HEADER TRANSFERASE 08-DEC-08 2W5A TITLE HUMAN NEK2 KINASE ADP-BOUND 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 COMPND 6 KINASE 1, HSPK 21, NEK2; COMPND 7 EC: 2.7.11.1; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS SER/THR PROTEIN KINASE, KINASE, NUCLEUS, MEIOSIS, MITOSIS, KEYWDS 2 CYTOPLASM, SERINE/THREONINE-PROTEIN KINASE, METAL-BINDING, KEYWDS 3 PHOSPHOPROTEIN, NUCLEOTIDE-BINDING, MAGNESIUM, CELL CYCLE, KEYWDS 4 ATP-BINDING, TRANSFERASE, CENTROSOME SPLITTING, KEYWDS 5 ALTERNATIVE SPLICING, COILED COIL, POLYMORPHISM, CELL KEYWDS 6 DIVISION EXPDTA X-RAY DIFFRACTION AUTHOR I.WESTWOOD,R.BAYLISS REVDAT 4 13-JUL-11 2W5A 1 REMARK SEQADV DBREF HETSYN REVDAT 4 2 FORMUL REVDAT 3 17-FEB-09 2W5A 1 JRNL REVDAT 2 20-JAN-09 2W5A 1 JRNL REVDAT 1 23-DEC-08 2W5A 0 JRNL AUTH I.WESTWOOD,D.M.CHEARY,J.E.BAXTER,M.W.RICHARDS, JRNL AUTH 2 R.L.VAN MONTFORT,A.M.FRY,R.BAYLISS JRNL TITL INSIGHTS INTO THE CONFORMATIONAL VARIABILITY AND JRNL TITL 2 REGULATION OF HUMAN NEK2 KINASE. JRNL REF J.MOL.BIOL. V. 386 476 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19124027 JRNL DOI 10.1016/J.JMB.2008.12.033 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 43905 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2241 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.7425 - 3.9010 0.99 2907 144 0.1686 0.1752 REMARK 3 2 3.9010 - 3.0982 1.00 2838 157 0.1585 0.1710 REMARK 3 3 3.0982 - 2.7072 0.99 2806 185 0.1669 0.1970 REMARK 3 4 2.7072 - 2.4599 0.99 2829 137 0.1701 0.1647 REMARK 3 5 2.4599 - 2.2837 0.99 2791 161 0.1605 0.1912 REMARK 3 6 2.2837 - 2.1491 0.99 2808 164 0.1556 0.1716 REMARK 3 7 2.1491 - 2.0416 0.99 2771 148 0.1575 0.1778 REMARK 3 8 2.0416 - 1.9527 0.98 2794 159 0.1585 0.2004 REMARK 3 9 1.9527 - 1.8776 0.97 2726 141 0.1732 0.1987 REMARK 3 10 1.8776 - 1.8128 0.96 2728 121 0.1709 0.1821 REMARK 3 11 1.8128 - 1.7561 0.95 2668 153 0.1758 0.2029 REMARK 3 12 1.7561 - 1.7060 0.94 2617 153 0.1826 0.2433 REMARK 3 13 1.7060 - 1.6611 0.91 2592 127 0.1899 0.2100 REMARK 3 14 1.6611 - 1.6205 0.79 2222 117 0.2016 0.2487 REMARK 3 15 1.6205 - 1.5837 0.68 1935 90 0.2163 0.2445 REMARK 3 16 1.5837 - 1.5500 0.59 1632 84 0.2217 0.2295 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 55.36 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.75410 REMARK 3 B22 (A**2) : -2.55310 REMARK 3 B33 (A**2) : 4.30730 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -3.96800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 2396 REMARK 3 ANGLE : 0.977 3245 REMARK 3 CHIRALITY : 0.066 351 REMARK 3 PLANARITY : 0.004 413 REMARK 3 DIHEDRAL : 17.264 916 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 3-36 REMARK 3 ORIGIN FOR THE GROUP (A): -32.7213 0.3635 16.2181 REMARK 3 T TENSOR REMARK 3 T11: 0.0422 T22: 0.0685 REMARK 3 T33: 0.0673 T12: -0.0300 REMARK 3 T13: 0.0320 T23: -0.0377 REMARK 3 L TENSOR REMARK 3 L11: 1.6560 L22: 0.6198 REMARK 3 L33: 0.2259 L12: 0.6071 REMARK 3 L13: 0.0247 L23: 0.0654 REMARK 3 S TENSOR REMARK 3 S11: -0.1456 