10 20 30 40 50 60 70 80 3V51 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/TRANSFERASE INHIBITOR 15-DEC-11 3V51
TITLE CALCIUM-DEPENDENT PROTEIN KINASE 1 FROM TOXOPLASMA GONDII (TGCDPK1) IN TITLE 2 COMPLEX WITH INHIBITOR RM-1-176
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN-DOMAIN PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 30-507; COMPND 5 SYNONYM: CALMODULIN-DOMAIN PROTEIN KINASE, PUTATIVE; COMPND 6 EC: 2.7.11.17; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOXOPLASMA GONDII; SOURCE 3 ORGANISM_TAXID: 5811; SOURCE 4 GENE: AAG53993, CDPK1, TGGT1_059880, TGVEG_042030; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: AVA0421
KEYWDS SERINE/THREONINE PROTEIN KINASE, CALCIUM-BINDING, ATP-BINDING, BUMPED KEYWDS 2 KINASE INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR E.A.MERRITT,E.T.LARSON
REVDAT 2 18-APR-12 3V51 1 JRNL REVDAT 1 14-MAR-12 3V51 0
JRNL AUTH E.T.LARSON,K.K.OJO,R.C.MURPHY,S.M.JOHNSON,Z.ZHANG,J.E.KIM, JRNL AUTH 2 D.J.LEIBLY,A.M.FOX,M.C.REID,E.J.DALE,B.G.PERERA,J.KIM, JRNL AUTH 3 S.N.HEWITT,W.G.HOL,C.L.VERLINDE,E.FAN,W.C.VAN VOORHIS, JRNL AUTH 4 D.J.MALY,E.A.MERRITT JRNL TITL MULTIPLE DETERMINANTS FOR SELECTIVE INHIBITION OF JRNL TITL 2 APICOMPLEXAN CALCIUM-DEPENDENT PROTEIN KINASE CDPK1. JRNL REF J.MED.CHEM. V. 55 2803 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22369268 JRNL DOI 10.1021/JM201725V
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.K.OJO,E.T.LARSON,K.R.KEYLOUN,L.J.CASTANEDA,A.E.DEROCHER, REMARK 1 AUTH 2 K.K.INAMPUDI,J.E.KIM,T.L.ARAKAKI,R.C.MURPHY,L.ZHANG, REMARK 1 AUTH 3 A.J.NAPULI,D.J.MALY,C.L.M.J.VERLINDE,F.S.BUCKNER,M.PARSONS, REMARK 1 AUTH 4 W.G.J.HOL,E.A.MERRITT,W.C.VAN VOORHIS REMARK 1 TITL TOXOPLASMA GONDII CALCIUM-DEPENDENT PROTEIN KINASE 1 IS A REMARK 1 TITL 2 TARGET FOR SELECTIVE KINASE INHIBITORS REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 17 602 2010 REMARK 1 REFN ISSN 1545-9993 REMARK 1 PMID 20436472 REMARK 1 DOI 10.1038/NSMB.1818 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.C.MURPHY,K.K.OJO,E.T.LARSON,A.CASTELLANOS-GONZALEZ, REMARK 1 AUTH 2 B.G.K.PERERA,K.R.KEYLOUN,J.E.KIM,J.G.BHANDARI,N.MULLER, REMARK 1 AUTH 3 C.L.M.J.VERLINDE,S.H.NAKAZAWA,W.G.J.HOL,F.S.BUCKNER, REMARK 1 AUTH 4 A.J.NAPULI,C.A.WHITE,E.A.MERRITT,W.C.VAN VOORHIS,D.J.MALY REMARK 1 TITL DISCOVERY OF POTENT AND SELECTIVE INHIBITORS OF REMARK 1 TITL 2 CALCIUM-DEPENDENT PROTEIN KINASE 1 (CDPK1) FROM C. PARVUM REMARK 1 TITL 3 AND T. GONDII REMARK 1 REF ACS MED.CHEM.LETT. V. 1 331 2010 REMARK 1 REFN ISSN 1948-5875 REMARK 1 PMID 21116453 REMARK 1 DOI 10.1021/ML100096T
REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 32270 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1664 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1963 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : -0.09000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.74000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.194 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.713 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3765 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2581 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5071 ; 1.205 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6291 ; 0.844 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 462 ; 5.088 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 175 ;36.930 ;24.