PDB Short entry for 6NCG HEADER TRANSFERASE 11-DEC-18 6NCG TITLE CRYSTAL STRUCTURE OF HUMAN VACCINIA-RELATED KINASE 2 (VRK-2) BOUND TO TITLE 2 PYRIDIN-BENZENESULFONAMIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE VRK2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 14-335; COMPND 5 SYNONYM: VACCINIA-RELATED KINASE 2; 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: VRK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS TRANSFERASE, PROTEIN KINASE DOMAIN, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.V.DOS REIS,C.G.CHIODI,G.P.DE SOUZA,C.GUIMARAES,A.MASCARELLO,F.GAMA, AUTHOR 2 M.FERREIRA,R.M.COUNAGO,K.B.MASSIRER,J.M.ELKINS,P.ARRUDA,A.M.EDWARDS, AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 01-JAN-20 6NCG 1 REMARK REVDAT 1 16-JAN-19 6NCG 0 JRNL AUTH C.V.DOS REIS,C.G.CHIODI,G.P.DE SOUZA,H.AZEVEDO,C.GUIMARAES, JRNL AUTH 2 A.MASCARELLO,F.GAMA,M.FERREIRA,R.M.COUNAGO,K.B.MASSIRER, JRNL AUTH 3 P.ARRUDA,J.M.ELKINS,A.M.EDWARDS, JRNL AUTH 4 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF HUMAN VACCINIA-RELATED KINASE 2 (VRK-2) JRNL TITL 2 BOUND TO PYRIDIN-BENZENESULFONAMIDE INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0218 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22794 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1241 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1680 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4466 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.63000 REMARK 3 B22 (A**2) : 11.70000 REMARK 3 B33 (A**2) : -7.08000 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): 0.553 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.332 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.393 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.890 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4631 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4116 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6305 ; 1.199 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9466 ; 0.779 ; 2.995 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 586 ; 5.043 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;28.996 ;24.022 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 683 ;14.575 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;13.401 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 696 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5191 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 943 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2374 ; 3.925 ; 6.918 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2373 ; 3.925 ; 6.917 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2950 ; 6.337 ;10.347 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2951 ; 6.336 ;10.349 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2257 ; 3.800 ; 6.982 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2254 ; 3.800 ; 6.962 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3350 ; 6.086 ;10.370 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 