HEADER TRANSFERASE 30-NOV-09 3KVW TITLE CRYSTAL STRUCTURE OF DUAL-SPECIFICITY TYROSINE PHOSPHORYLATION TITLE 2 REGULATED KINASE 2 (DYRK2) IN COMPLEX WITH AN INDIRUBIN LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE COMPND 3 2; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 146-552; COMPND 6 SYNONYM: DYRK2; COMPND 7 EC: 2.7.12.1; 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: DYRK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-R3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS DYRK2, DUAL-SPECIFICITY TYROSINE, KI-(Y)-PHOSPHORYLATION REGULATED KEYWDS 2 KINASE 2, PSK-H2, KINASE, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 3 APOPTOSIS, ATP-BINDING, NUCLEOTIDE-BINDING, SERINE/THREONINE-PROTEIN KEYWDS 4 KINASE, TRANSFERASE, TYROSINE-PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR P.FILIPPAKOPOULOS,V.MYRIANTHOPOULOS,M.KRITSANIDA,P.MAGIATIS, AUTHOR 2 A.L.SKALTSOUNIS,M.SOUNDARARAJAN,T.KROJER,O.GILEADI,E.HAPKA, AUTHOR 3 O.FEDOROV,G.BERRIDGE,J.WANG,L.SHRESTHA,M.VOLLMAR,F.VON DELFT, AUTHOR 4 C.H.ARROWSMITH,A.EDWARDS,J.WEIGELT,C.BOUNTRA,E.MIKROS,S.KNAPP, AUTHOR 5 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 5 09-OCT-24 3KVW 1 REMARK REVDAT 4 22-NOV-23 3KVW 1 REMARK REVDAT 3 01-NOV-23 3KVW 1 REMARK SEQADV LINK REVDAT 2 13-JUL-11 3KVW 1 VERSN REVDAT 1 05-JAN-10 3KVW 0 JRNL AUTH P.FILIPPAKOPOULOS,V.MYRIANTHOPOULOS,M.KRITSANIDA,P.MAGIATIS, JRNL AUTH 2 A.L.SKALTSOUNIS,M.SOUNDARARAJAN,T.KROJER,O.GILEADI,E.HAPKA, JRNL AUTH 3 O.FEDOROV,G.BERRIDGE,J.WANG,L.SHRESTHA,M.VOLLMAR, JRNL AUTH 4 F.VON DELFT,C.H.ARROWSMITH,A.EDWARDS,J.WEIGELT,C.BOUNTRA, JRNL AUTH 5 E.MIKROS,S.KNAPP JRNL TITL CRYSTAL STRUCTURE OF DUAL-SPECIFICITY TYROSINE JRNL TITL 2 PHOSPHORYLATION REGULATED KINASE 2 (DYRK2) IN COMPLEX WITH JRNL TITL 3 AN INDIRUBIN LIGAND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25247 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1721 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3188 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 48.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.69000 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): 0.276 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.227 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.006 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3358 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2273 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4554 ; 1.548 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5507 ; 0.939 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 412 ; 8.519 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;36.292 ;23.677 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 560 ;16.523 ;15.054 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;21.525 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3749 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 694 ; 0.007 ; 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): 2054 ; 3.633 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 839 ; 1.146 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3288 ; 5.217 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1304 ; 8.396 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1266 ;10.267 ;11.000 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 -16 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): 27.4044 -56.3736 39.2025 REMARK 3 T TENSOR