HEADER TRANSFERASE/TRANSFERASE INHIBITOR 05-JAN-12 3VN9 TITLE RIFINED CRYSTAL STRUCTURE OF NON-PHOSPHORYLATED MAP2K6 IN A PUTATIVE TITLE 2 AUTO-INHIBITION STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAP KINASE KINASE 6, MAPKK 6, MAPK/ERK KINASE 6, MEK 6, COMPND 5 STRESS-ACTIVATED PROTEIN KINASE KINASE 3, SAPK KINASE 3, SAPKK-3, COMPND 6 SAPKK3; 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: MAP2K6; 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: PET22(+) KEYWDS AUTO-INHIBITION STATE, ACTIVATION HELICES, MITOGEN-ACTIVATED PROTEIN KEYWDS 2 KINASE KINASE, AMP-PNP BINDING, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.KINOSHITA,H.MATSUZAKA,R.NAKAI,Y.KIRII,K.YOKOTA,T.TADA,T.MATSUMOTO REVDAT 4 08-NOV-23 3VN9 1 REMARK SEQADV LINK REVDAT 3 22-NOV-17 3VN9 1 REMARK REVDAT 2 08-AUG-12 3VN9 1 JRNL REVDAT 1 29-FEB-12 3VN9 0 SPRSDE 29-FEB-12 3VN9 3AN0 JRNL AUTH T.MATSUMOTO,T.KINOSHITA,H.MATSUZAKA,R.NAKAI,Y.KIRII, JRNL AUTH 2 K.YOKOTA,T.TADA JRNL TITL CRYSTAL STRUCTURE OF NON-PHOSPHORYLATED MAP2K6 IN A PUTATIVE JRNL TITL 2 AUTO-INHIBITION STATE JRNL REF J.BIOCHEM. V. 151 541 2012 JRNL REFN ISSN 0021-924X JRNL PMID 22383536 JRNL DOI 10.1093/JB/MVS023 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 10917 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) : 0.265 REMARK 3 R VALUE (WORKING SET) : 0.264 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1207 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 771 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4430 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.4550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2272 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 98.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.88000 REMARK 3 B22 (A**2) : 4.88000 REMARK 3 B33 (A**2) : -7.32000 REMARK 3 B12 (A**2) : 2.44000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.355 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.343 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.123 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2354 ; 0.030 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3194 ; 2.594 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 290 ; 7.581 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;38.099 ;24.842 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 416 ;21.030 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.967 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 361 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1728 ; 0.014 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3VN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000095257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12124 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 9.260 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.72 REMARK 200 R MERGE FOR SHELL (I) : 0.53900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3EQD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4000, 10% 2-PROPANOL, 0.1MOL/L REMARK 280 NA-HEPES-HCL, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 33.71767 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 67.43533 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 67.43533 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 33.71767 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 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 GLY A 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 ARG A 9 REMARK 465 ASN A 10 REMARK 465 PRO A 11 REMARK 465 GLY A 12 REMARK 465 LEU A 13 REMARK 465 LYS A 14 REMARK 465 