VAL A 229 -1 O LYS A 228 N ILE A 202 SHEET 1 C 2 ILE A 211 LEU A 213 0 SHEET 2 C 2 ILE A 219 ILE A 221 -1 O GLN A 220 N LEU A 212 SHEET 1 D 5 PHE B 82 GLU B 90 0 SHEET 2 D 5 SER B 94 GLU B 101 -1 O LEU B 98 N LYS B 86 SHEET 3 D 5 GLU B 107 GLU B 114 -1 O ILE B 112 N THR B 95 SHEET 4 D 5 LYS B 154 LEU B 159 -1 O PHE B 157 N LYS B 111 SHEET 5 D 5 LEU B 145 GLN B 150 -1 N TYR B 146 O GLY B 158 SHEET 1 E 2 ILE B 201 ILE B 202 0 SHEET 2 E 2 LYS B 228 VAL B 229 -1 O LYS B 228 N ILE B 202 SHEET 1 F 2 ILE B 211 LEU B 213 0 SHEET 2 F 2 ILE B 219 ILE B 221 -1 O GLN B 220 N LEU B 212 LINK C ASN A 240 N SEP A 241 1555 1555 1.34 LINK C SEP A 241 N PHE A 242 1555 1555 1.35 LINK C ASN B 240 N SEP B 241 1555 1555 1.35 LINK C SEP B 241 N PHE B 242 1555 1555 1.35 SITE 1 AC1 14 LEU A 88 GLU A 90 VAL A 96 ALA A 109 SITE 2 AC1 14 LYS A 111 GLU A 130 SER A 160 TYR A 161 SITE 3 AC1 14 ALA A 162 LYS A 163 GLY A 165 GLU A 209 SITE 4 AC1 14 LEU A 212 THR A 222 SITE 1 AC2 14 LEU B 88 GLY B 89 GLU B 90 VAL B 96 SITE 2 AC2 14 ALA B 109 SER B 160 ALA B 162 LYS B 163 SITE 3 AC2 14 GLY B 165 GLU B 209 ASN B 210 LEU B 212 SITE 4 AC2 14 THR B 222 ASP B 223 CRYST1 89.677 89.677 178.000 90.00 90.00 90.00 P 41 21 2 16 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 0.011151 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005618 0.00000