PDB Short entry for 2KUL HEADER TRANSFERASE 19-FEB-10 2KUL TITLE SOLUTION STRUCTURE OF HUMAN VACCINIA RELATED KINASE 1(VRK1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE VRK1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-360; COMPND 5 SYNONYM: VACCINIA-RELATED KINASE 1; COMPND 6 EC: 2.7.11.1; 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: VRK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET29B KEYWDS VRK1, VACCINIA RELATED KINASE, ATP-BINDING, KINASE, NUCLEOTIDE- KEYWDS 2 BINDING, SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.SHIN,H.YOON REVDAT 3 14-JUN-23 2KUL 1 REMARK REVDAT 2 26-FEB-20 2KUL 1 REMARK SEQADV REVDAT 1 23-FEB-11 2KUL 0 JRNL AUTH J.SHIN,H.YOON JRNL TITL SOLUTION STRUCTURE OF HUMAN VACCINIA RELATED KINASE 1(VRK1) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CNS 1.1 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN EXPLICIT WATER USING CNS REMARK 3 1.1 REMARK 4 REMARK 4 2KUL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000101591. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 0.3-0.5MM [U-100% 13C; U-100% REMARK 210 15N; U-80% 2H] VACCINIA RELATED- REMARK 210 KINASE 1; 0.3-0.5MM [U-100% 15N; REMARK 210 U-50% 2H] VACCINIA RELATED- REMARK 210 KINASE 1; 0.1-0.2MM [U-100% 15N] REMARK 210 VACCINIA RELATED-KINASE 1; 90% REMARK 210 H2O/10% D2O; 0.3-0.5MM [U-100% REMARK 210 13C; U-100% 15N; U-70% 2H] REMARK 210 VACCINIA RELATED-KINASE 1; 0.3- REMARK 210 0.5MM [13C;15N]-VAL,ILE,LEU; [U- REMARK 210 100% 2H] VACCINIA RELATED-KINASE REMARK 210 1; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HN(COCA)CB; 3D HNCO; 3D HN(CO)CA; REMARK 210 3D HN(CA)CO; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 LEU A 361 REMARK 465 GLU A 362 REMARK 465 HIS A 363 REMARK 465 HIS A 364 REMARK 465 HIS A 365 REMARK 465 HIS A 366 REMARK 465 HIS A 367 REMARK 465 HIS A 368 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HE1 TYR A 87 HG2 PRO A 111 1.21 REMARK 500 HG2 GLU A 73 HB2 LEU A 80 1.31 REMARK 500 HG3 ARG A 241 HA TYR A 311 1.35 REMARK 500 O LEU A 285 HG CYS A 289 1.56 REMARK 500 HH12 ARG A 103 OE2 GLU A 170 1.58 REMARK 500 HZ2 LYS A 35 OD2 ASP A 65 1.59 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 1 ALA A 6 108.62 179.67 REMARK 500 1 GLN A 8 109.69 -178.71 REMARK 500 1 ARG A 11 79.46 -157.64 REMARK 500 1 ALA A 15 80.09 -157.98 REMARK 500 1 GLU A 21 -63.00 69.16 REMARK 500 1 GLN A 22 -71.98 -66.21 REMARK 500 1 ALA A 24 -63.73 179.38 REMARK 500 1 PHE A 48 -59.02 177.93 REMARK 500 1 MET A 56 