ILE A 15 REMARK 465 PRO A 16 REMARK 465 LYS A 17 REMARK 465 GLU A 18 REMARK 465 ALA A 19 REMARK 465 PHE A 20 REMARK 465 GLU A 21 REMARK 465 GLN A 22 REMARK 465 PRO A 23 REMARK 465 GLN A 24 REMARK 465 THR A 25 REMARK 465 SER A 26 REMARK 465 SER A 27 REMARK 465 THR A 28 REMARK 465 PRO A 29 REMARK 465 PRO A 30 REMARK 465 ARG A 31 REMARK 465 ASP A 32 REMARK 465 LEU A 33 REMARK 465 ASP A 34 REMARK 465 SER A 35 REMARK 465 LYS A 36 REMARK 465 ALA A 37 REMARK 465 CYS A 38 REMARK 465 ILE A 39 REMARK 465 SER A 40 REMARK 465 ILE A 41 REMARK 465 GLY A 42 REMARK 465 ASN A 43 REMARK 465 HIS A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 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 49 CG CD CE NZ REMARK 470 ASP A 52 CG OD1 OD2 REMARK 470 ARG A 85 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 SER A 183 OG REMARK 470 ARG A 254 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 310 CG CD OE1 NE2 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 OE1 GLU A 54 CG2 VAL A 236 2445 2.00 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 MET A 57 N - CA - C ANGL. DEV. = -20.8 DEGREES REMARK 500 GLU A 58 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 LEU A 59 CA - CB - CG ANGL. DEV. = 19.0 DEGREES REMARK 500 GLY A 62 N - CA - C ANGL. DEV. = -20.8 DEGREES REMARK 500 ALA A 63 CA - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 TYR A 64 C - N - CA ANGL. DEV. = 18.9 DEGREES REMARK 500 PRO A 227 C - N - CD ANGL. DEV. = -22.1 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 ASN A 45 -71.34 -112.56 REMARK 500 PHE A 46 119.78 49.95 REMARK 500 LYS A 49 172.23 -53.95 REMARK 500 ALA A 50 -154.67 -125.66 REMARK 500 LEU A 59 72.80 -177.20 REMARK 500 TYR A 64 -41.77 70.83 REMARK 500 ARG A 85 156.51 -41.71 REMARK 500 ALA A 86 -5.39 -41.34 REMARK 500 THR A 87 -154.06 43.10 REMARK 500 VAL A 88 84.25 -167.55 REMARK 500 THR A 112 -69.77 -90.56 REMARK 500 VAL A 113 -43.13 152.61 REMARK 500 THR A 114 113.33 91.14 REMARK 500 ARG A 121 -120.55 -110.22 REMARK 500 GLU A 122 65.07 -69.27 REMARK 500 PHE A 139 -71.02 -51.37 REMARK 500 TYR A 140 -2.51 -52.13 REMARK 500 VAL A 143 -70.37 -55.61 REMARK 500 LEU A 190 -3.45 55.31 REMARK 500 PHE A 198 -73.12 -66.48 REMARK 500 THR A 211 -72.09 -99.33 REMARK 500 ALA A 214 -122.29 -100.99 REMARK 500 GLU A 228 106.22 -49.36 REMARK 500 LEU A 229 -66.62 29.99 REMARK 500 PRO A 256 0.11 -56.39 REMARK 500 SER A 259 -112.35 -41.16 REMARK 500 LYS A 268 -38.37 -39.40 REMARK 500 ALA A 280 -72.50 -57.15 REMARK 500 ASP A 281 -46.08 -20.71 REMARK 500 SER A 284 125.67 -39.95 REMARK 500 MET A 309 -9.51 -57.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 259 TRP A 260 -32.89 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 A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 197 OD2 REMARK 620 2 ANK A 401 O1A 131.0 REMARK 620 3 ANK A 401 O2B 117.8 89.5 REMARK 620 4 ANK A 401 O1G 67.4 91.2 67.0 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 ANK A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 DBREF 3VN9 A 1 334 UNP P52564 MP2K6_HUMAN 1 334 SEQADV 3VN9 HIS A 335 UNP P52564 EXPRESSION TAG SEQADV 3VN9 HIS A 336 UNP P52564 EXPRESSION TAG SEQADV 3VN9 HIS A 337 UNP P52564 EXPRESSION TAG SEQADV 3VN9 HIS A 338 UNP P52564 EXPRESSION TAG SEQADV 3VN9 HIS A 339 UNP P52564 EXPRESSION TAG SEQADV 3VN9 HIS A 340 UNP P52564 EXPRESSION TAG SEQRES 1 A 340 MET SER GLN SER LYS GLY LYS LYS ARG ASN PRO GLY LEU SEQRES 2 A 340 LYS ILE PRO LYS GLU ALA PHE GLU GLN PRO GLN THR SER SEQRES 3 A 340 SER THR PRO PRO ARG ASP LEU ASP SER LYS ALA CYS ILE SEQRES 4 A 340 SER ILE GLY ASN GLN ASN PHE