HEADER SIGNALING PROTEIN 18-AUG-17 5Y86 TITLE CRYSTAL STRUCTURE OF KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE COMPND 3 3; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: REGULATORY ERYTHROID KINASE,REDK; COMPND 6 EC: 2.7.12.1; COMPND 7 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: DYRK3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, INHIBITOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.L.KIM,J.S.CHA,Y.S.CHO,H.Y.KIM,N.P.CHANG,H.S.CHO REVDAT 3 22-NOV-23 5Y86 1 HETSYN REVDAT 2 30-MAY-18 5Y86 1 JRNL REVDAT 1 02-MAY-18 5Y86 0 JRNL AUTH K.KIM,J.S.CHA,Y.S.CHO,H.KIM,N.CHANG,H.J.KIM,H.S.CHO JRNL TITL CRYSTAL STRUCTURE OF HUMAN DUAL-SPECIFICITY JRNL TITL 2 TYROSINE-REGULATED KINASE 3 REVEALS NEW STRUCTURAL FEATURES JRNL TITL 3 AND INSIGHTS INTO ITS AUTO-PHOSPHORYLATION JRNL REF J. MOL. BIOL. V. 430 1521 2018 JRNL REFN ESSN 1089-8638 JRNL PMID 29634919 JRNL DOI 10.1016/J.JMB.2018.04.001 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 37563 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1964 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2717 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3208 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.48000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : -0.96000 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): 0.128 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.686 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3344 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3250 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4500 ; 2.167 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7477 ; 1.135 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 394 ; 4.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;31.588 ;22.770 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 589 ;14.926 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;23.811 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 469 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3652 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 787 ; 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): 1579 ; 2.396 ; 1.709 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1578 ; 2.395 ; 1.707 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1972 ; 3.573 ; 2.545 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1973 ; 3.573 ; 2.548 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1765 ; 4.021 ; 2.220 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1765 ; 4.021 ; 2.220 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2528 ; 6.155 ; 3.115 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14300 ; 8.200 ;17.038 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14106 ; 8.155 ;16.900 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 : 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 5Y86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 77.15 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 628287 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3K2L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M NAH2PO4 AND K2HPO4 (PH8.2), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 290.