PDB Short entry for 3DY7 HEADER TRANSFERASE 25-JUL-08 3DY7 TITLE X-RAY STRUCTURE OF THE HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 TITLE 2 (MEK1) IN A COMPLEX WITH LIGAND AND MGATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEIN KINASE DOMAIN, UNP RESIDUES 62-393; COMPND 5 SYNONYM: MAP KINASE KINASE 1, MAPKK 1, ERK ACTIVATOR KINASE 1, COMPND 6 MAPK/ERK KINASE 1, MEK1; COMPND 7 EC: 2.7.12.2; COMPND 8 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: MAP2K1, MEK1, PRKMK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24B KEYWDS DUAL SPECIFICITY PROTEIN KINASE, NON-ATP-COMPETITIVE KINASE KEYWDS 2 INHIBITOR, INHIBITOR-BOUND PROTEIN KINASE, ATP-BOUND PROTEIN KINASE, KEYWDS 3 ACETYLATION, ATP-BINDING, DISEASE MUTATION, NUCLEOTIDE-BINDING, KEYWDS 4 PHOSPHOPROTEIN, SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE, KEYWDS 5 TYROSINE-PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR J.F.OHREN,A.PAVLOVSKY,E.ZHANG REVDAT 2 30-AUG-23 3DY7 1 REMARK SEQADV LINK REVDAT 1 16-JUN-09 3DY7 0 JRNL AUTH H.TECLE,J.SHAO,Y.LI,M.KOTHE,S.KAZMIRSKI,J.PENZOTTI,Y.H.DING, JRNL AUTH 2 J.OHREN,D.MOSHINSKY,R.COLI,N.JHAWAR,E.BORA, JRNL AUTH 3 S.JACQUES-O'HAGAN,J.WU JRNL TITL BEYOND THE MEK-POCKET: CAN CURRENT MEK KINASE INHIBITORS BE JRNL TITL 2 UTILIZED TO SYNTHESIZE NOVEL TYPE III NCKIS? DOES THE JRNL TITL 3 MEK-POCKET EXIST IN KINASES OTHER THAN MEK? JRNL REF BIOORG.MED.CHEM.LETT. V. 19 226 2009 JRNL REFN ISSN 0960-894X JRNL PMID 19019675 JRNL DOI 10.1016/J.BMCL.2008.10.108 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.F.OHREN,H.CHEN,A.PAVLOVSKY,C.WHITEHEAD,E.ZHANG,P.KUFFA, REMARK 1 AUTH 2 C.YAN,P.MCCONNELL,C.SPESSARD,C.BANOTAI,W.T.MUELLER, REMARK 1 AUTH 3 A.DELANEY,C.OMER,J.SEBOLT-LEOPOLD,D.T.DUDLEY,I.K.LEUNG, REMARK 1 AUTH 4 C.FLAMME,J.WARMUS,M.KAUFMAN,S.BARRETT,H.TECLE,C.A.HASEMANN REMARK 1 TITL STRUCTURES OF HUMAN MAP KINASE KINASE 1 (MEK1) AND MEK2 REMARK 1 TITL 2 DESCRIBE NOVEL NONCOMPETITIVE KINASE INHIBITION. REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 11 1192 2004 REMARK 1 REFN ISSN 1545-9993 REMARK 1 PMID 15543157 REMARK 1 DOI 10.1038/NSMB859 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 11895 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) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 632 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3630 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2037 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 80.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.59000 REMARK 3 B22 (A**2) : 2.59000 REMARK 3 B33 (A**2) : -3.89000 REMARK 3 B12 (A**2) : 1.30000 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): 0.531 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.316 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.251 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.270 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2123 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2872 ; 1.290 ; 2.010 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 