18759 ;11.299 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 18760 ;11.298 ; 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 : 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 6NCG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1000238550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979100 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24095 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 29.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.30 REMARK 200 R MERGE FOR SHELL (I) : 1.77300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5UU1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27.5% PEG3350; 200 MM LISO4; 0.1M SBG REMARK 280 (EACH SODIUM-TARTRATE + BIS-TRIS + GLYCYLGLYCINE) PH 6.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 27.26400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.67300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.81250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.67300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.26400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.81250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 12 REMARK 465 MET A 13 REMARK 465 GLY A 38 REMARK 465 GLY A 39 REMARK 465 GLU A 53 REMARK 465 GLY A 133 REMARK 465 GLN A 134 REMARK 465 THR A 327 REMARK 465 LYS A 328 REMARK 465 GLY A 329 REMARK 465 GLN A 330 REMARK 465 SER A 331 REMARK 465 ILE A 332 REMARK 465 ASN A 333 REMARK 465 VAL A 334 REMARK 465 HIS A 335 REMARK 465 SER B 12 REMARK 465 MET B 13 REMARK 465 PRO B 14 REMARK 465 PHE B 15 REMARK 465 GLY B 38 REMARK 465 GLY B 39 REMARK 465 PRO B 52 REMARK 465 GLU B 53 REMARK 465 TYR B 64 REMARK 465 GLN B 65 REMARK 465 GLU B 66 REMARK 465 LYS B 112 REMARK 465 GLY B 113 REMARK 465 ASN B 196 REMARK 465 GLY B 197 REMARK 465 ASN B 198 REMARK 465 HIS B 199 REMARK 465 LYS B 200 REMARK 465 GLN B 201 REMARK 465 TYR B 202 REMARK 465 GLN B 203 REMARK 465 GLU B 204 REMARK 465 ASN B 205 REMARK 465 PRO B 206 REMARK 465 ARG B 207 REMARK 465 LYS B 208 REMARK 465 GLY B 209 REMARK 465 HIS B 210 REMARK 465 THR B 327 REMARK 465 LYS B 328 REMARK 465 GLY B 329 REMARK 465 GLN B 330 REMARK 465 SER B 331 REMARK 465 ILE B 332 REMARK 465 ASN B 333 REMARK 465 VAL B 334 REMARK 465 HIS B 335 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 PHE A 15 CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 20 CG1 CG2 REMARK 470 GLU A 25 CG CD OE1 OE2 REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 PHE A 40 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 50 CG OD1 ND2 REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 TYR A 64 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 65 CG CD OE1 NE2 REMARK 470 GLU A 66 CG CD OE1 OE2 REMARK 470 ASN A 67 CG OD1 ND2 REMARK 470 LEU A 70 CG CD1 CD2 REMARK 470 PHE A 71 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 75 CG CD CE NZ REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 GLU A 91 CG CD OE1 OE2 REMARK 470 ARG A 92 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 