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.23500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.26000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.23500 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: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 THR A 4 REMARK 465 ALA A 5 REMARK 465 ARG A 6 REMARK 465 GLY A 7 REMARK 465 PRO A 8 REMARK 465 GLY A 9 REMARK 465 ARG A 10 REMARK 465 LYS A 11 REMARK 465 ASP A 12 REMARK 465 ALA A 13 REMARK 465 GLY A 14 REMARK 465 PRO A 15 REMARK 465 PRO A 16 REMARK 465 GLY A 17 REMARK 465 ALA A 18 REMARK 465 GLY A 19 REMARK 465 LEU A 20 REMARK 465 PRO A 21 REMARK 465 PRO A 22 REMARK 465 GLN A 23 REMARK 465 GLN A 24 REMARK 465 ARG A 25 REMARK 465 ARG A 26 REMARK 465 LEU A 27 REMARK 465 GLY A 28 REMARK 465 ASP A 29 REMARK 465 GLY A 30 REMARK 465 VAL A 31 REMARK 465 TYR A 32 REMARK 465 ASP A 33 REMARK 465 THR A 34 REMARK 465 PHE A 35 REMARK 465 MET A 36 REMARK 465 MET A 37 REMARK 465 ILE A 38 REMARK 465 ASP A 39 REMARK 465 GLU A 40 REMARK 465 THR A 41 REMARK 465 LYS A 42 REMARK 465 CYS A 43 REMARK 465 PRO A 44 REMARK 465 PRO A 45 REMARK 465 CYS A 46 REMARK 465 SER A 47 REMARK 465 ASN A 48 REMARK 465 VAL A 49 REMARK 465 LEU A 50 REMARK 465 CYS A 51 REMARK 465 ASN A 52 REMARK 465 PRO A 53 REMARK 465 SER A 54 REMARK 465 GLU A 55 REMARK 465 PRO A 56 REMARK 465 PRO A 57 REMARK 465 PRO A 58 REMARK 465 PRO A 59 REMARK 465 ARG A 60 REMARK 465 ARG A 61 REMARK 465 LEU A 62 REMARK 465 ASN A 63 REMARK 465 MET A 64 REMARK 465 THR A 65 REMARK 465 THR A 66 REMARK 465 GLU A 67 REMARK 465 GLN A 68 REMARK 465 PHE A 69 REMARK 465 THR A 70 REMARK 465 GLY A 71 REMARK 465 ASP A 72 REMARK 465 HIS A 73 REMARK 465 THR A 74 REMARK 465 GLN A 75 REMARK 465 HIS A 76 REMARK 465 PHE A 77 REMARK 465 LEU A 78 REMARK 465 ASP A 79 REMARK 465 GLY A 80 REMARK 465 GLY A 81 REMARK 465 GLU A 82 REMARK 465 MET A 83 REMARK 465 LYS A 84 REMARK 465 VAL A 85 REMARK 465 GLU A 86 REMARK 465 GLN A 87 REMARK 465 LEU A 88 REMARK 465 PHE A 89 REMARK 465 GLN A 90 REMARK 465 GLU A 91 REMARK 465 PHE A 92 REMARK 465 GLY A 93 REMARK 465 ASN A 94 REMARK 465 ARG A 95 REMARK 465 LYS A 96 REMARK 465 SER A 97 REMARK 465 ASN A 98 REMARK 465 THR A 99 REMARK 465 ILE A 100 REMARK 465 GLN A 101 REMARK 465 SER A 102 REMARK 465 ASP A 103 REMARK 465 GLY A 104 REMARK 465 ILE A 105 REMARK 465 SER A 106 REMARK 465 ASP A 107 REMARK 465 SER A 108 REMARK 465 GLU A 109 REMARK 465 LYS A 110 REMARK 465 CYS A 111 REMARK 465 SER A 112 REMARK 465 PRO A 113 REMARK 465 THR A 114 REMARK 465 VAL A 115 REMARK 465 SER A 116 REMARK 465 GLN A 117 REMARK 465 GLY A 118 REMARK 465 LYS A 119 REMARK 465 SER A 120 REMARK 465 SER A 121 REMARK 465 ASP A 122 REMARK 465 CYS A 123 REMARK 465 LEU A 124 REMARK 465 ASN A 125 REMARK 465 THR A 126 REMARK 465 VAL A 127 REMARK 465 LYS A 128 REMARK 465 SER A 129 REMARK 465 ASN A 130 REMARK 465 SER A 131 REMARK 465 SER A 132 REMARK 465 SER A 133 REMARK 465 LYS A 134 REMARK 465 ALA A 135 REMARK 465 PRO A 136 REMARK 465 LYS A 137 REMARK 465 ILE A 533 REMARK 465 ASP A 534 REMARK 465 LYS A 535 REMARK 465 VAL A 536 REMARK 465 SER A 537 REMARK 465 GLY A 538 REMARK 