258 ; 5.398 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 86 ;38.711 ;24.070 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 369 ;21.377 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;20.828 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 315 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1567 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1297 ; 0.563 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2092 ; 1.063 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 826 ; 1.264 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 780 ; 2.258 ; 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 REMARK 4 REMARK 4 3DY7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SINGLE CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12527 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 93.4 REMARK 200 DATA REDUNDANCY : 5.970 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : 0.41300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1S9J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8K, AMMONIUM PHOSPHATE, IMIDAZOLE REMARK 280 -MALATE, DTT, PH 5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 85.92867 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 42.96433 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 85.92867 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 42.96433 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: 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 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 61 REMARK 465 SER A 222 REMARK 465 PHE A 223 REMARK 465 VAL A 224 REMARK 465 ASP A 267 REMARK 465 ALA A 268 REMARK 465 LYS A 269 REMARK 465 GLU A 270 REMARK 465 LEU A 271 REMARK 465 GLU A 272 REMARK 465 LEU A 273 REMARK 465 MET A 274 REMARK 465 PHE A 275 REMARK 465 GLY A 276 REMARK 465 CYS A 277 REMARK 465 GLN A 278 REMARK 465 VAL A 279 REMARK 465 GLU A 280 REMARK 465 GLY A 281 REMARK 465 ASP A 282 REMARK 465 ALA A 283 REMARK 465 ALA A 284 REMARK 465 GLU A 285 REMARK 465 THR A 286 REMARK 465 PRO A 287 REMARK 465 PRO A 288 REMARK 465 ARG A 289 REMARK 465 PRO A 290 REMARK 465 ARG A 291 REMARK 465 THR A 292 REMARK 465 PRO A 293 REMARK 465 GLY A 294 REMARK 465 ARG A 295 REMARK 465 PRO A 296 REMARK 465 LEU A 297 REMARK 465 SER A 298 REMARK 465 SER A 299 REMARK 465 TYR A 300 REMARK 465 GLY A 301 REMARK 465 MET A 302 REMARK 465 ASP A 303 REMARK 465 SER A 304 REMARK 465 ARG A 305 REMARK 465 PRO A 306 REMARK 465 ASP A 365 REMARK 465 ALA A 366 REMARK 465 GLU A 367 REMARK 465 GLU A 368 REMARK 465 VAL A 369 REMARK 465 ASP A 370 REMARK 465 PHE A 371 REMARK 465 ALA A 372 REMARK 465 GLY A 373 REMARK 465 TRP A 374 REMARK 465 LEU A 375 REMARK 465 CYS A 376 REMARK 465 SER A 377 REMARK 465 THR A 378 REMARK 465 ILE A 379 REMARK 465 GLY A 380 REMARK 465 LEU A 381 REMARK 465 ASN A 382 REMARK 465 GLN A 383 REMARK 465 PRO A 384 REMARK 465 SER A 385 REMARK 465 THR A 386 REMARK 465 PRO A 387 REMARK 465 THR A 388 REMARK 465 HIS A 389 REMARK 465 ALA A 390 REMARK 465 ALA A 391 REMARK 465 GLY A 392 