HEADER TRANSFERASE 18-AUG-18 6HDP TITLE HUMAN DYRK2 BOUND TO SCORZODIHYDROSTILBENE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE COMPND 3 2; COMPND 4 CHAIN: A; COMPND 5 EC: 2.7.12.1; COMPND 6 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: DYRK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS KINASE, STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.ELKINS,M.SOUNDARARAJAN,P.PROKSCH,L.MEIJER,M.VOLLMAR,T.KROJER, AUTHOR 2 C.BOUNTRA,A.M.EDWARDS,C.ARROWSMITH,S.KNAPP REVDAT 2 17-JAN-24 6HDP 1 LINK REVDAT 1 28-AUG-19 6HDP 0 JRNL AUTH J.M.ELKINS,S.KNAPP JRNL TITL DYRK2 BOUND TO SCORZODIHYDROSTILBENE A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23351 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1261 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1669 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3235 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.59000 REMARK 3 B22 (A**2) : 0.59000 REMARK 3 B33 (A**2) : -1.18000 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): 0.263 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.503 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3418 ; 0.007 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 2980 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4634 ; 1.198 ; 1.678 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6952 ; 0.814 ; 1.639 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 418 ; 7.498 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;32.434 ;22.088 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 568 ;15.332 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.557 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 424 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3858 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 637 ; 0.002 ; 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): 1666 ; 1.929 ; 5.111 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1665 ; 1.926 ; 5.106 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2083 ; 3.081 ; 7.657 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2084 ; 3.081 ; 7.662 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1752 ; 2.085 ; 5.258 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1752 ; 2.081 ; 5.259 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2546 ; 3.279 ; 7.827 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3809 ; 5.558 ;59.116 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3785 ; 5.532 ;58.878 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 61 A 91 REMARK 3 ORIGIN FOR THE GROUP (A): 60.0670 29.1630 38.4120 REMARK 3 T TENSOR REMARK 3 T11: 0.1641 T22: 0.2625 REMARK 3 T33: 0.0747 T12: 0.0015 REMARK 3 T13: -0.0787 T23: 0.0836 REMARK 3 L TENSOR REMARK 3 L11: 5.0568 L22: 2.0017 REMARK 3 L33: 22.6989 L12: -0.9966 REMARK 3 L13: -4.3795 L23: 1.9069 REMARK 3 S TENSOR REMARK 3 S11: 0.0887 S12: -0.3252 S13: 0.0245 REMARK 3 S21: 0.2277 S22: -0.0254 S23: -0.1582 REMARK 3 S31: -0.7570 S32: -0.2015 S33: -0.0633 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 92 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): 45.6470 27.9670 21.3400 REMARK 3 T TENSOR REMARK 3 T11: 0.1681 T22: 0.0411 REMARK 3 T33: 0.0222 T12: 0.0104 REMARK 3 T13: -0.0451 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 5.9124 L22: 0.9328 REMARK 3 L33: 1.4179 L12: 0.3462 REMARK 3 L13: -0.7401 L23: 0.0084 REMARK 3 S TENSOR REMARK 3 S11: -0.0503 S12: 0.1925 S13: -0.0903 REMARK 3 S21: -0.1752 S22: -0.0533 S23: 0.0230 REMARK 3 S31: 0.0015 S32: -0.0721 S33: 0.1036 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 232 A 467 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4120 28.7920 12.1600 REMARK 3 T TENSOR REMARK 3 T11: 0.0314 T22: 0.1572 REMARK 3 T33: 0.0670 T12: 0.0231 REMARK 3 T13: -0.0036 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 2.1520 L22: 1.5566 REMARK 3 L33: 2.9992 L12: -0.2113 REMARK 3 L13: 0.4565 L23: 0.2050 REMARK 3 S TENSOR REMARK 3 S11: -0.0725 S12: -0.0262 S13: 0.1961 REMARK 3 S21: 0.0008 S22: -0.0885 S23: 0.2320 REMARK 3 S31: -0.0757 S32: -0.5438 S33: 0.1610 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6HDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-11 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 : DIAMOND REMARK 200 BEAMLINE : I03 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24654 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 84.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.83700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4AZF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M SODIUM MALATE AND 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.26350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.26350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.18600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.26350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.26350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.18600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.26350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.26350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 74.18600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.26350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.26350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.18600 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 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: 50 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 502 LIES ON A SPECIAL POSITION. 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 51 REMARK 465 HIS 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 SER A 58 REMARK 465 SER A 59 REMARK 465 GLY A 60 REMARK 465 PRO A 470 REMARK 465 THR A 471 REMARK 465 GLY A 472 REMARK 465 GLU A 473 REMARK 465 LYS A 474 REMARK 465 THR A 475 REMARK 465 SER A 476 REMARK 465 VAL A 477 REMARK 465 LYS A 478 REMARK 465 ARG A 479 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 VAL A 61 CG1 CG2 REMARK 470 MET A 73 CG SD CE REMARK 470 LYS A 77 CE NZ REMARK 470 LYS A 88 NZ REMARK 470 LYS A 93 CE NZ REMARK 470 LYS A 116 CD CE NZ REMARK 470 LYS A 153 NZ REMARK 470 LYS A 157 CE NZ REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 ARG A 188 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 202 CD CE NZ REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 LYS A 243 CE NZ REMARK 470 ARG A 305 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 325 CD NE CZ NH1 NH2 REMARK 470 LYS A 371 NZ REMARK 470 LYS A 377 CE NZ REMARK 470 LYS A 380 CG CD CE NZ REMARK 470 LYS A 386 CG CD CE NZ REMARK 470 SER A 398 OG REMARK 470 ASP A 431 CG OD1 OD2 REMARK 470 ARG A 463 CD NE CZ NH1 NH2 REMARK 470 ARG A 465 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 468 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 ASP A 62 65.93 71.64 REMARK 500 ARG A 148 -51.26 -145.99 REMARK 500 SER A 232 -151.31 -102.88 REMARK 500 ASP A 275 42.28 -150.14 REMARK 