HEADER TRANSFERASE 06-MAY-20 6YZ4 TITLE CRYSTAL STRUCTURE OF MKK7 (MAP2K7) WITH IBRUTINIB BOUND AT ALLOSTERIC TITLE 2 SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAPKK 7,JNK-ACTIVATING KINASE 2,MAPK/ERK KINASE 7,MEK 7, COMPND 5 STRESS-ACTIVATED PROTEIN KINASE KINASE 4,SAPKK4,C-JUN N-TERMINAL COMPND 6 KINASE KINASE 2,JNKK 2; 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: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: -R3-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS KINASE, KINASE INHIBITOR, ALLOSTERIC, MKK7, MEK7, MAP2K7, MAP2K, MEK, KEYWDS 2 JNK SIGNALING, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 3 SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAIKUAD,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 24-JAN-24 6YZ4 1 REMARK REVDAT 3 28-OCT-20 6YZ4 1 JRNL REVDAT 2 02-SEP-20 6YZ4 1 JRNL REVDAT 1 12-AUG-20 6YZ4 0 JRNL AUTH M.SCHRODER,L.TAN,J.WANG,Y.LIANG,N.S.GRAY,S.KNAPP,A.CHAIKUAD JRNL TITL CATALYTIC DOMAIN PLASTICITY OF MKK7 REVEALS STRUCTURAL JRNL TITL 2 MECHANISMS OF ALLOSTERIC ACTIVATION AND DIVERSE TARGETING JRNL TITL 3 OPPORTUNITIES. JRNL REF CELL CHEM BIOL V. 27 1285 2020 JRNL REFN ESSN 2451-9456 JRNL PMID 32783966 JRNL DOI 10.1016/J.CHEMBIOL.2020.07.014 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 37213 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1893 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2709 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2295 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.09000 REMARK 3 B33 (A**2) : 0.10000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.511 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2461 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2427 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3299 ; 1.610 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5589 ; 0.827 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 6.030 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;31.198 ;23.714 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 451 ;13.565 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;20.430 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 355 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2828 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 547 ; 0.001 ; 0.020 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 118 A 172 REMARK 3 ORIGIN FOR THE GROUP (A): -0.9505 37.2410 -0.3345 REMARK 3 T TENSOR REMARK 3 T11: 0.0618 T22: 0.0304 REMARK 3 T33: 0.0189 T12: -0.0047 REMARK 3 T13: -0.0237 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 4.8574 L22: 0.8881 REMARK 3 L33: 5.6094 L12: 0.6825 REMARK 3 L13: -3.0821 L23: -0.2128 REMARK 3 S TENSOR REMARK 3 S11: 0.0953 S12: 0.0425 S13: 0.1115 REMARK 3 S21: -0.0071 S22: -0.0647 S23: 0.0290 REMARK 3 S31: -0.1690 S32: -0.0517 S33: -0.0307 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 173 A 298 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8888 29.3212 13.2105 REMARK 3 T TENSOR REMARK 3 T11: 0.0722 T22: 0.0351 REMARK 3 T33: 0.0237 T12: -0.0148 REMARK 3 T13: 0.0081 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 2.5610 L22: 1.4313 REMARK 3 L33: 0.4328 L12: -1.8894 REMARK 3 L13: 0.8878 L23: -0.5939 REMARK 3 S TENSOR REMARK 3 S11: 0.0114 S12: -0.0327 S13: -0.1391 REMARK 3 S21: 0.0179 S22: -0.0091 S23: 0.1265 REMARK 3 S31: 0.0061 S32: -0.0749 S33: -0.0024 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 299 A 420 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0396 17.5485 21.0789 REMARK 3 T TENSOR REMARK 3 T11: 0.0206 T22: 0.0077 REMARK 3 T33: 0.0082 T12: -0.0020 REMARK 3 T13: 0.0009 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 1.5094 L22: 3.0759 REMARK 3 L33: 2.6747 L12: 0.3978 REMARK 3 L13: -0.3900 L23: -0.9374 REMARK 3 S TENSOR REMARK 3 S11: -0.0292 S12: 0.0155 S13: -0.0618 REMARK 3 S21: 0.1167 S22: 0.0102 S23: 0.0631 REMARK 3 S31: 0.1006 S32: -0.1170 S33: 0.0190 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 6YZ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108587. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.02823 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39163 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.535 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.78100 REMARK 200 R SYM FOR SHELL (I) : 0.78100 REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 2DYL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG3350, 0.1 M TRIS PH 7.8, 0.25 M REMARK 280 AMMONIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 26.75500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.58500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.33500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.58500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.75500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.33500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 2490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 33.0 KCAL/MOL 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 SER A 115 REMARK 465 MET A 116 REMARK 465 SER A 144 REMARK 465 GLY A 145 REMARK 465 THR A 146 REMARK 465 CYS A 147 REMARK 465 VAL A 285 REMARK 465 ASP A 286 REMARK 465 SER A 287 REMARK 465 LYS A 288 REMARK 465 ALA A 289 REMARK 465 LYS A 290 REMARK 465 THR A 291 REMARK 465 ARG A 292 REMARK 465 SER A 293 REMARK 465 ALA A 294 REMARK 465 ARG A 421 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 117 CG CD CE NZ REMARK 470 ARG A 283 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 284 CG CD1 CD2 REMARK 470 THR A 311 OG1 CG2 REMARK 470 LYS A 312 CG CD CE NZ REMARK 470 ASP A 314 CG OD1 OD2 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 SER A 419 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 634 O HOH A 679 2.15 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 182 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = -3.4 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 259 53.99 -150.71 REMARK 500 CYS A 296 46.58 -103.96 REMARK 500 LYS A 312 63.86 -107.80 REMARK 500 ASP A 314 38.48 -89.80 REMARK 500 ASP A 316 -159.38 -123.62 REMARK 500 SER A 419 -71.48 -76.80 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 EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1E8 A 514 DBREF 6YZ4 A 116 421 UNP O14733 MP2K7_HUMAN 100 405 SEQADV 6YZ4 SER A 115 UNP O14733 EXPRESSION TAG SEQRES 1 A 307 SER MET LYS GLN THR GLY TYR LEU THR ILE GLY GLY GLN SEQRES 2 A 307 ARG TYR GLN ALA GLU ILE ASN ASP LEU GLU ASN LEU GLY SEQRES 3 A 307 GLU MET GLY SER GLY THR CYS GLY GLN VAL TRP LYS MET SEQRES 4 A 307 ARG PHE ARG LYS THR GLY HIS VAL ILE ALA VAL LYS GLN SEQRES 5 A 307 MET ARG ARG SER GLY ASN LYS GLU GLU ASN LYS ARG ILE SEQRES 6 A 307 LEU MET ASP LEU ASP VAL VAL LEU LYS SER HIS ASP CYS SEQRES 7 A 307 PRO TYR ILE VAL GLN CYS PHE GLY THR PHE ILE THR ASN SEQRES 8 A 307 THR ASP VAL PHE ILE ALA MET GLU LEU MET GLY THR CYS SEQRES 9 A 307 ALA GLU LYS LEU LYS LYS ARG MET GLN GLY PRO ILE PRO SEQRES 10 A 307 GLU ARG ILE LEU GLY LYS MET THR VAL ALA ILE VAL LYS SEQRES 11 A 307 ALA LEU TYR TYR LEU LYS GLU LYS HIS GLY VAL ILE HIS