GLN A 94 CG CD OE1 NE2 REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 PHE A 111 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 ARG A 114 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 130 CG CD CE NZ REMARK 470 LYS A 139 CG CD CE NZ REMARK 470 LYS A 177 CG CD CE NZ REMARK 470 LEU A 189 CG CD1 CD2 REMARK 470 GLN A 203 CG CD OE1 NE2 REMARK 470 ARG A 207 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 208 CG CD CE NZ REMARK 470 GLN A 252 CG CD OE1 NE2 REMARK 470 ASN A 253 CG OD1 ND2 REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 ASP A 269 CG OD1 OD2 REMARK 470 GLN A 307 CG CD OE1 NE2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 LYS B 19 CG CD CE NZ REMARK 470 ASP B 22 CG OD1 OD2 REMARK 470 GLN B 28 CG CD OE1 NE2 REMARK 470 VAL B 30 CG1 CG2 REMARK 470 LYS B 33 CG CD CE NZ REMARK 470 LYS B 34 CG CD CE NZ REMARK 470 PHE B 40 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 42 CG CD1 CD2 REMARK 470 THR B 49 OG1 CG2 REMARK 470 ASN B 50 CG OD1 ND2 REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 LYS B 54 CG CD CE NZ REMARK 470 ASN B 67 CG OD1 ND2 REMARK 470 LEU B 70 CG CD1 CD2 REMARK 470 PHE B 71 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 83 CG CD CE NZ REMARK 470 LYS B 87 CG CD CE NZ REMARK 470 LYS B 88 CG CD CE NZ REMARK 470 LYS B 93 CG CD CE NZ REMARK 470 SER B 106 OG REMARK 470 GLU B 110 CG CD OE1 OE2 REMARK 470 PHE B 111 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER B 132 OG REMARK 470 GLN B 134 CG CD OE1 NE2 REMARK 470 ASN B 135 CG OD1 ND2 REMARK 470 LYS B 177 CG CD CE NZ REMARK 470 ASP B 180 CG OD1 OD2 REMARK 470 CYS B 194 SG REMARK 470 ASN B 211 CG OD1 ND2 REMARK 470 LYS B 247 CG CD CE NZ REMARK 470 GLU B 251 CG CD OE1 OE2 REMARK 470 GLN B 252 CG CD OE1 NE2 REMARK 470 ASN B 253 CG OD1 ND2 REMARK 470 LYS B 255 CG CD CE NZ REMARK 470 SER B 284 OG REMARK 470 LYS B 311 CG CD CE NZ REMARK 470 HIS B 316 CG ND1 CD2 CE1 NE2 REMARK 470 LEU B 320 CG CD1 CD2 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 ILE A 35 41.93 -101.11 REMARK 500 GLN A 65 -165.85 -162.79 REMARK 500 LYS A 112 -128.79 54.99 REMARK 500 ASP A 186 62.42 60.55 REMARK 500 TYR A 187 23.63 -76.78 REMARK 500 LYS A 208 47.52 -93.06 REMARK 500 GLN B 134 -123.69 56.74 REMARK 500 ASP B 166 37.34 -158.48 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 KJD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KJD B 600 DBREF 6NCG A 14 335 UNP Q86Y07 VRK2_HUMAN 14 335 DBREF 6NCG B 14 335 UNP Q86Y07 VRK2_HUMAN 14 335 SEQADV 6NCG SER A 12 UNP Q86Y07 EXPRESSION TAG SEQADV 6NCG MET A 13 UNP Q86Y07 EXPRESSION TAG SEQADV 6NCG SER B 12 UNP Q86Y07 EXPRESSION TAG SEQADV 6NCG MET B 13 UNP Q86Y07 EXPRESSION TAG SEQRES 1 A 324 SER MET PRO PHE PRO GLU GLY LYS VAL LEU ASP ASP MET SEQRES 2 A 324 GLU GLY ASN GLN TRP VAL LEU GLY LYS LYS ILE GLY SER SEQRES 3 A 324 GLY GLY PHE GLY LEU ILE TYR LEU ALA PHE PRO THR ASN SEQRES 4 A 324 LYS PRO GLU LYS ASP ALA ARG HIS VAL VAL LYS VAL GLU SEQRES 5 A 324 TYR GLN GLU ASN GLY PRO LEU PHE SER GLU