465 LYS A 539 REMARK 465 ARG A 540 REMARK 465 VAL A 541 REMARK 465 VAL A 542 REMARK 465 ASN A 543 REMARK 465 PRO A 544 REMARK 465 ALA A 545 REMARK 465 SER A 546 REMARK 465 ALA A 547 REMARK 465 PHE A 548 REMARK 465 GLN A 549 REMARK 465 GLY A 550 REMARK 465 LEU A 551 REMARK 465 GLY A 552 REMARK 465 SER A 553 REMARK 465 LYS A 554 REMARK 465 LEU A 555 REMARK 465 PRO A 556 REMARK 465 PRO A 557 REMARK 465 VAL A 558 REMARK 465 VAL A 559 REMARK 465 GLY A 560 REMARK 465 ILE A 561 REMARK 465 ALA A 562 REMARK 465 ASN A 563 REMARK 465 LYS A 564 REMARK 465 LEU A 565 REMARK 465 LYS A 566 REMARK 465 ALA A 567 REMARK 465 ASN A 568 REMARK 465 LEU A 569 REMARK 465 MET A 570 REMARK 465 SER A 571 REMARK 465 GLU A 572 REMARK 465 THR A 573 REMARK 465 ASN A 574 REMARK 465 GLY A 575 REMARK 465 SER A 576 REMARK 465 ILE A 577 REMARK 465 PRO A 578 REMARK 465 LEU A 579 REMARK 465 CYS A 580 REMARK 465 SER A 581 REMARK 465 VAL A 582 REMARK 465 LEU A 583 REMARK 465 PRO A 584 REMARK 465 LYS A 585 REMARK 465 LEU A 586 REMARK 465 ILE A 587 REMARK 465 SER A 588 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 O3P TPO A 512 O HOH A 701 2.15 REMARK 500 O HOH A 777 O HOH A 944 2.15 REMARK 500 O3 PO4 A 603 O HOH A 702 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 414 O2 GOL A 612 3645 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 243 CD GLU A 243 OE1 0.077 REMARK 500 GLU A 497 CD GLU A 497 OE1 0.082 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 ARG A 178 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 178 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 202 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 202 NE - CZ - NH2 ANGL. DEV. = -9.0 DEGREES REMARK 500 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LYS A 265 N - CA - C ANGL. DEV. = -20.5 DEGREES REMARK 500 THR A 266 CB - CA - C ANGL. DEV. = -17.5 DEGREES REMARK 500 MET A 269 CG - SD - CE ANGL. DEV. = 10.8 DEGREES REMARK 500 ASP A 355 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 ARG A 373 NE - CZ - NH2 ANGL. DEV. = -4.2 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 ARG A 208 -50.16 -136.02 REMARK 500 LEU A 212 -90.16 -112.39 REMARK 500 LEU A 291 -164.87 -111.59 REMARK 500 SER A 292 -157.01 -94.84 REMARK 500 ASP A 335 41.38 -152.30 REMARK 500 GLN A 371 154.26 75.29 REMARK 500 SER A 387 -154.73 -156.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1050 DISTANCE = 6.06 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HRM A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 612 DBREF 5Y86 A 1 588 UNP O43781 DYRK3_HUMAN 1 588 SEQRES 1 A 588 MET GLY GLY THR ALA ARG GLY PRO GLY ARG LYS ASP ALA SEQRES 2 A 588 GLY PRO PRO GLY ALA GLY LEU PRO PRO GLN GLN ARG ARG SEQRES 3 A 588 LEU GLY ASP GLY VAL TYR ASP THR PHE MET MET ILE ASP SEQRES 4 A 588 GLU THR LYS CYS PRO PRO CYS SER ASN VAL LEU CYS ASN SEQRES 5 A 588 PRO SER GLU PRO PRO PRO PRO ARG ARG LEU ASN MET THR SEQRES 6 A 588 THR GLU GLN PHE THR GLY ASP HIS THR GLN HIS PHE LEU SEQRES 7 A 588 ASP GLY GLY GLU MET LYS VAL GLU GLN LEU PHE GLN GLU SEQRES 8 A 588 PHE GLY ASN ARG LYS SER ASN THR ILE GLN SER ASP GLY SEQRES 9 A 588 ILE SER ASP SER GLU LYS CYS SER PRO THR VAL SER