REMARK 3 T11: 0.4077 T22: 0.4210 REMARK 3 T33: 0.2874 T12: 0.0234 REMARK 3 T13: 0.1647 T23: -0.0522 REMARK 3 L TENSOR REMARK 3 L11: 0.3552 L22: 5.6692 REMARK 3 L33: 9.9832 L12: 0.5074 REMARK 3 L13: 0.9797 L23: -1.2304 REMARK 3 S TENSOR REMARK 3 S11: 0.0655 S12: -0.2438 S13: 0.1529 REMARK 3 S21: 0.5223 S22: 0.0166 S23: 0.1829 REMARK 3 S31: -0.2340 S32: -0.0098 S33: -0.0821 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 86 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): 28.1143 -46.0365 21.5560 REMARK 3 T TENSOR REMARK 3 T11: 0.1132 T22: 0.1698 REMARK 3 T33: 0.1153 T12: 0.0010 REMARK 3 T13: 0.0327 T23: 0.0576 REMARK 3 L TENSOR REMARK 3 L11: 0.9403 L22: 7.0182 REMARK 3 L33: 2.1559 L12: -0.6103 REMARK 3 L13: -0.0002 L23: 0.7837 REMARK 3 S TENSOR REMARK 3 S11: 0.0085 S12: 0.2321 S13: 0.0099 REMARK 3 S21: -0.2706 S22: -0.0741 S23: -0.0198 REMARK 3 S31: -0.0890 S32: 0.0538 S33: 0.0655 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 395 REMARK 3 ORIGIN FOR THE GROUP (A): 29.8838 -16.6622 12.7602 REMARK 3 T TENSOR REMARK 3 T11: 0.1198 T22: 0.0267 REMARK 3 T33: 0.0601 T12: -0.0412 REMARK 3 T13: -0.0203 T23: 0.0137 REMARK 3 L TENSOR REMARK 3 L11: 2.3680 L22: 2.7143 REMARK 3 L33: 3.4385 L12: 0.0548 REMARK 3 L13: -0.0629 L23: -0.8991 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: 0.0952 S13: 0.1767 REMARK 3 S21: 0.1096 S22: -0.1143 S23: -0.2170 REMARK 3 S31: -0.2958 S32: 0.2251 S33: 0.1456 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 396 A 463 REMARK 3 ORIGIN FOR THE GROUP (A): 27.4235 -4.0742 9.6506 REMARK 3 T TENSOR REMARK 3 T11: 0.3867 T22: 0.0413 REMARK 3 T33: 0.2674 T12: -0.0360 REMARK 3 T13: -0.0308 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 2.0512 L22: 1.3005 REMARK 3 L33: 4.3220 L12: 0.2067 REMARK 3 L13: 1.1370 L23: 0.4576 REMARK 3 S TENSOR REMARK 3 S11: -0.1474 S12: -0.0746 S13: 0.5120 REMARK 3 S21: 0.1823 S22: -0.0900 S23: 0.0240 REMARK 3 S31: -0.8795 S32: -0.1923 S33: 0.2375 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 U VALUES: RESIDUAL ONLY REMARK 4 REMARK 4 3KVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056512. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.9802 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25294 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 46.552 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : 0.10500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.88500 REMARK 200 R SYM FOR SHELL (I) : 0.88500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB ENTRY 3K2L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA(ACETATE), 0.1M CACODYLATE PH REMARK 280 6.5, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 42.14000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.56000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.14000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.14000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.56000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.14000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.14000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 74.56000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.14000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.14000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.56000 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 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 -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 