173.99 63.21 REMARK 500 1 GLU A 60 -55.56 -144.82 REMARK 500 1 ASN A 77 105.49 68.63 REMARK 500 1 SER A 116 147.82 -171.27 REMARK 500 1 HIS A 171 -65.07 -97.49 REMARK 500 1 GLU A 172 -44.31 -162.05 REMARK 500 1 ASN A 189 80.78 -159.57 REMARK 500 1 ASP A 197 65.49 68.74 REMARK 500 1 LEU A 200 36.38 -88.78 REMARK 500 1 GLU A 207 -63.96 70.31 REMARK 500 1 LYS A 211 -88.44 -81.04 REMARK 500 1 GLU A 212 139.45 173.05 REMARK 500 1 LYS A 214 33.15 -155.24 REMARK 500 1 LYS A 218 -56.21 -156.03 REMARK 500 1 CYS A 220 -60.08 -134.32 REMARK 500 1 HIS A 221 96.85 52.98 REMARK 500 1 SER A 229 -174.04 62.49 REMARK 500 1 ASP A 231 -72.65 -49.69 REMARK 500 1 SER A 239 -159.95 -85.47 REMARK 500 1 LYS A 266 14.07 -157.22 REMARK 500 1 GLU A 292 -82.66 -159.59 REMARK 500 1 LYS A 293 29.67 -144.13 REMARK 500 1 PRO A 296 37.90 -98.85 REMARK 500 1 ASP A 310 -96.96 68.48 REMARK 500 1 TYR A 311 -38.10 -136.89 REMARK 500 1 THR A 312 29.17 -158.38 REMARK 500 1 GLU A 313 -71.46 -68.21 REMARK 500 1 LYS A 338 78.10 58.30 REMARK 500 1 LEU A 339 -169.66 65.36 REMARK 500 1 LEU A 349 -162.73 -114.10 REMARK 500 1 LYS A 357 -50.55 -168.00 REMARK 500 2 SER A 14 29.99 -154.74 REMARK 500 2 ALA A 20 -82.75 -171.04 REMARK 500 2 PHE A 23 84.15 -169.37 REMARK 500 2 ALA A 24 -162.49 -176.22 REMARK 500 2 LYS A 34 36.12 71.07 REMARK 500 2 PHE A 48 -79.08 171.71 REMARK 500 2 CYS A 50 76.48 65.52 REMARK 500 2 ALA A 54 36.93 -93.39 REMARK 500 2 SER A 61 86.85 -66.77 REMARK 500 2 ALA A 66 91.80 60.76 REMARK 500 2 PRO A 74 -171.45 -63.38 REMARK 500 REMARK 500 THIS ENTRY HAS 878 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KTY RELATED DB: PDB REMARK 900 THE SAME PROTEIN REFINED BY CYANA REMARK 900 RELATED ID: 16738 RELATED DB: BMRB DBREF 2KUL A 1 360 UNP Q99986 VRK1_HUMAN 1 360 SEQADV 2KUL LEU A 361 UNP Q99986 EXPRESSION TAG SEQADV 2KUL GLU A 362 UNP Q99986 EXPRESSION TAG SEQADV 2KUL HIS A 363 UNP Q99986 EXPRESSION TAG SEQADV 2KUL HIS A 364 UNP Q99986 EXPRESSION TAG SEQADV 2KUL HIS A 365 UNP Q99986 EXPRESSION TAG SEQADV 2KUL HIS A 366 UNP Q99986 EXPRESSION TAG SEQADV 2KUL HIS A 367 UNP Q99986 EXPRESSION TAG SEQADV 2KUL HIS A 368 UNP Q99986 EXPRESSION TAG SEQRES 1 A 368 MET PRO ARG VAL LYS ALA ALA GLN ALA GLY ARG GLN SER SEQRES 2 A 368 SER ALA LYS ARG HIS LEU ALA GLU GLN PHE ALA VAL GLY SEQRES 3 A 368 GLU ILE ILE THR ASP MET ALA LYS LYS GLU TRP LYS VAL SEQRES 4 A 368 GLY LEU PRO ILE GLY GLN GLY GLY PHE GLY CYS ILE TYR SEQRES 5 A 368 LEU ALA ASP MET ASN SER SER GLU SER VAL GLY SER ASP SEQRES 6 A 368 ALA PRO CYS