GLN SEQRES 10 A 588 GLY LYS SER SER ASP CYS LEU ASN THR VAL LYS SER ASN SEQRES 11 A 588 SER SER SER LYS ALA PRO LYS VAL VAL PRO LEU THR PRO SEQRES 12 A 588 GLU GLN ALA LEU LYS GLN TYR LYS HIS HIS LEU THR ALA SEQRES 13 A 588 TYR GLU LYS LEU GLU ILE ILE ASN TYR PRO GLU ILE TYR SEQRES 14 A 588 PHE VAL GLY PRO ASN ALA LYS LYS ARG HIS GLY VAL ILE SEQRES 15 A 588 GLY GLY PRO ASN ASN GLY GLY TYR ASP ASP ALA ASP GLY SEQRES 16 A 588 ALA TYR ILE HIS VAL PRO ARG ASP HIS LEU ALA TYR ARG SEQRES 17 A 588 TYR GLU VAL LEU LYS ILE ILE GLY LYS GLY SER PHE GLY SEQRES 18 A 588 GLN VAL ALA ARG VAL TYR ASP HIS LYS LEU ARG GLN TYR SEQRES 19 A 588 VAL ALA LEU LYS MET VAL ARG ASN GLU LYS ARG PHE HIS SEQRES 20 A 588 ARG GLN ALA ALA GLU GLU ILE ARG ILE LEU GLU HIS LEU SEQRES 21 A 588 LYS LYS GLN ASP LYS THR GLY SER MET ASN VAL ILE HIS SEQRES 22 A 588 MET LEU GLU SER PHE THR PHE ARG ASN HIS VAL CYS MET SEQRES 23 A 588 ALA PHE GLU LEU LEU SER ILE ASP LEU TYR GLU LEU ILE SEQRES 24 A 588 LYS LYS ASN LYS PHE GLN GLY PHE SER VAL GLN LEU VAL SEQRES 25 A 588 ARG LYS PHE ALA GLN SER ILE LEU GLN SER LEU ASP ALA SEQRES 26 A 588 LEU HIS LYS ASN LYS ILE ILE HIS CYS ASP LEU LYS PRO SEQRES 27 A 588 GLU ASN ILE LEU LEU LYS HIS HIS GLY ARG SER SEP THR SEQRES 28 A 588 LYS VAL ILE ASP PHE GLY SER SER CYS PHE GLU TYR GLN SEQRES 29 A 588 LYS LEU TYR THR PTR ILE GLN SER ARG PHE TYR ARG ALA SEQRES 30 A 588 PRO GLU ILE ILE LEU GLY SER ARG TYR SER THR PRO ILE SEQRES 31 A 588 ASP ILE TRP SER PHE GLY CYS ILE LEU ALA GLU LEU LEU SEQRES 32 A 588 THR GLY GLN PRO LEU PHE PRO GLY GLU ASP GLU GLY ASP SEQRES 33 A 588 GLN LEU ALA CYS MET MET GLU LEU LEU GLY MET PRO PRO SEQRES 34 A 588 PRO LYS LEU LEU GLU GLN SER LYS ARG ALA LYS TYR PHE SEQRES 35 A 588 ILE ASN SEP LYS GLY ILE PRO ARG TYR CYS SER VAL THR SEQRES 36 A 588 THR GLN ALA ASP GLY ARG VAL VAL LEU VAL GLY GLY ARG SEQRES 37 A 588 SER ARG ARG GLY LYS LYS ARG GLY PRO PRO GLY SER LYS SEQRES 38 A 588 ASP TRP GLY THR ALA LEU LYS GLY CYS ASP ASP TYR LEU SEQRES 39 A 588 PHE ILE GLU PHE LEU LYS ARG CYS LEU HIS TRP ASP PRO SEQRES 40 A 588 SER ALA ARG LEU TPO PRO ALA GLN ALA LEU ARG HIS PRO SEQRES 41 A 588 TRP ILE SER LYS SER VAL PRO ARG PRO LEU THR THR ILE SEQRES 42 A 588 ASP LYS VAL SER GLY LYS ARG VAL VAL ASN PRO ALA SER SEQRES 43 A 588 ALA PHE GLN GLY LEU GLY SER LYS LEU PRO PRO VAL VAL SEQRES 44 A 588 GLY ILE ALA ASN LYS LEU LYS ALA ASN LEU MET SER GLU SEQRES 45 A 588 THR ASN GLY SER ILE PRO LEU CYS SER VAL LEU PRO LYS SEQRES 46 A 588 LEU ILE SER MODRES 5Y86 SEP A 350 SER MODIFIED RESIDUE MODRES 5Y86 PTR A 369 TYR MODIFIED RESIDUE MODRES 5Y86 SEP A 445 SER MODIFIED RESIDUE MODRES 5Y86 TPO A 512 THR MODIFIED RESIDUE HET SEP A 350 10 HET PTR A 369 16 HET SEP A 445 10 HET TPO A 512 11 HET HRM A 601 16 HET PO4 A 602 5 HET PO4 A 603 5 HET EDO A 604 4 HET EDO A 605 4 HET EDO A 606 4 HET EDO A 607 4 HET EDO A 608 4 HET EDO A 609 4 HET EDO A 610 4 HET EDO A 611 4 HET GOL A 612 6 HETNAM SEP PHOSPHOSERINE HETNAM PTR O-PHOSPHOTYROSINE HETNAM TPO PHOSPHOTHREONINE HETNAM HRM 7-METHOXY-1-METHYL-9H-BETA-CARBOLINE HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN SEP PHOSPHONOSERINE HETSYN PTR PHOSPHONOTYROSINE HETSYN TPO