PDB Short entry for 2JAV HEADER TRANSFERASE 30-NOV-06 2JAV TITLE HUMAN KINASE WITH PYRROLE-INDOLINONE LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE NEK2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 1-271; COMPND 5 SYNONYM: NIMA-RELATED PROTEIN KINASE 2, NIMA-LIKE PROTEIN KINASE 1, COMPND 6 HSPK 21, NEVER IN MITOSIS GENE A-RELATED KINASE 2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS TRANSFERASE, PHOSPHORYLATION, NUCLEOTIDE-BINDING, ATP-BINDING, CELL KEYWDS 2 DIVISION, METAL-BINDING, NUCLEAR PROTEIN, SERINE/THREONINE-PROTEIN KEYWDS 3 KINASE, SERINE/THREONINE PROTEIN KINASE, KINASE, MEIOSIS, MITOSIS, KEYWDS 4 MAGNESIUM, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR A.C.W.PIKE,P.RELLOS,S.DAS,O.FEDOROV,E.PAPAGRIGORIOU,J.E.DEBRECZENI, AUTHOR 2 A.P.TURNBULL,F.GORREC,J.BRAY,M.SUNDSTROM,C.H.ARROWSMITH,A.EDWARDS, AUTHOR 3 J.WEIGELT,F.VON DELFT,S.KNAPP REVDAT 7 13-DEC-23 2JAV 1 REMARK REVDAT 6 08-MAY-19 2JAV 1 REMARK REVDAT 5 24-JAN-18 2JAV 1 AUTHOR REVDAT 4 13-JUL-11 2JAV 1 VERSN REVDAT 3 24-FEB-09 2JAV 1 VERSN REVDAT 2 06-MAR-07 2JAV 1 JRNL REVDAT 1 04-DEC-06 2JAV 0 SPRSDE 04-DEC-06 2JAV 2CL1 JRNL AUTH P.RELLOS,F.J.IVINS,J.E.BAXTER,A.C.W.PIKE,T.J.NOTT, JRNL AUTH 2 D.-M.PARKINSON,S.DAS,S.HOWELL,O.FEDOROV,Q.Y.SHEN,A.M.FRY, JRNL AUTH 3 S.KNAPP,S.J.SMERDON JRNL TITL STRUCTURE AND REGULATION OF THE HUMAN NEK2 CENTROSOMAL JRNL TITL 2 KINASE JRNL REF J.BIOL.CHEM. V. 282 6833 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17197699 JRNL DOI 10.1074/JBC.M609721200 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14883 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 796 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1019 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2014 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 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) : 32.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.93000 REMARK 3 B22 (A**2) : -1.95000 REMARK 3 B33 (A**2) : 0.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.77000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.286 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.237 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.164 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.818 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2119 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2858 ; 1.225 ; 1.980 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 249 ; 5.514 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;34.673 ;23.204 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 380 ;16.232 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.300 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 304 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1604 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 932 ; 0.187 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1423 ; 0.295 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 117 ; 0.136 ; 0.200 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): 34 ; 0.168 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.177 ; 0.200 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): 1297 ; 0.552 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2019 ; 0.895 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 970 ; 1.238 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 839 ; 1.922 ; 4.500 