S12: 0.2028 S13: -0.2518 REMARK 3 S21: -0.0670 S22: 0.1025 S23: -0.0319 REMARK 3 S31: -0.0195 S32: -0.0995 S33: 0.0356 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 37-63 REMARK 3 ORIGIN FOR THE GROUP (A): -22.7973 3.3028 1.1060 REMARK 3 T TENSOR REMARK 3 T11: 0.1689 T22: 0.2915 REMARK 3 T33: 0.0843 T12: -0.0152 REMARK 3 T13: -0.0575 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: -0.0260 L22: 0.9910 REMARK 3 L33: 0.2414 L12: 0.0484 REMARK 3 L13: -0.3232 L23: 0.0916 REMARK 3 S TENSOR REMARK 3 S11: -0.2556 S12: 0.0070 S13: 0.1698 REMARK 3 S21: -0.1442 S22: 0.1689 S23: -0.1885 REMARK 3 S31: 0.0345 S32: -0.0228 S33: 0.0085 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 64-128 REMARK 3 ORIGIN FOR THE GROUP (A): -19.0359 8.2337 19.8479 REMARK 3 T TENSOR REMARK 3 T11: 0.0189 T22: 0.0354 REMARK 3 T33: 0.0251 T12: -0.0081 REMARK 3 T13: 0.0109 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 1.1018 L22: 0.8453 REMARK 3 L33: 1.2668 L12: 0.6365 REMARK 3 L13: 0.1068 L23: 0.4339 REMARK 3 S TENSOR REMARK 3 S11: -0.0090 S12: 0.0721 S13: 0.0237 REMARK 3 S21: -0.0086 S22: -0.0324 S23: 0.0802 REMARK 3 S31: 0.0131 S32: -0.1696 S33: 0.0922 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 129-156 REMARK 3 ORIGIN FOR THE GROUP (A): -14.6256 9.0048 18.3151 REMARK 3 T TENSOR REMARK 3 T11: 0.0902 T22: 0.0847 REMARK 3 T33: 0.0096 T12: -0.0133 REMARK 3 T13: 0.0211 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 0.8649 L22: 2.7448 REMARK 3 L33: -1.4255 L12: -0.3405 REMARK 3 L13: 0.1767 L23: 0.1495 REMARK 3 S TENSOR REMARK 3 S11: 0.0458 S12: 0.1834 S13: 0.0222 REMARK 3 S21: -0.4654 S22: 0.0028 S23: -0.0619 REMARK 3 S31: 0.0453 S32: -0.0404 S33: 0.0184 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 157-184 REMARK 3 ORIGIN FOR THE GROUP (A): -18.6231 19.4386 7.5994 REMARK 3 T TENSOR REMARK 3 T11: 0.2105 T22: 0.2039 REMARK 3 T33: 0.1201 T12: -0.0819 REMARK 3 T13: -0.0755 T23: 0.0364 REMARK 3 L TENSOR REMARK 3 L11: 0.3074 L22: 0.6846 REMARK 3 L33: -0.1826 L12: -0.0529 REMARK 3 L13: 0.1695 L23: -0.0225 REMARK 3 S TENSOR REMARK 3 S11: -0.1692 S12: 0.1730 S13: 0.0769 REMARK 3 S21: -0.4240 S22: 0.2673 S23: 0.2999 REMARK 3 S31: 0.0197 S32: -0.0954 S33: -0.0145 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 185-214 REMARK 3 ORIGIN FOR THE GROUP (A): -7.1340 21.6359 14.9434 REMARK 3 T TENSOR REMARK 3 T11: 0.1103 T22: 0.0542 REMARK 3 T33: 0.0115 T12: -0.0200 REMARK 3 T13: -0.0188 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 2.7771 L22: 3.2275 REMARK 3 L33: -0.9638 L12: -0.4011 REMARK 3 L13: -0.0733 L23: 0.5440 REMARK 3 S TENSOR REMARK 3 S11: 0.0048 S12: 0.3756 S13: 0.0060 REMARK 3 S21: -0.5145 S22: 0.0321 S23: 0.1654 REMARK 3 S31: -0.1405 S32: -0.0981 S33: -0.0586 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN A AND RESID 215-252 REMARK 3 ORIGIN FOR THE GROUP (A): -5.9830 28.6325 21.6295 REMARK 3 T TENSOR REMARK 3 T11: 0.0629 T22: 0.0268 REMARK 3 T33: 0.0161 T12: -0.0072 REMARK 3 T13: 0.0053 