PHOSPHONOTHREONINE HETSYN HRM 7-METHOXY-1-METHYL-9H-PYRIDO[3,4-B]INDOL; HARMINE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 1 PTR C9 H12 N O6 P FORMUL 1 TPO C4 H10 N O6 P FORMUL 2 HRM C13 H12 N2 O FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 EDO 8(C2 H6 O2) FORMUL 13 GOL C3 H8 O3 FORMUL 14 HOH *350(H2 O) HELIX 1 AA1 THR A 142 TYR A 150 1 9 HELIX 2 AA2 THR A 155 ILE A 162 1 8 HELIX 3 AA3 ILE A 163 TYR A 165 5 3 HELIX 4 AA4 GLY A 184 GLY A 189 1 6 HELIX 5 AA5 GLU A 243 ASP A 264 1 22 HELIX 6 AA6 ASP A 294 ASN A 302 1 9 HELIX 7 AA7 SER A 308 ASN A 329 1 22 HELIX 8 AA8 LYS A 337 GLU A 339 5 3 HELIX 9 AA9 ASP A 355 SER A 359 5 5 HELIX 10 AB1 SER A 372 ARG A 376 5 5 HELIX 11 AB2 ALA A 377 GLY A 383 1 7 HELIX 12 AB3 THR A 388 GLY A 405 1 18 HELIX 13 AB4 ASP A 413 GLY A 426 1 14 HELIX 14 AB5 PRO A 429 GLN A 435 1 7 HELIX 15 AB6 ARG A 438 PHE A 442 5 5 HELIX 16 AB7 ASP A 482 LEU A 487 1 6 HELIX 17 AB8 ASP A 492 LEU A 503 1 12 HELIX 18 AB9 ASP A 506 ARG A 510 5 5 HELIX 19 AC1 TPO A 512 HIS A 519 1 8 SHEET 1 AA1 6 HIS A 204 LEU A 205 0 SHEET 2 AA1 6 TYR A 209 GLY A 218 -1 O TYR A 209 N LEU A 205 SHEET 3 AA1 6 GLY A 221 ASP A 228 -1 O VAL A 223 N GLY A 216 SHEET 4 AA1 6 GLN A 233 VAL A 240 -1 O GLN A 233 N ASP A 228 SHEET 5 AA1 6 HIS A 283 PHE A 288 -1 O MET A 286 N LYS A 238 SHEET 6 AA1 6 MET A 274 PHE A 280 -1 N PHE A 278 O CYS A 285 SHEET 1 AA2 2 ILE A 331 ILE A 332 0 SHEET 2 AA2 2 CYS A 360 PHE A 361 -1 O CYS A 360 N ILE A 332 SHEET 1 AA3 2 ILE A 341 LEU A 343 0 SHEET 2 AA3 2 THR A 351 VAL A 353 -1 O LYS A 352 N LEU A 342 SHEET 1 AA4 2 SER A 453 THR A 456 0 SHEET 2 AA4 2 VAL A 462 VAL A 465 -1 O VAL A 463 N THR A 455 SHEET 1 AA5 2 GLY A 467 ARG A 468 0 SHEET 2 AA5 2 LYS A 474 ARG A 475 -1 O ARG A 475 N GLY A 467 LINK C SER A 349 N SEP A 350 1555 1555 1.31 LINK C SEP A 350 N THR A 351 1555 1555 1.34 LINK C THR A 368 N PTR A 369 1555 1555 1.31 LINK C PTR A 369 N ILE A 370 1555 1555 1.33 LINK C ASN A 444 N SEP A 445 1555 1555 1.31 LINK C SEP A 445 N LYS A 446 1555 1555 1.29 LINK C LEU A 511 N TPO A 512 1555 1555 1.31 LINK C TPO A 512 N PRO A 513 1555 1555 1.34 SITE 1 AC1 10 ALA A 236 LYS A 238 PHE A 288 GLU A 289 SITE 2 AC1 10 LEU A 290 LEU A 291 LEU A 342 ILE A 354 SITE 3 AC1 10 ASP A 355 HOH A 735 SITE 1 AC2 6 LYS A 151 GLY A 218 SER A 219 LYS A 337 SITE 2 AC2 6 HOH A 745 HOH A 897 SITE 1 AC3 5 ARG A 313 LYS A 314 LYS A 524 HOH A 702 SITE 2 AC3 5 HOH A 734 SITE 1 AC4 3 ARG A 178 LYS A 440 TYR A 441 SITE 1 AC5 4 LYS A 151 LYS A 159 PTR A 369 ARG A 376 SITE 1 AC6 8 ILE A 448 PRO A 520 SER A 523 LYS A 524 SITE 2 AC6 8 SER A 525 HOH A 744 HOH A 755 HOH A 768 SITE 1 AC7 3 ARG A 208 PHE A 278 HOH A 922 SITE 1 AC8 4 SER A 308 VAL A 309 ARG A 461 HOH A 947 SITE 1 AC9 4 LEU A 343 HIS A 346 GLY A 347 ARG A 348 SITE 1 AD1 2 ARG A 450 CYS A 452 SITE 1 AD2 4 TYR A 296 GLU A 297 LYS A 300 HOH A 707 SITE 1 AD3 9 TYR A 157 GLY A 180 VAL A 181 ILE A 182 SITE 2 AD3 9 ASP A 413 GLU A 414 GLY A 415 HOH A 704 SITE 3 AD3 9 HOH A 927 CRYST1 43.000 76.520 148.470 90.00 90.00 90.00 P 2 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 0.023256 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006735 0.00000