LEU LYS PHE SEQRES 6 A 324 TYR GLN ARG VAL ALA LYS LYS ASP CYS ILE LYS LYS TRP SEQRES 7 A 324 ILE GLU ARG LYS GLN LEU ASP TYR LEU GLY ILE PRO LEU SEQRES 8 A 324 PHE TYR GLY SER GLY LEU THR GLU PHE LYS GLY ARG SER SEQRES 9 A 324 TYR ARG PHE MET VAL MET GLU ARG LEU GLY ILE ASP LEU SEQRES 10 A 324 GLN LYS ILE SER GLY GLN ASN GLY THR PHE LYS LYS SER SEQRES 11 A 324 THR VAL LEU GLN LEU GLY ILE ARG MET LEU ASP VAL LEU SEQRES 12 A 324 GLU TYR ILE HIS GLU ASN GLU TYR VAL HIS GLY ASP ILE SEQRES 13 A 324 LYS ALA ALA ASN LEU LEU LEU GLY TYR LYS ASN PRO ASP SEQRES 14 A 324 GLN VAL TYR LEU ALA ASP TYR GLY LEU SER TYR ARG TYR SEQRES 15 A 324 CYS PRO ASN GLY ASN HIS LYS GLN TYR GLN GLU ASN PRO SEQRES 16 A 324 ARG LYS GLY HIS ASN GLY THR ILE GLU PHE THR SER LEU SEQRES 17 A 324 ASP ALA HIS LYS GLY VAL ALA LEU SER ARG ARG SER ASP SEQRES 18 A 324 VAL GLU ILE LEU GLY TYR CYS MET LEU ARG TRP LEU CYS SEQRES 19 A 324 GLY LYS LEU PRO TRP GLU GLN ASN LEU LYS ASP PRO VAL SEQRES 20 A 324 ALA VAL GLN THR ALA LYS THR ASN LEU LEU ASP GLU LEU SEQRES 21 A 324 PRO GLN SER VAL LEU LYS TRP ALA PRO SER GLY SER SER SEQRES 22 A 324 CYS CYS GLU ILE ALA GLN PHE LEU VAL CYS ALA HIS SER SEQRES 23 A 324 LEU ALA TYR ASP GLU LYS PRO ASN TYR GLN ALA LEU LYS SEQRES 24 A 324 LYS ILE LEU ASN PRO HIS GLY ILE PRO LEU GLY PRO LEU SEQRES 25 A 324 ASP PHE SER THR LYS GLY GLN SER ILE ASN VAL HIS SEQRES 1 B 324 SER MET PRO PHE PRO GLU GLY LYS VAL LEU ASP ASP MET SEQRES 2 B 324 GLU GLY ASN GLN TRP VAL LEU GLY LYS LYS ILE GLY SER SEQRES 3 B 324 GLY GLY PHE GLY LEU ILE TYR LEU ALA PHE PRO THR ASN SEQRES 4 B 324 LYS PRO GLU LYS ASP ALA ARG HIS VAL VAL LYS VAL GLU SEQRES 5 B 324 TYR GLN GLU ASN GLY PRO LEU PHE SER GLU LEU LYS PHE SEQRES 6 B 324 TYR GLN ARG VAL ALA LYS LYS ASP CYS ILE LYS LYS TRP SEQRES 7 B 324 ILE GLU ARG LYS GLN LEU ASP TYR LEU GLY ILE PRO LEU SEQRES 8 B 324 PHE TYR GLY SER GLY LEU THR GLU PHE LYS GLY ARG SER SEQRES 9 B 324 TYR ARG PHE MET VAL MET GLU ARG LEU GLY ILE ASP LEU SEQRES 10 B 324 GLN LYS ILE SER GLY GLN ASN GLY THR PHE LYS LYS SER SEQRES 11 B 324 THR VAL LEU GLN LEU GLY ILE ARG MET LEU ASP VAL LEU SEQRES 12 B 324 GLU TYR ILE HIS GLU ASN GLU TYR VAL HIS GLY ASP ILE SEQRES 13 B 324 LYS ALA ALA ASN LEU LEU LEU GLY TYR LYS ASN PRO ASP SEQRES 14 B 324 GLN VAL TYR LEU ALA ASP TYR GLY LEU SER TYR ARG TYR SEQRES 15 B 324 CYS PRO ASN GLY ASN HIS LYS GLN TYR GLN GLU ASN PRO SEQRES 16 B 324 ARG LYS GLY HIS ASN GLY THR ILE GLU PHE THR SER LEU SEQRES 17 B 324 ASP ALA HIS LYS GLY VAL ALA LEU SER ARG ARG SER ASP SEQRES 18 B 324 VAL GLU ILE LEU GLY TYR CYS MET LEU ARG TRP LEU CYS SEQRES 19 B 324 GLY LYS LEU PRO TRP GLU GLN ASN LEU LYS ASP PRO VAL SEQRES 20 B 324 ALA VAL GLN THR ALA LYS THR ASN LEU LEU ASP GLU LEU SEQRES 21 B 324 PRO GLN SER VAL LEU LYS TRP ALA PRO SER GLY SER SER SEQRES 22 B 324 CYS CYS GLU ILE ALA GLN PHE LEU VAL CYS ALA HIS SER SEQRES 23 B 324 LEU ALA TYR ASP GLU LYS PRO ASN TYR GLN ALA LEU LYS SEQRES 24 B 324 LYS ILE LEU ASN PRO HIS GLY ILE PRO LEU GLY PRO LEU SEQRES 25 B 324 ASP PHE SER THR