500 ASP A 295 77.41 62.03 REMARK 500 GLU A 302 -7.81 -53.51 REMARK 500 ARG A 305 -168.48 178.83 REMARK 500 VAL A 306 85.99 162.26 REMARK 500 GLN A 311 153.79 71.47 REMARK 500 SER A 409 172.92 -56.60 REMARK 500 ARG A 464 88.78 -154.59 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 ASN A 114 ALA A 115 148.65 REMARK 500 ARG A 305 VAL A 306 133.57 REMARK 500 ARG A 305 VAL A 306 -144.22 REMARK 500 VAL A 306 TYR A 307 135.71 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 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 613 O REMARK 620 2 HOH A 613 O 80.5 REMARK 620 3 HOH A 694 O 83.3 93.7 REMARK 620 4 HOH A 694 O 93.7 83.3 176.1 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 FZ5 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 502 DBREF 6HDP A 73 479 UNP Q92630 DYRK2_HUMAN 73 479 SEQADV 6HDP MET A 51 UNP Q92630 INITIATING METHIONINE SEQADV 6HDP HIS A 52 UNP Q92630 EXPRESSION TAG SEQADV 6HDP HIS A 53 UNP Q92630 EXPRESSION TAG SEQADV 6HDP HIS A 54 UNP Q92630 EXPRESSION TAG SEQADV 6HDP HIS A 55 UNP Q92630 EXPRESSION TAG SEQADV 6HDP HIS A 56 UNP Q92630 EXPRESSION TAG SEQADV 6HDP HIS A 57 UNP Q92630 EXPRESSION TAG SEQADV 6HDP SER A 58 UNP Q92630 EXPRESSION TAG SEQADV 6HDP SER A 59 UNP Q92630 EXPRESSION TAG SEQADV 6HDP GLY A 60 UNP Q92630 EXPRESSION TAG SEQADV 6HDP VAL A 61 UNP Q92630 EXPRESSION TAG SEQADV 6HDP ASP A 62 UNP Q92630 EXPRESSION TAG SEQADV 6HDP LEU A 63 UNP Q92630 EXPRESSION TAG SEQADV 6HDP GLY A 64 UNP Q92630 EXPRESSION TAG SEQADV 6HDP THR A 65 UNP Q92630 EXPRESSION TAG SEQADV 6HDP GLU A 66 UNP Q92630 EXPRESSION TAG SEQADV 6HDP ASN A 67 UNP Q92630 EXPRESSION TAG SEQADV 6HDP LEU A 68 UNP Q92630 EXPRESSION TAG SEQADV 6HDP TYR A 69 UNP Q92630 EXPRESSION TAG SEQADV 6HDP PHE A 70 UNP Q92630 EXPRESSION TAG SEQADV 6HDP GLN A 71 UNP Q92630 EXPRESSION TAG SEQADV 6HDP SER A 72 UNP Q92630 EXPRESSION TAG SEQRES 1 A 429 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 429 GLY THR GLU ASN LEU TYR PHE GLN SER MET GLY LYS VAL SEQRES 3 A 429 LYS ALA THR PRO MET THR PRO GLU GLN ALA MET LYS GLN SEQRES 4 A 429 TYR MET GLN LYS LEU THR ALA PHE GLU HIS HIS GLU ILE SEQRES 5 A 429 PHE SER TYR PRO GLU ILE TYR PHE LEU GLY LEU ASN ALA SEQRES 6 A 429 LYS LYS ARG GLN GLY MET THR GLY GLY PRO ASN ASN GLY SEQRES 7 A 429 GLY TYR ASP ASP ASP GLN GLY SER TYR VAL GLN VAL PRO SEQRES 8 A 429 HIS ASP HIS VAL ALA TYR ARG TYR GLU VAL LEU LYS VAL SEQRES 9 A 429 ILE GLY LYS GLY SER PHE GLY GLN VAL VAL LYS ALA TYR SEQRES 10 A 429 ASP HIS LYS VAL HIS GLN HIS VAL ALA LEU LYS MET VAL SEQRES 11 A 429 ARG ASN GLU LYS ARG PHE HIS ARG GLN ALA ALA GLU GLU SEQRES 12 A 429 ILE ARG ILE LEU GLU HIS LEU ARG LYS GLN ASP LYS ASP SEQRES 13 A 429 ASN THR MET ASN VAL ILE HIS MET LEU GLU ASN PHE THR SEQRES 14 A 429 PHE ARG ASN HIS ILE CYS MET THR PHE GLU LEU LEU SER SEQRES 15 A 429 MET ASN LEU TYR GLU LEU ILE LYS LYS ASN LYS PHE GLN SEQRES 16 A 429 GLY PHE SER LEU PRO LEU VAL ARG LYS PHE ALA HIS SER SEQRES 17 A 429 ILE LEU GLN CYS LEU ASP ALA LEU HIS LYS ASN ARG ILE SEQRES 18 A 429 ILE HIS CYS ASP LEU LYS PRO GLU ASN ILE LEU LEU LYS SEQRES 19 A 429 GLN GLN GLY ARG SER GLY ILE LYS VAL ILE ASP PHE GLY SEQRES 20 A 429 SER SER CYS TYR GLU HIS GLN ARG VAL TYR THR PTR ILE SEQRES 21 A 429 GLN SER ARG PHE TYR ARG ALA PRO GLU VAL ILE LEU GLY SEQRES 22 A 429 ALA ARG TYR GLY MET PRO ILE ASP MET TRP SER LEU GLY SEQRES 23 A 429 CYS ILE LEU ALA GLU LEU LEU THR GLY TYR PRO LEU LEU SEQRES 24 A 429 PRO GLY GLU ASP GLU GLY ASP GLN LEU ALA CYS MET