GLU VAL LYS ALA ASP ASP SEQRES 5 A 340 LEU GLU PRO ILE MET GLU LEU GLY ARG GLY ALA TYR GLY SEQRES 6 A 340 VAL VAL GLU LYS MET ARG HIS VAL PRO SER GLY GLN ILE SEQRES 7 A 340 MET ALA VAL LYS ARG ILE ARG ALA THR VAL ASN SER GLN SEQRES 8 A 340 GLU GLN LYS ARG LEU LEU MET ASP LEU ASP ILE SER MET SEQRES 9 A 340 ARG THR VAL ASP CYS PRO PHE THR VAL THR PHE TYR GLY SEQRES 10 A 340 ALA LEU PHE ARG GLU GLY ASP VAL TRP ILE CYS MET GLU SEQRES 11 A 340 LEU MET ASP THR SER LEU ASP LYS PHE TYR LYS GLN VAL SEQRES 12 A 340 ILE ASP LYS GLY GLN THR ILE PRO GLU ASP ILE LEU GLY SEQRES 13 A 340 LYS ILE ALA VAL SER ILE VAL LYS ALA LEU GLU HIS LEU SEQRES 14 A 340 HIS SER LYS LEU SER VAL ILE HIS ARG ASP VAL LYS PRO SEQRES 15 A 340 SER ASN VAL LEU ILE ASN ALA LEU GLY GLN VAL LYS MET SEQRES 16 A 340 CYS ASP PHE GLY ILE SER GLY TYR LEU VAL ASP SER VAL SEQRES 17 A 340 ALA LYS THR ILE ASP ALA GLY CYS LYS PRO TYR MET ALA SEQRES 18 A 340 PRO GLU ARG ILE ASN PRO GLU LEU ASN GLN LYS GLY TYR SEQRES 19 A 340 SER VAL LYS SER ASP ILE TRP SER LEU GLY ILE THR MET SEQRES 20 A 340 ILE GLU LEU ALA ILE LEU ARG PHE PRO TYR ASP SER TRP SEQRES 21 A 340 GLY THR PRO PHE GLN GLN LEU LYS GLN VAL VAL GLU GLU SEQRES 22 A 340 PRO SER PRO GLN LEU PRO ALA ASP LYS PHE SER ALA GLU SEQRES 23 A 340 PHE VAL ASP PHE THR SER GLN CYS LEU LYS LYS ASN SER SEQRES 24 A 340 LYS GLU ARG PRO THR TYR PRO GLU LEU MET GLN HIS PRO SEQRES 25 A 340 PHE PHE THR LEU HIS GLU SER LYS GLY THR ASP VAL ALA SEQRES 26 A 340 SER PHE VAL LYS LEU ILE LEU GLY ASP HIS HIS HIS HIS SEQRES 27 A 340 HIS HIS HET ANK A 401 31 HET MG A 402 1 HETNAM ANK 9-{5-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOAMINO) HETNAM 2 ANK PHOSPHORYL]OXY}PHOSPHORYL]-BETA-L-RIBOFURANOSYL}-9H- HETNAM 3 ANK PURIN-6-AMINE HETNAM MG MAGNESIUM ION FORMUL 2 ANK C10 H17 N6 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *18(H2 O) HELIX 1 1 SER A 90 ARG A 105 1 16 HELIX 2 2 LEU A 136 LYS A 146 1 11 HELIX 3 3 PRO A 151 LEU A 173 1 23 HELIX 4 4 GLY A 199 VAL A 205 1 7 HELIX 5 5 ASP A 206 ASP A 213 1 8 HELIX 6 6 ALA A 221 ASN A 226 1 6 HELIX 7 7 SER A 235 LEU A 253 1 19 HELIX 8 8 THR A 262 GLU A 273 1 12 HELIX 9 9 PRO A 279 PHE A 283 5 5 HELIX 10 10 SER A 284 LEU A 295 1 12 HELIX 11 11 ASN A 298 ARG A 302 5 5 HELIX 12 12 THR A 304 MET A 309 1 6 HELIX 13 13 HIS A 311 GLU A 318 1 8 HELIX 14 14 VAL A 324 GLY A 333 1 10 SHEET 1 A 5 LEU A 53 ARG A 61 0 SHEET 2 A 5 GLY A 65 HIS A 72 -1 O VAL A 67 N GLY A 60 SHEET 3 A 5 GLN A 77 ILE A 84 -1 O MET A 79 N MET A 70 SHEET 4 A 5 VAL A 125 MET A 129 -1 O VAL A 125 N ILE A 84 SHEET 5 A 5 PHE A 115 PHE A 120 -1 N GLY A 117 O CYS A 128 SHEET 1 B 3 THR A 134 SER A 135 0 SHEET 2 B 3 VAL A 185 ILE A 187 -1 O ILE A 187 N THR A 134 SHEET 3 B 3 VAL A 193 MET A 195 -1 O LYS A 194 N LEU A 186 LINK OD2 ASP A 197 MG MG A 402 1555 1555 2.04 LINK O1A ANK A 401 MG MG A 402 1555 1555 1.70 LINK O2B ANK A 401 MG MG A 402 1555 1555 2.51 LINK O1G ANK A 401 MG MG A 402 1555 1555 2.92 CISPEP 1 PHE A 46 GLU A 47 0 -1.58 CISPEP 2 LYS A 49 ALA A 50 0 -4.92 CISPEP 3 ALA A 50 ASP A 51 0 -2.79 SITE 1 AC1 19 GLY A 60 ALA A 63 TYR A 64 VAL A 67 SITE 2 AC1 19 ALA A 80 LYS A 82 MET A 129 GLU A 130 SITE 3 AC1 19 MET A 132 SER A 135 LYS A 138 ASP A 179 SITE 4 AC1 19 LYS A 181 SER A 183 ASN A 184 ASP A 197 SITE 5 AC1 19 SER A 201 LYS A 210 MG A 402 SITE 1 AC2 3 ASN A 184 ASP A 197 ANK A 401 CRYST1 83.456 83.456 101.153 90.00 90.00 120.00 P 31 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 0.011982 0.006918 0.000000 0.00000 SCALE2 0.000000 0.013836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009886 0.00000