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 : 2 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 3 A 90 REMARK 3 ORIGIN FOR THE GROUP (A): -3.9591 2.2859 10.5005 REMARK 3 T TENSOR REMARK 3 T11: 0.4429 T22: 0.0551 REMARK 3 T33: 0.1932 T12: 0.0085 REMARK 3 T13: -0.3760 T23: -0.1895 REMARK 3 L TENSOR REMARK 3 L11: 13.4988 L22: 4.4903 REMARK 3 L33: 4.6756 L12: -3.1466 REMARK 3 L13: 4.8513 L23: -1.4348 REMARK 3 S TENSOR REMARK 3 S11: 1.0386 S12: 1.6194 S13: -1.5073 REMARK 3 S21: -1.4248 S22: -0.4728 S23: 0.6732 REMARK 3 S31: 0.7313 S32: 0.2933 S33: -0.5658 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 91 A 279 REMARK 3 ORIGIN FOR THE GROUP (A): 12.8160 19.1608 22.8707 REMARK 3 T TENSOR REMARK 3 T11: -0.1575 T22: -0.1417 REMARK 3 T33: -0.2082 T12: 0.0032 REMARK 3 T13: 0.0174 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 2.5486 L22: 4.3558 REMARK 3 L33: 2.0580 L12: 0.0526 REMARK 3 L13: 0.0378 L23: 0.2130 REMARK 3 S TENSOR REMARK 3 S11: 0.0445 S12: 0.3536 S13: 0.0935 REMARK 3 S21: -0.5251 S22: -0.0189 S23: 0.0503 REMARK 3 S31: -0.0078 S32: -0.0305 S33: -0.0256 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.DIETHYLAMINO TAIL OF LIGAND IS DISORDERED AND HAS NOT REMARK 3 BEEN INCLUDED IN THE FINAL MODEL. REMARK 4 REMARK 4 2JAV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1290030685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15620 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 65.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 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: PDB ENTRY 1OL7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG6000, 200 MM MGCL2. SITTING REMARK 280 DROPS, 150NL AND 50NL PROTEIN AND RESERVOIR MIX., VAPOR REMARK 280 DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.46200 REMARK 290 SMTRY3 2 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, THR 175 TO ALA 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 PRO A 2 REMARK 465 ARG A 77 REMARK 465 THR A 78 REMARK 465 ASN A 79 REMARK 465 THR A 80 REMARK 465 ASP A 132 REMARK 465 GLY A 133 REMARK 465 GLY A 134 REMARK 465 HIS A 135 REMARK 465 THR A 136 REMARK 465 VAL A 137 REMARK 465 LEU A 138 REMARK 465 HIS A 139 REMARK 465 ARG A 140 REMARK 465 ASN A 167 REMARK 465 HIS A 168 REMARK 465 ASP A 169 REMARK 465 THR A 170 REMARK 465 SER A 171 REMARK 465 PHE A 172 REMARK 465 ALA A 173 REMARK 465 LYS A 174 REMARK 465 ALA A 175 REMARK 465 PHE A 176 REMARK 465 VAL A 177 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 SER A 3 OG REMARK 470 ARG A 4 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 6 OE1 OE2 REMARK 470 SER A 18 OG REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 ASP A 30 CG OD1 OD2 REMARK 470 MET A 44 CG SD CE REMARK 470 LYS A 49 CG CD CE NZ REMARK 470 GLN A 50 CG CD OE1 NE2 REMARK 470 MET A 51 CG SD CE REMARK 470 LEU A 52 CG CD1 CD2 REMARK 470 ASN A 57 CG OD1 ND2 REMARK 470 LEU A 58 CG CD1 CD2 REMARK 470 LEU A 59 CG CD1 CD2 REMARK 470 GLU A 61 OE1 OE2 REMARK 470 LYS A 63 CD CE NZ REMARK 470 ARG A 73 NE CZ NH1 NH2 REMARK 470 LYS A 100 NZ REMARK 470 ARG A 130 CD NE CZ NH1 NH2 REMARK 470 ARG A 190 CD NE CZ NH1 NH2 REMARK 470 MET A 191 SD CE REMARK 470 LYS A 222 NZ REMARK 470 LYS A 227 NZ REMARK 470 GLU A 230 CD OE1 OE2 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 SER A 3 N SER A 3 CA 0.125 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 TYR A 181 -49.58 67.83 REMARK 500 SER A 184 150.87 -49.74 