REMARK 465 VAL A 393 REMARK 465 LEU A 394 REMARK 465 GLU A 395 REMARK 465 HIS A 396 REMARK 465 HIS A 397 REMARK 465 HIS A 398 REMARK 465 HIS A 399 REMARK 465 HIS A 400 REMARK 465 HIS A 401 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 104 CG CD CE NZ REMARK 480 LYS A 156 CG CD CE NZ REMARK 480 LYS A 157 CG CD CE NZ REMARK 480 LYS A 168 CG CD CE NZ REMARK 480 GLU A 348 CG CD OE1 OE2 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 LYS A 157 CB LYS A 157 CG -0.360 REMARK 500 LYS A 168 CB LYS A 168 CG -0.239 REMARK 500 GLU A 348 CB GLU A 348 CG -0.195 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 ILE A 310 CB - CA - C ANGL. DEV. = -12.3 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 136 77.31 42.99 REMARK 500 GLU A 138 114.41 -168.01 REMARK 500 ARG A 189 -10.30 86.81 REMARK 500 ASP A 190 53.27 -157.55 REMARK 500 ALA A 220 -31.23 -34.90 REMARK 500 THR A 226 -78.94 -68.47 REMARK 500 SER A 241 -148.39 -168.22 REMARK 500 PRO A 265 157.69 -45.73 REMARK 500 PRO A 326 150.91 -45.21 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 A9001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 195 OD1 REMARK 620 2 ASP A 208 OD1 105.7 REMARK 620 3 ATP A9000 O1B 81.3 136.6 REMARK 620 4 ATP A9000 O2A 148.2 88.7 69.2 REMARK 620 N 1 2 3 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 9001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 9000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1CX A 9002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S9J RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE HUMAN MITOGEN-ACTIVATED PROTEIN KINASE REMARK 900 KINASE 1 (MEK1) IN A COMPLEX WITH LIGAND AND MGATP REMARK 900 RELATED ID: 1S9I RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE HUMAN MITOGEN-ACTIVATED PROTEIN KINASE REMARK 900 KINASE 2 (MEK2) IN A COMPLEX WITH LIGAND AND MGATP DBREF 3DY7 A 62 393 UNP Q02750 MP2K1_HUMAN 62 393 SEQADV 3DY7 MET A 61 UNP Q02750 EXPRESSION TAG SEQADV 3DY7 LEU A 394 UNP Q02750 EXPRESSION TAG SEQADV 3DY7 GLU A 395 UNP Q02750 EXPRESSION TAG SEQADV 3DY7 HIS A 396 UNP Q02750 EXPRESSION TAG SEQADV 3DY7 HIS A 397 UNP Q02750 EXPRESSION TAG SEQADV 3DY7 HIS A 398 UNP Q02750 EXPRESSION TAG SEQADV 3DY7 HIS A 399 UNP Q02750 EXPRESSION TAG SEQADV 3DY7 HIS A 400 UNP Q02750 EXPRESSION TAG SEQADV 3DY7 HIS A 401 UNP Q02750 EXPRESSION TAG SEQRES 1 A 341 MET GLU LEU LYS ASP ASP ASP PHE GLU LYS ILE SER GLU SEQRES 2 A 341 LEU GLY ALA GLY ASN GLY GLY VAL VAL PHE LYS VAL SER SEQRES 3 A 341 HIS LYS PRO SER GLY LEU VAL MET ALA ARG LYS LEU ILE SEQRES 4 A 341 HIS LEU GLU ILE LYS PRO ALA ILE ARG ASN GLN ILE ILE SEQRES 5 A 341 ARG GLU LEU GLN VAL LEU HIS GLU CYS ASN SER PRO TYR SEQRES 6 A 341 ILE VAL GLY PHE TYR GLY ALA PHE TYR SER ASP GLY GLU SEQRES 7 A 341 ILE SER ILE CYS MET GLU HIS MET ASP GLY GLY SER LEU SEQRES 8 A 341 ASP GLN VAL LEU LYS LYS ALA GLY ARG ILE PRO GLU GLN SEQRES 9 A 341 ILE LEU GLY LYS VAL SER ILE ALA VAL ILE LYS GLY LEU SEQRES 10 A 341 THR TYR LEU ARG GLU LYS HIS LYS ILE MET HIS ARG ASP SEQRES 11 A 341 VAL LYS PRO SER ASN