SEQRES 12 A 307 ARG ASP VAL LYS PRO SER ASN ILE LEU LEU ASP GLU ARG SEQRES 13 A 307 GLY GLN ILE LYS LEU CYS ASP PHE GLY ILE SER GLY ARG SEQRES 14 A 307 LEU VAL ASP SER LYS ALA LYS THR ARG SER ALA GLY CYS SEQRES 15 A 307 ALA ALA TYR MET ALA PRO GLU ARG ILE ASP PRO PRO ASP SEQRES 16 A 307 PRO THR LYS PRO ASP TYR ASP ILE ARG ALA ASP VAL TRP SEQRES 17 A 307 SER LEU GLY ILE SER LEU VAL GLU LEU ALA THR GLY GLN SEQRES 18 A 307 PHE PRO TYR LYS ASN CYS LYS THR ASP PHE GLU VAL LEU SEQRES 19 A 307 THR LYS VAL LEU GLN GLU GLU PRO PRO LEU LEU PRO GLY SEQRES 20 A 307 HIS MET GLY PHE SER GLY ASP PHE GLN SER PHE VAL LYS SEQRES 21 A 307 ASP CYS LEU THR LYS ASP HIS ARG LYS ARG PRO LYS TYR SEQRES 22 A 307 ASN LYS LEU LEU GLU HIS SER PHE ILE LYS ARG TYR GLU SEQRES 23 A 307 THR LEU GLU VAL ASP VAL ALA SER TRP PHE LYS ASP VAL SEQRES 24 A 307 MET ALA LYS THR GLU SER PRO ARG HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 509 4 HET DMS A 510 4 HET DMS A 511 4 HET DMS A 512 4 HET DMS A 513 4 HET 1E8 A 514 33 HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM 1E8 1-{(3R)-3-[4-AMINO-3-(4-PHENOXYPHENYL)-1H-PYRAZOLO[3,4- HETNAM 2 1E8 D]PYRIMIDIN-1-YL]PIPERIDIN-1-YL}PROP-2-EN-1-ONE HETSYN EDO ETHYLENE GLYCOL HETSYN 1E8 IMBRUVICA; PCI-32765 FORMUL 2 EDO 9(C2 H6 O2) FORMUL 11 DMS 4(C2 H6 O S) FORMUL 15 1E8 C25 H24 N6 O2 FORMUL 16 HOH *310(H2 O) HELIX 1 AA1 GLU A 132 ASN A 134 5 3 HELIX 2 AA2 ASN A 172 LYS A 188 1 17 HELIX 3 AA3 ALA A 219 GLN A 227 1 9 HELIX 4 AA4 PRO A 231 GLY A 254 1 24 HELIX 5 AA5 LYS A 261 SER A 263 5 3 HELIX 6 AA6 CYS A 296 MET A 300 5 5 HELIX 7 AA7 ALA A 301 ILE A 305 5 5 HELIX 8 AA8 ASP A 316 GLY A 334 1 19 HELIX 9 AA9 THR A 343 GLU A 354 1 12 HELIX 10 AB1 SER A 366 LEU A 377 1 12 HELIX 11 AB2 ASP A 380 ARG A 384 5 5 HELIX 12 AB3 LYS A 386 LEU A 391 1 6 HELIX 13 AB4 HIS A 393 LEU A 402 1 10 HELIX 14 AB5 ASP A 405 THR A 417 1 13 SHEET 1 AA1 2 GLY A 120 ILE A 124 0 SHEET 2 AA1 2 GLN A 127 ALA A 131 -1 O TYR A 129 N LEU A 122 SHEET 1 AA2 5 LEU A 136 GLU A 141 0 SHEET 2 AA2 5 VAL A 150 PHE A 155 -1 O LYS A 152 N GLY A 140 SHEET 3 AA2 5 VAL A 161 ARG A 168 -1 O VAL A 164 N TRP A 151 SHEET 4 AA2 5 ASP A 207 GLU A 213 -1 O MET A 212 N ALA A 163 SHEET 5 AA2 5 CYS A 198 ILE A 203 -1 N PHE A 202 O PHE A 209 SHEET 1 AA3 3 THR A 217 CYS A 218 0 SHEET 2 AA3 3 ILE A 265 LEU A 267 -1 O LEU A 267 N THR A 217 SHEET 3 AA3 3 ILE A 273 LEU A 275 -1 O LYS A 274 N LEU A 266 SITE 1 AC1 3 HIS A 160 VAL A 161 HOH A 606 SITE 1 AC2 4 GLU A 213 MET A 215 ASP A 277 HOH A 761 SITE 1 AC3 3 THR A 201 EDO A 504 HOH A 826 SITE 1 AC4 7 THR A 201 ILE A 203 ILE A 305 ASP A 306 SITE 2 AC4 7 EDO A 503 HOH A 605 HOH A 714 SITE 1 AC5 6 PRO A 231 GLU A 232 MET A 363 GLY A 364 SITE 2 AC5 6 HOH A 796 HOH A 806 SITE 1 AC6 4 GLU A 251 LYS A 252 HIS A 253 GLY A 254 SITE 1 AC7 4 ARG A 156 TYR A 247 ASN A 388 LEU A 391 SITE 1 AC8 2 TYR A 338 CYS A 341 SITE 1 AC9 5 GLN A 353 GLU A 354 GLU A 355 LYS A 379 SITE 2 AC9 5 HOH A 803 SITE 1 AD1 7 ALA A 131 GLU A 132 ILE A 133 LEU A 136 SITE 2 AD1 7 PHE A 202 1E8 A 514 HOH A 631 SITE 1 AD2 1 THR A 158 SITE 1 AD3 6 THR A 123 LEU A 187 CYS A 198 PHE A 199 SITE 2 AD3 6 GLY A 200 HOH A 609 SITE 1 AD4 4 GLU A 141 VAL A 150 TRP A 151 LYS A 416 SITE 1 AD5 12 TYR A 121 LEU A 122 ILE A 133 ASN A 138 SITE 2 AD5 12 TRP A 151 MET A 153 GLY A 200 THR A 201 SITE 3 AD5 12 PHE A 209 GLN A 227 DMS A 510 HOH A 645 CRYST1 53.510 74.670 87.170 90.00 90.00 90.00 P 21 21 21 4 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 0.018688 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011472 0.00000