REMARK 500 LEU A 212 17.11 58.71 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 5Z5 A1280 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CL1 RELATED DB: PDB REMARK 900 HUMAN KINASE WITH PYRROLE-INDOLINONE LIGAND REMARK 999 REMARK 999 SEQUENCE REMARK 999 C-TERMINAL HEXA-HISTIDINE TAG DBREF 2JAV A 1 271 UNP P51955 NEK2_HUMAN 1 271 DBREF 2JAV A 272 279 PDB 2JAV 2JAV 272 279 SEQADV 2JAV ALA A 175 UNP P51955 THR 175 ENGINEERED MUTATION SEQRES 1 A 279 MET PRO SER ARG ALA GLU ASP TYR GLU VAL LEU TYR THR SEQRES 2 A 279 ILE GLY THR GLY SER TYR GLY ARG CYS GLN LYS ILE ARG SEQRES 3 A 279 ARG LYS SER ASP GLY LYS ILE LEU VAL TRP LYS GLU LEU SEQRES 4 A 279 ASP TYR GLY SER MET THR GLU ALA GLU LYS GLN MET LEU SEQRES 5 A 279 VAL SER GLU VAL ASN LEU LEU ARG GLU LEU LYS HIS PRO SEQRES 6 A 279 ASN ILE VAL ARG TYR TYR ASP ARG ILE ILE ASP ARG THR SEQRES 7 A 279 ASN THR THR LEU TYR ILE VAL MET GLU TYR CYS GLU GLY SEQRES 8 A 279 GLY ASP LEU ALA SER VAL ILE THR LYS GLY THR LYS GLU SEQRES 9 A 279 ARG GLN TYR LEU ASP GLU GLU PHE VAL LEU ARG VAL MET SEQRES 10 A 279 THR GLN LEU THR LEU ALA LEU LYS GLU CYS HIS ARG ARG SEQRES 11 A 279 SER ASP GLY GLY HIS THR VAL LEU HIS ARG ASP LEU LYS SEQRES 12 A 279 PRO ALA ASN VAL PHE LEU ASP GLY LYS GLN ASN VAL LYS SEQRES 13 A 279 LEU GLY ASP PHE GLY LEU ALA ARG ILE LEU ASN HIS ASP SEQRES 14 A 279 THR SER PHE ALA LYS ALA PHE VAL GLY THR PRO TYR TYR SEQRES 15 A 279 MET SER PRO GLU GLN MET ASN ARG MET SER TYR ASN GLU SEQRES 16 A 279 LYS SER ASP ILE TRP SER LEU GLY CYS LEU LEU TYR GLU SEQRES 17 A 279 LEU CYS ALA LEU MET PRO PRO PHE THR ALA PHE SER GLN SEQRES 18 A 279 LYS GLU LEU ALA GLY LYS ILE ARG GLU GLY LYS PHE ARG SEQRES 19 A 279 ARG ILE PRO TYR ARG TYR SER ASP GLU LEU ASN GLU ILE SEQRES 20 A 279 ILE THR ARG MET LEU ASN LEU LYS ASP TYR HIS ARG PRO SEQRES 21 A 279 SER VAL GLU GLU ILE LEU GLU ASN PRO LEU ILE LEU GLU SEQRES 22 A 279 HIS HIS HIS HIS HIS HIS HET 5Z5 A1280 23 HETNAM 5Z5 5-[(Z)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE) HETNAM 2 5Z5 METHYL]-N-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H- HETNAM 3 5Z5 PYRROLE-3-CARBOXAMIDE FORMUL 2 5Z5 C17 H16 CL N3 O2 FORMUL 3 HOH *107(H2 O) HELIX 1 1 ARG A 4 GLU A 6 5 3 HELIX 2 2 THR A 45 LEU A 59 1 15 HELIX 3 3 LEU A 94 ARG A 105 1 12 HELIX 4 4 ASP A 109 SER A 131 1 23 HELIX 5 5 LYS A 143 ALA A 145 5 3 HELIX 6 6 ASP A 159 LEU A 166 1 8 HELIX 7 7 SER A 184 ASN A 189 1 6 HELIX 8 8 ASN A 194 LEU A 212 1 19 HELIX 9 9 SER A 220 GLY A 231 1 12 HELIX 10 10 SER A 241 LEU A 252 1 12 HELIX 11 11 LYS A 255 ARG A 259 5 5 HELIX 12 12 SER A 261 GLU A 267 1 7 HELIX 13 13 LEU A 272 HIS A 276 5 5 SHEET 1 AA 5 TYR A 8 THR A 16 0 SHEET 2 AA 5 GLY A 20 ARG A 27 -1 O CYS A 22 N ILE A 14 SHEET 3 AA 5 ILE A 33 LEU A 39 -1 O LEU A 34 N ILE A 25 SHEET 4 AA 5 LEU A 82 GLU A 87 -1 O LEU A 82 N LEU A 39 SHEET 5 AA 5 TYR A 70 ILE A 75 -1 N TYR A 71 O VAL A 85 SHEET 1 AB 3 GLY A 92 ASP A 93 0 SHEET 2 AB 3 VAL A 147 LEU A 149 -1 N LEU A 149 O GLY A 92 SHEET 3 AB 3 VAL A 155 LEU A 157 -1 O LYS A 156 N PHE A 148 SITE 1 AC1 12 ILE A 14 VAL A 35 LYS A 37 VAL A 68 SITE 2 AC1 12 MET A 86 GLU A 87 TYR A 88 CYS A 89 SITE 3 AC1 12 GLU A 90 GLY A 92 PHE A 148 LEU A 162 CRYST1 41.634 56.924 66.012 90.00 95.98 90.00 P 1 21 1 2 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 0.024019 0.000000 0.002516 0.00000 SCALE2 0.000000 0.017567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015232 0.00000