ILE LEU VAL ASN SER ARG GLY GLU SEQRES 12 A 341 ILE LYS LEU CYS ASP PHE GLY VAL SER GLY GLN LEU ILE SEQRES 13 A 341 ASP SER MET ALA ASN SER PHE VAL GLY THR ARG SER TYR SEQRES 14 A 341 MET SER PRO GLU ARG LEU GLN GLY THR HIS TYR SER VAL SEQRES 15 A 341 GLN SER ASP ILE TRP SER MET GLY LEU SER LEU VAL GLU SEQRES 16 A 341 MET ALA VAL GLY ARG TYR PRO ILE PRO PRO PRO ASP ALA SEQRES 17 A 341 LYS GLU LEU GLU LEU MET PHE GLY CYS GLN VAL GLU GLY SEQRES 18 A 341 ASP ALA ALA GLU THR PRO PRO ARG PRO ARG THR PRO GLY SEQRES 19 A 341 ARG PRO LEU SER SER TYR GLY MET ASP SER ARG PRO PRO SEQRES 20 A 341 MET ALA ILE PHE GLU LEU LEU ASP TYR ILE VAL ASN GLU SEQRES 21 A 341 PRO PRO PRO LYS LEU PRO SER GLY VAL PHE SER LEU GLU SEQRES 22 A 341 PHE GLN ASP PHE VAL ASN LYS CYS LEU ILE LYS ASN PRO SEQRES 23 A 341 ALA GLU ARG ALA ASP LEU LYS GLN LEU MET VAL HIS ALA SEQRES 24 A 341 PHE ILE LYS ARG SER ASP ALA GLU GLU VAL ASP PHE ALA SEQRES 25 A 341 GLY TRP LEU CYS SER THR ILE GLY LEU ASN GLN PRO SER SEQRES 26 A 341 THR PRO THR HIS ALA ALA GLY VAL LEU GLU HIS HIS HIS SEQRES 27 A 341 HIS HIS HIS HET MG A9001 1 HET ATP A9000 31 HET 1CX A9002 24 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 1CX (5S)-4,5-DIFLUORO-6-[(2-FLUORO-4-IODOPHENYL)IMINO]-N- HETNAM 2 1CX (2-HYDROXYETHOXY)CYCLOHEXA-1,3-DIENE-1-CARBOXAMIDE FORMUL 2 MG MG 2+ FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 1CX C15 H12 F3 I N2 O3 HELIX 1 1 LYS A 104 GLN A 116 1 13 HELIX 2 2 VAL A 117 CYS A 121 5 5 HELIX 3 3 LEU A 151 GLY A 159 1 9 HELIX 4 4 PRO A 162 LYS A 185 1 24 HELIX 5 5 LYS A 192 SER A 194 5 3 HELIX 6 6 SER A 212 MET A 219 1 8 HELIX 7 7 SER A 231 GLY A 237 1 7 HELIX 8 8 VAL A 242 GLY A 259 1 18 HELIX 9 9 ALA A 309 GLU A 320 1 12 HELIX 10 10 SER A 331 LEU A 342 1 12 HELIX 11 11 ASP A 351 VAL A 357 1 7 HELIX 12 12 HIS A 358 SER A 364 1 7 SHEET 1 A 5 PHE A 68 ALA A 76 0 SHEET 2 A 5 GLY A 80 HIS A 87 -1 O VAL A 82 N LEU A 74 SHEET 3 A 5 VAL A 93 ILE A 99 -1 O LEU A 98 N VAL A 81 SHEET 4 A 5 ILE A 139 GLU A 144 -1 O MET A 143 N ALA A 95 SHEET 5 A 5 PHE A 129 TYR A 134 -1 N PHE A 133 O SER A 140 SHEET 1 B 3 GLY A 149 SER A 150 0 SHEET 2 B 3 ILE A 196 ASN A 199 -1 O VAL A 198 N GLY A 149 SHEET 3 B 3 GLU A 203 LEU A 206 -1 O LYS A 205 N LEU A 197 LINK OD1 ASN A 195 MG MG A9001 1555 1555 2.35 LINK OD1 ASP A 208 MG MG A9001 1555 1555 1.79 LINK O1B ATP A9000 MG MG A9001 1555 1555 2.18 LINK O2A ATP A9000 MG MG A9001 1555 1555 2.12 CISPEP 1 ILE A 263 PRO A 264 0 -0.58 SITE 1 AC1 2 ASN A 195 ASP A 208 SITE 1 AC2 17 LEU A 74 GLY A 75 GLY A 77 ASN A 78 SITE 2 AC2 17 GLY A 80 ALA A 95 LYS A 97 MET A 143 SITE 3 AC2 17 GLU A 144 MET A 146 SER A 150 GLN A 153 SITE 4 AC2 17 LYS A 192 SER A 194 ASN A 195 LEU A 197 SITE 5 AC2 17 ASP A 208 SITE 1 AC3 6 GLY A 80 LYS A 97 ILE A 141 ASP A 208 SITE 2 AC3 6 PHE A 209 SER A 212 CRYST1 81.754 81.754 128.893 90.00 90.00 120.00 P 62 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 0.012232 0.007062 0.000000 0.00000 SCALE2 0.000000 0.014124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007758 0.00000