ILE SEQRES 25 A 429 GLU LEU LEU GLY MET PRO SER GLN LYS LEU LEU ASP ALA SEQRES 26 A 429 SER LYS ARG ALA LYS ASN PHE VAL SER SEP LYS GLY TYR SEQRES 27 A 429 PRO ARG TYR CYS THR VAL THR THR LEU SER ASP GLY SER SEQRES 28 A 429 VAL VAL LEU ASN GLY GLY ARG SER ARG ARG GLY LYS LEU SEQRES 29 A 429 ARG GLY PRO PRO GLU SER ARG GLU TRP GLY ASN ALA LEU SEQRES 30 A 429 LYS GLY CYS ASP ASP PRO LEU PHE LEU ASP PHE LEU LYS SEQRES 31 A 429 GLN CYS LEU GLU TRP ASP PRO ALA VAL ARG MET THR PRO SEQRES 32 A 429 GLY GLN ALA LEU ARG HIS PRO TRP LEU ARG ARG ARG LEU SEQRES 33 A 429 PRO LYS PRO PRO THR GLY GLU LYS THR SER VAL LYS ARG MODRES 6HDP PTR A 309 TYR MODIFIED RESIDUE MODRES 6HDP SEP A 385 SER MODIFIED RESIDUE HET PTR A 309 16 HET SEP A 385 10 HET FZ5 A 501 33 HET NA A 502 1 HETNAM PTR O-PHOSPHOTYROSINE HETNAM SEP PHOSPHOSERINE HETNAM FZ5 SCORZODIHYDROSTILBENE A HETNAM NA SODIUM ION HETSYN PTR PHOSPHONOTYROSINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 PTR C9 H12 N O6 P FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 FZ5 C23 H28 O10 FORMUL 3 NA NA 1+ FORMUL 4 HOH *164(H2 O) HELIX 1 AA1 ASP A 62 GLU A 66 5 5 HELIX 2 AA2 THR A 82 MET A 91 1 10 HELIX 3 AA3 GLN A 92 LEU A 94 5 3 HELIX 4 AA4 THR A 95 ILE A 102 1 8 HELIX 5 AA5 PHE A 103 TYR A 105 5 3 HELIX 6 AA6 GLY A 124 GLY A 129 1 6 HELIX 7 AA7 GLU A 183 LYS A 202 1 20 HELIX 8 AA8 ASN A 234 ASN A 242 1 9 HELIX 9 AA9 SER A 248 ASN A 269 1 22 HELIX 10 AB1 LYS A 277 GLU A 279 5 3 HELIX 11 AB2 SER A 312 ARG A 316 5 5 HELIX 12 AB3 ALA A 317 GLY A 323 1 7 HELIX 13 AB4 MET A 328 GLY A 345 1 18 HELIX 14 AB5 ASP A 353 GLY A 366 1 14 HELIX 15 AB6 SER A 369 ALA A 375 1 7 HELIX 16 AB7 ARG A 378 PHE A 382 5 5 HELIX 17 AB8 GLU A 422 LEU A 427 1 6 HELIX 18 AB9 ASP A 432 LEU A 443 1 12 HELIX 19 AC1 THR A 452 HIS A 459 1 8 SHEET 1 AA1 2 ASN A 67 TYR A 69 0 SHEET 2 AA1 2 LYS A 77 THR A 79 -1 O LYS A 77 N TYR A 69 SHEET 1 AA2 6 HIS A 144 VAL A 145 0 SHEET 2 AA2 6 TYR A 149 GLY A 158 -1 O TYR A 149 N VAL A 145 SHEET 3 AA2 6 GLY A 161 ASP A 168 -1 O VAL A 163 N GLY A 156 SHEET 4 AA2 6 GLN A 173 VAL A 180 -1 O LEU A 177 N VAL A 164 SHEET 5 AA2 6 HIS A 223 PHE A 228 -1 O MET A 226 N LYS A 178 SHEET 6 AA2 6 MET A 214 PHE A 220 -1 N PHE A 218 O CYS A 225 SHEET 1 AA3 2 ILE A 271 ILE A 272 0 SHEET 2 AA3 2 CYS A 300 TYR A 301 -1 O CYS A 300 N ILE A 272 SHEET 1 AA4 2 ILE A 281 LEU A 283 0 SHEET 2 AA4 2 ILE A 291 VAL A 293 -1 O LYS A 292 N LEU A 282 SHEET 1 AA5 2 VAL A 394 THR A 396 0 SHEET 2 AA5 2 VAL A 402 LEU A 404 -1 O VAL A 403 N THR A 395 SHEET 1 AA6 2 GLY A 407 ARG A 408 0 SHEET 2 AA6 2 LEU A 414 ARG A 415 -1 O ARG A 415 N GLY A 407 LINK C ATHR A 308 N PTR A 309 1555 1555 1.33 LINK C BTHR A 308 N PTR A 309 1555 1555 1.35 LINK C PTR A 309 N ILE A 310 1555 1555 1.34 LINK C SER A 384 N SEP A 385 1555 1555 1.34 LINK C SEP A 385 N LYS A 386 1555 1555 1.34 LINK NA NA A 502 O HOH A 613 1555 1555 3.16 LINK NA NA A 502 O HOH A 613 1555 7555 3.16 LINK NA NA A 502 O HOH A 694 1555 1555 2.32 LINK NA NA A 502 O HOH A 694 1555 7555 2.32 SITE 1 AC1 18 ILE A 155 VAL A 163 ALA A 176 LYS A 178 SITE 2 AC1 18 GLU A 193 PHE A 228 GLU A 229 LEU A 230 SITE 3 AC1 18 LEU A 231 SER A 232 MET A 233 ASN A 234 SITE 4 AC1 18 GLU A 237 LEU A 282 ILE A 294 ASP A 295 SITE 5 AC1 18 HOH A 657 HOH A 735 SITE 1 AC2 1 HOH A 694 CRYST1 84.527 84.527 148.372 90.00 90.00 90.00 P 42 21 2 8 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 0.011831 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006740 0.00000