GLY A 400 REMARK 465 SER A 401 REMARK 465 ARG A 464 REMARK 465 ARG A 465 REMARK 465 LEU A 466 REMARK 465 PRO A 467 REMARK 465 LYS A 468 REMARK 465 PRO A 469 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 -11 CG1 CG2 REMARK 470 GLN A -1 CD OE1 NE2 REMARK 470 SER A 0 OG REMARK 470 MET A 73 CG SD CE REMARK 470 LYS A 77 CE NZ REMARK 470 LYS A 88 CD CE NZ REMARK 470 GLN A 92 CD OE1 NE2 REMARK 470 LYS A 93 CD CE NZ REMARK 470 LYS A 116 CD CE NZ REMARK 470 GLN A 134 CD OE1 NE2 REMARK 470 LYS A 153 CE NZ REMARK 470 LYS A 157 CG CD CE NZ REMARK 470 GLU A 183 CD OE1 OE2 REMARK 470 ARG A 185 CG CD NE CZ NH1 NH2 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 ARG A 253 CZ NH1 NH2 REMARK 470 GLN A 286 CD OE1 NE2 REMARK 470 GLN A 304 CG CD OE1 NE2 REMARK 470 ARG A 305 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 306 CG1 CG2 REMARK 470 ARG A 325 CD NE CZ NH1 NH2 REMARK 470 LYS A 371 CG CD CE NZ REMARK 470 LYS A 377 CD CE NZ REMARK 470 LYS A 380 CG CD CE NZ REMARK 470 LYS A 386 CG CD CE NZ REMARK 470 ASP A 431 CG OD1 OD2 REMARK 470 ARG A 463 CD NE CZ NH1 NH2 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 352 CB GLU A 352 CG -0.118 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 GLY A -12 N - CA - C ANGL. DEV. = 15.6 DEGREES REMARK 500 VAL A 306 N - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 ARG A 313 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SEP A -14 -151.99 -77.23 REMARK 500 MET A 73 72.80 43.55 REMARK 500 ARG A 148 -45.82 -141.43 REMARK 500 ASP A 204 52.98 -117.30 REMARK 500 LEU A 231 -162.38 -118.67 REMARK 500 SER A 232 -157.40 -107.74 REMARK 500 CYS A 274 -3.21 78.54 REMARK 500 ASP A 275 43.29 -151.01 REMARK 500 ASP A 295 75.68 64.30 REMARK 500 GLN A 304 -146.48 -133.26 REMARK 500 ARG A 305 -177.98 23.61 REMARK 500 ARG A 305 162.66 -24.60 REMARK 500 VAL A 306 -64.15 -174.08 REMARK 500 TYR A 307 88.63 87.73 REMARK 500 GLN A 311 159.88 69.36 REMARK 500 SEP A 385 -59.67 -5.27 REMARK 500 LYS A 428 42.12 37.62 REMARK 500 LEU A 462 -66.15 -96.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A -13 GLY A -12 140.87 REMARK 500 VAL A -11 ASP A -10 -142.93 REMARK 500 ARG A 305 VAL A 306 -52.74 REMARK 500 ARG A 305 VAL A 306 78.98 REMARK 500 SER A 398 ASP A 399 143.73 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 IRB A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 480 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3K2L RELATED DB: PDB REMARK 900 THE SAME PROTEIN, APO FORM REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS ENTRY USES SKIP NUMBERING TO CLARIFY THE EXPRESSION TAG REGION. DBREF 3KVW A 73 479 UNP Q92630 DYRK2_HUMAN 146 552 SEQADV 3KVW MET A -21 UNP Q92630 INITIATING METHIONINE SEQADV 3KVW HIS A -20 UNP Q92630 EXPRESSION TAG SEQADV 3KVW HIS A -19 UNP Q92630 EXPRESSION TAG SEQADV 3KVW HIS A -18 UNP Q92630 EXPRESSION TAG SEQADV 3KVW HIS A -17 UNP Q92630 EXPRESSION TAG SEQADV 3KVW HIS A -16 UNP Q92630 EXPRESSION TAG SEQADV 3KVW HIS A -15 UNP Q92630 EXPRESSION TAG SEQADV 3KVW SEP A -14 UNP Q92630 EXPRESSION TAG SEQADV 3KVW SER A -13 UNP Q92630 EXPRESSION TAG SEQADV 3KVW GLY A -12 UNP Q92630 EXPRESSION TAG SEQADV 3KVW VAL A -11 UNP Q92630 EXPRESSION TAG SEQADV 3KVW ASP A -10 UNP Q92630 EXPRESSION TAG SEQADV 3KVW LEU A -9 UNP Q92630 EXPRESSION TAG SEQADV 3KVW GLY A -8 UNP Q92630 EXPRESSION TAG SEQADV 3KVW THR A -7 UNP Q92630 EXPRESSION TAG SEQADV 3KVW GLU A -6 UNP Q92630 EXPRESSION TAG SEQADV 3KVW ASN A -5 UNP Q92630 EXPRESSION TAG SEQADV 3KVW LEU A -4 UNP Q92630 EXPRESSION TAG SEQADV 3KVW TYR A -3 UNP Q92630 EXPRESSION TAG SEQADV 3KVW PHE A -2 UNP Q92630 EXPRESSION TAG SEQADV 3KVW GLN A -1 UNP Q92630 EXPRESSION TAG SEQADV 3KVW SER A 0 UNP Q92630 EXPRESSION TAG SEQRES 1 A 429 MET HIS HIS HIS HIS HIS HIS SEP 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 3KVW SEP A -14 SER PHOSPHOSERINE MODRES 3KVW PTR A 309 TYR O-PHOSPHOTYROSINE MODRES 3KVW SEP A 385 SER PHOSPHOSERINE HET SEP A -14 10 HET PTR A 309 17 HET SEP A 385 10 HET IRB A 1 25 HET CL A 480 1 HET CL A 2 1 HET CL A 3 1 HET CL A 4 1 HETNAM SEP PHOSPHOSERINE HETNAM PTR O-PHOSPHOTYROSINE HETNAM IRB (2Z,3E)-7'-BROMO-3-(HYDROXYIMINO)-2'-OXO-1,1',2',3- HETNAM 2 IRB TETRAHYDRO-2,3'-BIINDOLE-5-CARBOXYLIC ACID HETNAM CL CHLORIDE ION HETSYN SEP PHOSPHONOSERINE HETSYN PTR PHOSPHONOTYROSINE HETSYN IRB INDIRUBIN-3'-MONOXIME DERIVATIVE, (2Z,3E)-7'-BROMO-3- HETSYN 2 IRB (HYDROXYIMINO)-2'-OXO-[2,3'-BIINDOLINYLIDENE]-5- HETSYN 3 IRB CARBOXYLIC ACID FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 1 PTR C9 H12 N O6 P FORMUL 2 IRB C17 H10 BR N3 O4 FORMUL 3 CL 4(CL 1-) FORMUL 7 HOH *107(H2 O) HELIX 1 1 ASP A -10 GLU A -6 5 5 HELIX 2 2 THR A 82 MET A 91 1 10 HELIX 3 3 GLN A 92 LEU A 94 5 3 HELIX 4 4 THR A 95 ILE A 102 1 8 HELIX 5 5 PHE A 103 TYR A 105 5 3 HELIX 6 6 GLY A 124 GLY A 129 1 6 HELIX 7 7 GLU A 183 LYS A 202 1 20 HELIX 8 8 ASN A 234 ASN A 242 1 9 HELIX 9 9 SER A 248 ARG A 270 1 23 HELIX 10 10 LYS A 277 GLU A 279 5 3 HELIX 11 11 SER A 312 ARG A 316 5 5 HELIX 12 12 ALA A 317 GLY A 323 1 7 HELIX 13 13 MET A 328 GLY A 345 1 18 HELIX 14 14 ASP A 353 GLY A 366 1 14 HELIX 15 15 SER A 369 ALA A 375 1 7 HELIX 16 16 ARG A 378 VAL A 383 1 6 HELIX 17 17 GLU A 422 LEU A 427 1 6 HELIX 18 18 ASP A 432 LEU A 443 1 12 HELIX 19 19 THR A 452 ARG A 458 1 7 SHEET 1 A 2 ASN A -5 PHE A -2 0 SHEET 2 A 2 VAL A 76 THR A 79 -1 O LYS A 77 N TYR A -3 SHEET 1 B 6 HIS A 144 VAL A 145 0 SHEET 2 B 6 TYR A 149 LYS A 157 -1 O TYR A 149 N VAL A 145 SHEET 3 B 6 GLY A 161 ASP A 168 -1 O TYR A 167 N GLU A 150 SHEET 4 B 6 GLN A 173 VAL A 180 -1 O VAL A 175 N ALA A 166 SHEET 5 B 6 HIS A 223 PHE A 228 -1 O MET A 226 N LYS A 178 SHEET 6 B 6 MET A 214 PHE A 220 -1 N LEU A 215 O THR A 227 SHEET 1 C 2 ILE A 271 ILE A 272 0 SHEET 2 C 2 CYS A 300 TYR A 301 -1 O CYS A 300 N ILE A 272 SHEET 1 D 2 ILE A 281 LEU A 283 0 SHEET 2 D 2 ILE A 291 VAL A 293 -1 O LYS A 292 N LEU A 282 SHEET 1 E 2 VAL A 394 THR A 395 0 SHEET 2 E 2 VAL A 403 LEU A 404 -1 O VAL A 403 N THR A 395 SHEET 1 F 2 GLY A 407 ARG A 408 0 SHEET 2 F 2 LEU A 414 ARG A 415 -1 O ARG A 415 N GLY A 407 LINK C HIS A -15 N SEP A -14 1555 1555 1.33 LINK C SEP A -14 N SER A -13 1555 1555 1.34 LINK C ATHR A 308 N APTR A 309 1555 1555 1.32 LINK C BTHR A 308 N BPTR A 309 1555 1555 1.34 LINK C PTR A 309 N ILE A 310 1555 1555 1.33 LINK C SER A 384 N SEP A 385 1555 1555 1.33 LINK C SEP A 385 N LYS A 386 1555 1555 1.34 SITE 1 AC1 12 ILE A 155 VAL A 163 ALA A 176 LYS A 178 SITE 2 AC1 12 PHE A 228 LEU A 230 LEU A 231 SER A 232 SITE 3 AC1 12 ILE A 294 ASP A 295 HOH A 508 HOH A 509 SITE 1 AC2 3 SEP A -14 TYR A 167 HIS A 172 SITE 1 AC3 2 SEP A -14 HIS A 174 SITE 1 AC4 3 HOH A 38 ARG A 421 ALA A 426 CRYST1 84.280 84.280 149.120 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 0.011865 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006706 0.00000