HEADER TRANSFERASE 27-MAR-20 6YG2 TITLE CRYSTAL STRUCTURE OF MKK7 (MAP2K7) IN COMPLEX WITH IBRUTNIB, WITH TITLE 2 COVALENT AND ALLOSTERIC BINDING MODES 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, MKK7, MEK7, MAP2K7, MAP2K, MEK, JNK KEYWDS 2 SIGNALING, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAIKUAD,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 24-JAN-24 6YG2 1 REMARK REVDAT 3 28-OCT-20 6YG2 1 JRNL REVDAT 2 02-SEP-20 6YG2 1 JRNL REVDAT 1 12-AUG-20 6YG2 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22831 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1176 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1659 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2290 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 114 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : -0.30000 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): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.917 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2494 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2433 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3346 ; 1.491 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5601 ; 0.762 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 5.959 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;32.721 ;23.883 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;13.806 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.320 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 358 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2999 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 551 ; 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 : 4 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 178 REMARK 3 ORIGIN FOR THE GROUP (A): -1.7350 39.0952 40.9819 REMARK 3 T TENSOR REMARK 3 T11: 0.0637 T22: 0.0540 REMARK 3 T33: 0.0291 T12: -0.0013 REMARK 3 T13: 0.0389 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 6.1514 L22: 1.5830 REMARK 3 L33: 5.9655 L12: -0.5416 REMARK 3 L13: 2.9261 L23: 0.5325 REMARK 3 S TENSOR REMARK 3 S11: 0.0375 S12: 0.0446 S13: 0.1131 REMARK 3 S21: 0.0612 S22: -0.0887 S23: 0.0025 REMARK 3 S31: -0.0244 S32: 0.0095 S33: 0.0512 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 179 A 275 REMARK 3 ORIGIN FOR THE GROUP (A): 10.6525 45.1107 31.0383 REMARK 3 T TENSOR REMARK 3 T11: 0.0668 T22: 0.0839 REMARK 3 T33: 0.0261 T12: 0.0275 REMARK 3 T13: -0.0062 T23: -0.0395 REMARK 3 L TENSOR REMARK 3 L11: 2.8568 L22: 1.4082 REMARK 3 L33: 0.4987 L12: 1.9076 REMARK 3 L13: -1.1047 L23: -0.7958 REMARK 3 S TENSOR REMARK 3 S11: -0.0110 S12: 0.1246 S13: 0.0367 REMARK 3 S21: -0.0834 S22: 0.0166 S23: 0.0595 REMARK 3 S31: 0.0494 S32: -0.0667 S33: -0.0057 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 276 A 316 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0082 55.7607 14.5087 REMARK 3 T TENSOR REMARK 3 T11: 0.7587 T22: 0.7397 REMARK 3 T33: 0.7187 T12: -0.0033 REMARK 3 T13: -0.1034 T23: -0.1251 REMARK 3 L TENSOR REMARK 3 L11: 1.5884 L22: 3.1479 REMARK 3 L33: 0.2202 L12: 2.2072 REMARK 3 L13: -0.5773 L23: -0.8080 REMARK 3 S TENSOR REMARK 3 S11: -0.3404 S12: 0.5271 S13: 0.5150 REMARK 3 S21: -0.3508 S22: 0.5864 S23: 0.8947 REMARK 3 S31: 0.1339 S32: -0.2142 S33: -0.2460 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 317 A 420 REMARK 3 ORIGIN FOR THE GROUP (A): 20.7772 57.5362 24.2878 REMARK 3 T TENSOR REMARK 3 T11: 0.0216 T22: 0.0498 REMARK 3 T33: 0.0177 T12: -0.0071 REMARK 3 T13: 0.0053 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.7782 L22: 2.9370 REMARK 3 L33: 3.1695 L12: -0.2932 REMARK 3 L13: 1.3082 L23: -1.2573 REMARK 3 S TENSOR REMARK 3 S11: -0.0554 S12: 0.0118 S13: 0.1415 REMARK 3 S21: -0.0923 S22: -0.0077 S23: -0.1042 REMARK 3 S31: -0.1768 S32: 0.0697 S33: 0.0632 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 6YG2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107566. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24057 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.90100 REMARK 200 R SYM FOR SHELL (I) : 0.90100 REMARK 200 FOR SHELL : 0.800 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 (%): 50.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG3350, 0.1 M AMMONIUM ACETATE, REMARK 280 0.1 M TRIS, PH 7.8, 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 26.55550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.33300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.47750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.33300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.55550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.47750 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: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 31.0 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 LYS A 117 REMARK 465 ARG A 283 REMARK 465 LEU A 284 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 GLY A 295 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 GLN A 118 CG CD OE1 NE2 REMARK 470 THR A 146 OG1 CG2 REMARK 470 CYS A 147 SG REMARK 470 PHE A 278 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 281 OG 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 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 SER A 144 92.85 -67.10 REMARK 500 CYS A 147 -75.43 -95.86 REMARK 500 ASP A 259 55.10 -147.28 REMARK 500 ASP A 277 -8.67 -158.89 REMARK 500 LEU A 377 30.46 -96.70 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 DMS 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 1E8 A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8E8 A 514 DBREF 6YG2 A 116 421 UNP O14733 MP2K7_HUMAN 116 421 SEQADV 6YG2 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 DMS A 509 4 HET DMS A 510 4 HET DMS A 511 4 HET DMS A 512 4 HET 1E8 A 513 33 HET 8E8 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 HETNAM 8E8 1-[(3~{R})-3-[4-AZANYL-3-(4-PHENOXYPHENYL)PYRAZOLO[3,4- HETNAM 2 8E8 D]PYRIMIDIN-1-YL]PIPERIDIN-1-YL]PROPAN-1-ONE HETSYN EDO ETHYLENE GLYCOL HETSYN 1E8 IMBRUVICA; PCI-32765 HETSYN 8E8 IBRUTINIB (BOUND FORM) FORMUL 2 EDO 8(C2 H6 O2) FORMUL 10 DMS 4(C2 H6 O S) FORMUL 14 1E8 C25 H24 N6 O2 FORMUL 15 8E8 C25 H26 N6 O2 FORMUL 16 HOH *182(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 ILE A 317 GLY A 334 1 18 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 ALA A 131 N GLY A 120 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 ILE A 162 N MET A 153 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 LINK SG CYS A 218 CAA 8E8 A 514 1555 1555 1.61 SITE 1 AC1 2 THR A 201 DMS A 511 SITE 1 AC2 5 ARG A 156 TYR A 247 ASN A 388 GLU A 392 SITE 2 AC2 5 HOH A 687 SITE 1 AC3 2 LYS A 244 HOH A 674 SITE 1 AC4 4 HIS A 160 VAL A 161 LEU A 214 HOH A 725 SITE 1 AC5 2 THR A 158 HIS A 160 SITE 1 AC6 4 LYS A 223 GLY A 334 GLN A 335 PHE A 336 SITE 1 AC7 5 MET A 142 GLY A 216 THR A 217 LYS A 221 SITE 2 AC7 5 8E8 A 514 SITE 1 AC8 3 LYS A 252 HIS A 253 GLY A 254 SITE 1 AC9 6 ARG A 270 GLY A 271 VAL A 404 ASP A 405 SITE 2 AC9 6 VAL A 406 ALA A 407 SITE 1 AD1 6 GLY A 120 ALA A 131 GLU A 132 LEU A 136 SITE 2 AD1 6 PHE A 202 1E8 A 513 SITE 1 AD2 7 THR A 123 LEU A 187 CYS A 198 PHE A 199 SITE 2 AD2 7 GLY A 200 EDO A 501 HOH A 707 SITE 1 AD3 6 PRO A 231 GLU A 232 MET A 363 GLY A 364 SITE 2 AD3 6 HOH A 718 HOH A 742 SITE 1 AD4 13 TYR A 121 LEU A 122 ILE A 133 LEU A 136 SITE 2 AD4 13 ASN A 138 MET A 153 GLY A 200 THR A 201 SITE 3 AD4 13 PHE A 202 PHE A 209 GLN A 227 DMS A 510 SITE 4 AD4 13 HOH A 633 SITE 1 AD5 16 MET A 142 SER A 144 GLY A 145 LYS A 165 SITE 2 AD5 16 ILE A 179 ASP A 182 LEU A 183 MET A 212 SITE 3 AD5 16 GLU A 213 LEU A 214 MET A 215 CYS A 218 SITE 4 AD5 16 LYS A 221 ASP A 277 PHE A 278 EDO A 507 CRYST1 53.111 74.955 86.666 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 0.018828 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013341 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011539 0.00000