LYS GLY GLN SER ILE ASN VAL HIS HET KJD A 401 26 HET SO4 A 402 5 HET KJD B 600 26 HETNAM KJD 4-[6-AMINO-5-(3,5-DIFLUORO-4-HYDROXYPHENYL)PYRIDIN-3- HETNAM 2 KJD YL]BENZENE-1-SULFONAMIDE HETNAM SO4 SULFATE ION FORMUL 3 KJD 2(C17 H13 F2 N3 O3 S) FORMUL 4 SO4 O4 S 2- FORMUL 6 HOH *41(H2 O) HELIX 1 AA1 PRO A 69 ALA A 81 1 13 HELIX 2 AA2 LYS A 82 GLN A 94 1 13 HELIX 3 AA3 LEU A 128 SER A 132 1 5 HELIX 4 AA4 LYS A 139 ASN A 160 1 22 HELIX 5 AA5 LYS A 168 ALA A 170 5 3 HELIX 6 AA6 ASP A 186 SER A 190 5 5 HELIX 7 AA7 CYS A 194 ASN A 198 5 5 HELIX 8 AA8 SER A 218 LYS A 223 1 6 HELIX 9 AA9 SER A 228 GLY A 246 1 19 HELIX 10 AB1 LEU A 248 LEU A 254 5 7 HELIX 11 AB2 ASP A 256 GLU A 270 1 15 HELIX 12 AB3 PRO A 272 ALA A 279 1 8 HELIX 13 AB4 CYS A 285 SER A 297 1 13 HELIX 14 AB5 ASN A 305 ASN A 314 1 10 HELIX 15 AB6 PRO B 69 ALA B 81 1 13 HELIX 16 AB7 LYS B 82 GLN B 94 1 13 HELIX 17 AB8 LEU B 128 SER B 132 1 5 HELIX 18 AB9 LYS B 139 ASN B 160 1 22 HELIX 19 AC1 LYS B 168 ALA B 170 5 3 HELIX 20 AC2 SER B 218 LYS B 223 1 6 HELIX 21 AC3 SER B 228 GLY B 246 1 19 HELIX 22 AC4 LEU B 248 LEU B 254 5 7 HELIX 23 AC5 ASP B 256 GLU B 270 1 15 HELIX 24 AC6 PRO B 272 ALA B 279 1 8 HELIX 25 AC7 CYS B 285 SER B 297 1 13 HELIX 26 AC8 ASN B 305 ASN B 314 1 10 SHEET 1 AA1 6 VAL A 20 ASP A 22 0 SHEET 2 AA1 6 GLN A 28 LYS A 34 -1 O TRP A 29 N LEU A 21 SHEET 3 AA1 6 LEU A 42 PRO A 48 -1 O PHE A 47 N VAL A 30 SHEET 4 AA1 6 HIS A 58 VAL A 62 -1 O VAL A 60 N TYR A 44 SHEET 5 AA1 6 ARG A 114 GLU A 122 -1 O MET A 119 N LYS A 61 SHEET 6 AA1 6 PHE A 103 PHE A 111 -1 N TYR A 104 O VAL A 120 SHEET 1 AA2 3 LEU A 124 ASP A 127 0 SHEET 2 AA2 3 LEU A 172 GLY A 175 -1 O LEU A 174 N GLY A 125 SHEET 3 AA2 3 VAL A 182 LEU A 184 -1 O TYR A 183 N LEU A 173 SHEET 1 AA3 7 VAL B 20 ASP B 23 0 SHEET 2 AA3 7 GLN B 28 GLY B 36 -1 O TRP B 29 N LEU B 21 SHEET 3 AA3 7 LEU B 42 PRO B 48 -1 O PHE B 47 N VAL B 30 SHEET 4 AA3 7 HIS B 58 VAL B 62 -1 O VAL B 60 N TYR B 44 SHEET 5 AA3 7 TYR B 116 GLU B 122 -1 O MET B 121 N VAL B 59 SHEET 6 AA3 7 PHE B 103 THR B 109 -1 N TYR B 104 O VAL B 120 SHEET 7 AA3 7 VAL B 20 ASP B 23 -1 N ASP B 22 O LEU B 108 SHEET 1 AA4 3 LEU B 124 ASP B 127 0 SHEET 2 AA4 3 LEU B 172 GLY B 175 -1 O LEU B 174 N GLY B 125 SHEET 3 AA4 3 VAL B 182 LEU B 184 -1 O TYR B 183 N LEU B 173 SHEET 1 AA5 2 TYR B 162 VAL B 163 0 SHEET 2 AA5 2 TYR B 191 ARG B 192 -1 O TYR B 191 N VAL B 163 CISPEP 1 LEU A 271 PRO A 272 0 -6.00 CISPEP 2 LEU B 271 PRO B 272 0 -0.58 SITE 1 AC1 10 ILE A 35 ILE A 43 GLU A 73 TYR A 77 SITE 2 AC1 10 MET A 121 GLU A 122 LEU A 124 ALA A 185 SITE 3 AC1 10 ASP A 186 ARG B 114 SITE 1 AC2 7 ARG A 230 GLU A 234 ALA A 295 HIS A 296 SITE 2 AC2 7 HOH A 501 HOH A 503 SER B 281 SITE 1 AC3 12 ILE B 35 ILE B 43 VAL B 59 LYS B 61 SITE 2 AC3 12 GLU B 73 TYR B 77 MET B 121 GLU B 122 SITE 3 AC3 12 LEU B 124 GLY B 125 LYS B 130 ALA B 185 CRYST1 54.528 67.625 171.346 90.00 90.00 90.00 P 21 21 21 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 0.018339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005836 0.00000