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.9011 L22: -0.0812 REMARK 3 L33: 1.0777 L12: 0.3851 REMARK 3 L13: 0.0682 L23: 0.4707 REMARK 3 S TENSOR REMARK 3 S11: -0.0715 S12: 0.1138 S13: 0.0658 REMARK 3 S21: 0.0055 S22: 0.0012 S23: -0.0488 REMARK 3 S31: -0.1850 S32: -0.0345 S33: -0.0101 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN A AND RESID 253-279 REMARK 3 ORIGIN FOR THE GROUP (A): -0.6010 12.0891 23.3782 REMARK 3 T TENSOR REMARK 3 T11: 0.0472 T22: 0.0221 REMARK 3 T33: 0.0471 T12: -0.0132 REMARK 3 T13: 0.0335 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 0.4121 L22: 0.9248 REMARK 3 L33: 0.5395 L12: 0.4800 REMARK 3 L13: -0.0506 L23: -0.5070 REMARK 3 S TENSOR REMARK 3 S11: -0.0562 S12: 0.0613 S13: -0.1114 REMARK 3 S21: -0.0809 S22: 0.0665 S23: -0.2017 REMARK 3 S31: 0.0888 S32: 0.0063 S33: 0.0364 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2W5A COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-08. REMARK 100 THE PDBE ID CODE IS EBI-38277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45663 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.55 REMARK 200 RESOLUTION RANGE LOW (A) : 26.23 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.6 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.80 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS, PH 8.5 2-10% REMARK 280 PEG8000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 49.73350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.55150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.73350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.55150 REMARK 290 SMTRY3 4 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 1 REMARK 465 PRO A 2 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 ASN A 167 REMARK 465 HIS A 168 REMARK 465 ASP A 169 REMARK 465 SER A 192 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 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 79 CG OD1 ND2 REMARK 470 LYS A 103 CD CE NZ REMARK 470 ARG A 105 NE CZ NH1 NH2 REMARK 470 ARG A 130 NE CZ NH1 NH2 REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 REMARK 470 MET A 191 CG SD CE 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 THR A 80 48.74 39.79 REMARK 500 PHE A 176 -75.36 -84.48 REMARK 500 ARG A 190 124.70 -171.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1281 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A1280 O2B REMARK 620 2 HOH A2221 O 101.7 REMARK 620 3 ADP A1280 O1A 86.9 87.8 REMARK 620 4 HOH A2347 O 83.8 164.8 78.2 REMARK 620 5 HOH A2220 O 91.1 95.3 176.6 98.8 REMARK 620 6 HOH A2207 O 162.7 93.8 86.1 79.3 95.