VAL VAL LYS VAL GLU PRO SER ASP ASN GLY SEQRES 7 A 368 PRO LEU PHE THR GLU LEU LYS PHE TYR GLN ARG ALA ALA SEQRES 8 A 368 LYS PRO GLU GLN ILE GLN LYS TRP ILE ARG THR ARG LYS SEQRES 9 A 368 LEU LYS TYR LEU GLY VAL PRO LYS TYR TRP GLY SER GLY SEQRES 10 A 368 LEU HIS ASP LYS ASN GLY LYS SER TYR ARG PHE MET ILE SEQRES 11 A 368 MET ASP ARG PHE GLY SER ASP LEU GLN LYS ILE TYR GLU SEQRES 12 A 368 ALA ASN ALA LYS ARG PHE SER ARG LYS THR VAL LEU GLN SEQRES 13 A 368 LEU SER LEU ARG ILE LEU ASP ILE LEU GLU TYR ILE HIS SEQRES 14 A 368 GLU HIS GLU TYR VAL HIS GLY ASP ILE LYS ALA SER ASN SEQRES 15 A 368 LEU LEU LEU ASN TYR LYS ASN PRO ASP GLN VAL TYR LEU SEQRES 16 A 368 VAL ASP TYR GLY LEU ALA TYR ARG TYR CYS PRO GLU GLY SEQRES 17 A 368 VAL HIS LYS GLU TYR LYS GLU ASP PRO LYS ARG CYS HIS SEQRES 18 A 368 ASP GLY THR ILE GLU PHE THR SER ILE ASP ALA HIS ASN SEQRES 19 A 368 GLY VAL ALA PRO SER ARG ARG GLY ASP LEU GLU ILE LEU SEQRES 20 A 368 GLY TYR CYS MET ILE GLN TRP LEU THR GLY HIS LEU PRO SEQRES 21 A 368 TRP GLU ASP ASN LEU LYS ASP PRO LYS TYR VAL ARG ASP SEQRES 22 A 368 SER LYS ILE ARG TYR ARG GLU ASN ILE ALA SER LEU MET SEQRES 23 A 368 ASP LYS CYS PHE PRO GLU LYS ASN LYS PRO GLY GLU ILE SEQRES 24 A 368 ALA LYS TYR MET GLU THR VAL LYS LEU LEU ASP TYR THR SEQRES 25 A 368 GLU LYS PRO LEU TYR GLU ASN LEU ARG ASP ILE LEU LEU SEQRES 26 A 368 GLN GLY LEU LYS ALA ILE GLY SER LYS ASP ASP GLY LYS SEQRES 27 A 368 LEU ASP LEU SER VAL VAL GLU ASN GLY GLY LEU LYS ALA SEQRES 28 A 368 LYS THR ILE THR LYS LYS ARG LYS LYS LEU GLU HIS HIS SEQRES 29 A 368 HIS HIS HIS HIS HELIX 1 1 PRO A 79 ALA A 91 1 13 HELIX 2 2 LYS A 92 ARG A 103 1 12 HELIX 3 3 LEU A 138 ASN A 145 1 8 HELIX 4 4 SER A 150 GLU A 170 1 21 HELIX 5 5 LYS A 179 SER A 181 5 3 HELIX 6 6 ASP A 197 ALA A 201 5 5 HELIX 7 7 THR A 228 GLY A 235 1 8 HELIX 8 8 SER A 239 GLY A 257 1 19 HELIX 9 9 ASP A 267 ASN A 281 1 15 HELIX 10 10 ASN A 281 LYS A 288 1 8 HELIX 11 11 PRO A 296 LEU A 309 1 14 HELIX 12 12 LEU A 316 ILE A 331 1 16 SHEET 1 A 6 ILE A 28 THR A 30 0 SHEET 2 A 6 GLU A 36 PRO A 42 -1 O TRP A 37 N ILE A 29 SHEET 3 A 6 TYR A 52 ALA A 54 -1 O LEU A 53 N GLY A 40 SHEET 4 A 6 CYS A 68 PRO A 74 -1 O VAL A 70 N TYR A 52 SHEET 5 A 6 LYS A 124 ASP A 132 -1 O ARG A 127 N GLU A 73 SHEET 6 A 6 SER A 116 LYS A 121 -1 N HIS A 119 O TYR A 126 SHEET 1 B 3 PHE A 134 ASP A 137 0 SHEET 2 B 3 LEU A 183 ASN A 186 -1 O LEU A 185 N SER A 136 SHEET 3 B 3 ASN A 189 LEU A 195 -1 O TYR A 194 N LEU A 184 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000