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A1280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1285 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W5B RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE ATPGAMMAS-BOUND REMARK 900 RELATED ID: 2JAV RELATED DB: PDB REMARK 900 HUMAN KINASE WITH PYRROLE-INDOLINONE LIGAND REMARK 900 RELATED ID: 2W5H RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE ATPGAMMAS-BOUND REMARK 999 REMARK 999 SEQUENCE REMARK 999 C-TERMINAL LEHHHHHH AFFINITY TAG FROM VECTOR SEQUENCE DBREF 2W5A A 1 271 UNP P51955 NEK2_HUMAN 1 271 SEQADV 2W5A LEU A 272 UNP P51955 EXPRESSION TAG SEQADV 2W5A GLU A 273 UNP P51955 EXPRESSION TAG SEQADV 2W5A HIS A 274 UNP P51955 EXPRESSION TAG SEQADV 2W5A HIS A 275 UNP P51955 EXPRESSION TAG SEQADV 2W5A HIS A 276 UNP P51955 EXPRESSION TAG SEQADV 2W5A HIS A 277 UNP P51955 EXPRESSION TAG SEQADV 2W5A HIS A 278 UNP P51955 EXPRESSION TAG SEQADV 2W5A HIS A 279 UNP P51955 EXPRESSION TAG 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 THR 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 ADP A1280 27 HET MG A1281 1 HET EDO A1282 4 HET EDO A1283 4 HET EDO A1284 4 HET EDO A1285 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 4(C2 H6 O2) FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG MG 2+ FORMUL 5 HOH *355(H2 O) HELIX 1 1 ARG A 4 GLU A 6 5 3 HELIX 2 2 THR A 45 LEU A 62 1 18 HELIX 3 3 ARG A 77 ASN A 79 5 3 HELIX 4 4 LEU A 94 GLU A 104 1 11 HELIX 5 5 ASP A 109 SER A 131 1 23 HELIX 6 6 LYS A 143 ALA A 145 5 3 HELIX 7 7 GLY A 161 LEU A 166 1 6 HELIX 8 8 THR A 170 GLY A 178 1 9 HELIX 9 9 SER A 184 ARG A 190 1 7 HELIX 10 10 ASN A 194 LEU A 212 1 19 HELIX 11 11 SER A 220 GLY A 231 1 12 HELIX 12 12 SER A 241 LEU A 252 1 12 HELIX 13 13 LYS A 255 ARG A 259 5 5 HELIX 14 14 SER A 261 GLU A 267 1 7 HELIX 15 15 LEU A 272 HIS A 276 5 5 SHEET 1 AA 5 TYR A 8 THR A 16 0 SHEET 2 AA 5 ARG A 21 ARG A 27 -1 O CYS A 22 N ILE A 14 SHEET 3 AA 5 ILE A 33 ASP A 40 -1 O LEU A 34 N ILE A 25 SHEET 4 AA 5 THR A 81 GLU A 87 -1 O LEU A 82 N LEU A 39 SHEET 5 AA 5 TYR A 70 ASP A 76 -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 LINK MG MG A1281 O2B ADP A1280 1555 1555 2.21 LINK MG MG A1281 O HOH A2221 1555 1555 2.37 LINK MG MG A1281 O1A ADP A1280 1555 1555 2.23 LINK MG MG A1281 O HOH A2347 1555 1555 2.46 LINK MG MG A1281 O HOH A2220 1555 1555 2.37 LINK MG MG A1281 O HOH A2207 1555 1555 2.31 SITE 1 AC1 23 GLY A 17 SER A 18 CYS A 22 LYS A 37 SITE 2 AC1 23 GLU A 87 TYR A 88 CYS A 89 ASP A 93 SITE 3 AC1 23 PHE A 148 ARG A 164 MG A1281 HOH A2034 SITE 4 AC1 23 HOH A2158 HOH A2159 HOH A2205 HOH A2207 SITE 5 AC1 23 HOH A2342 HOH A2343 HOH A2344 HOH A2345 SITE 6 AC1 23 HOH A2346 HOH A2347 HOH A2348 SITE 1 AC2 7 LYS A 37 ARG A 164 ADP A1280 HOH A2207 SITE 2 AC2 7 HOH A2220 HOH A2221 HOH A2347 SITE 1 AC3 6 LEU A 11 LYS A 152 GLN A 153 HOH A2337 SITE 2 AC3 6 HOH A2349 HOH A2350 SITE 1 AC4 6 HIS A 139 ARG A 140 ASP A 159 HOH A2110 SITE 2 AC4 6 HOH A2351 HOH A2352 SITE 1 AC5 8 LEU A 122 ARG A 235 ASP A 242 HIS A 276 SITE 2 AC5 8 HIS A 277 HOH A2109 HOH A2278 HOH A2353 SITE 1 AC6 4 GLU A 246 ILE A 247 GLU A 264 ASN A 268 CRYST1 99.467 57.103 80.213 90.00 132.99 90.00 C 1 2 1 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 0.010054 0.000000 0.009372 0.00000 SCALE2 0.000000 0.017512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017043 0.00000