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 710 ;14.338 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.719 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 560 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4149 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 743 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 7 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 43 A 94 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8930 16.2660 73.2860 REMARK 3 T TENSOR REMARK 3 T11: 0.0794 T22: 0.0418 REMARK 3 T33: 0.1575 T12: 0.0026 REMARK 3 T13: -0.0535 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.9552 L22: 2.0808 REMARK 3 L33: 2.8661 L12: -0.9225 REMARK 3 L13: 1.1313 L23: -0.7264 REMARK 3 S TENSOR REMARK 3 S11: -0.1171 S12: -0.0704 S13: 0.1609 REMARK 3 S21: 0.3320 S22: 0.0197 S23: -0.2081 REMARK 3 S31: -0.3147 S32: 0.0241 S33: 0.0974 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 95 A 214 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0540 14.0040 58.2380 REMARK 3 T TENSOR REMARK 3 T11: 0.0083 T22: 0.0691 REMARK 3 T33: 0.1902 T12: 0.0043 REMARK 3 T13: -0.0194 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.7599 L22: 1.2355 REMARK 3 L33: 2.8713 L12: -0.4162 REMARK 3 L13: 0.6098 L23: -0.7759 REMARK 3 S TENSOR REMARK 3 S11: -0.0104 S12: 0.0157 S13: 0.0224 REMARK 3 S21: -0.0118 S22: -0.0778 S23: -0.1521 REMARK 3 S31: 0.1030 S32: 0.1478 S33: 0.0881 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 215 A 334 REMARK 3 ORIGIN FOR THE GROUP (A): 7.5990 21.2290 40.5380 REMARK 3 T TENSOR REMARK 3 T11: 0.0780 T22: 0.1072 REMARK 3 T33: 0.1487 T12: 0.0252 REMARK 3 T13: -0.0025 T23: 0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.7053 L22: 2.5417 REMARK 3 L33: 1.8538 L12: -0.3517 REMARK 3 L13: -0.0642 L23: 0.5090 REMARK 3 S TENSOR REMARK 3 S11: 0.0959 S12: 0.1462 S13: 0.0937 REMARK 3 S21: -0.3966 S22: -0.0587 S23: -0.1997 REMARK 3 S31: 0.0185 S32: 0.1494 S33: -0.0373 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 335 A 375 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0710 34.7360 76.0030 REMARK 3 T TENSOR REMARK 3 T11: 0.1882 T22: 0.1980 REMARK 3 T33: 0.3031 T12: 0.1255 REMARK 3 T13: -0.0689 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.5229 L22: 0.7207 REMARK 3 L33: 11.9246 L12: 0.0986 REMARK 3 L13: 1.0300 L23: 0.6734 REMARK 3 S TENSOR REMARK 3 S11: -0.1460 S12: -0.1062 S13: 0.0081 REMARK 3 S21: 0.2721 S22: 0.2179 S23: -0.1382 REMARK 3 S31: -0.3817 S32: -0.2592 S33: -0.0719 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 376 A 413 REMARK 3 ORIGIN FOR THE GROUP (A): 25.5930 23.4180 85.1370 REMARK 3 T TENSOR REMARK 3 T11: 0.1363 T22: 0.1642 REMARK 3 T33: 0.3240 T12: -0.0134 REMARK 3 T13: -0.1365 T23: 0.0373 REMARK 3 L TENSOR REMARK 3 L11: 7.8164 L22: 7.4816 REMARK 3 L33: 6.0211 L12: -2.2140 REMARK 3 L13: 2.9627 L23: -2.5344 REMARK 3 S TENSOR REMARK 3 S11: -0.0124 S12: 0.1424 S13: -0.4068 REMARK 3 S21: -0.2915 S22: 0.3432 S23: 0.7641 REMARK 3 S31: 0.2790 S32: -0.4253 S33: -0.3308 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 414 A 442 REMARK 3 ORIGIN FOR THE GROUP (A): 33.7950 29.1390 80.5380 REMARK 3 T TENSOR REMARK 3 T11: 0.4787 T22: 0.3630 REMARK 3 T33: 0.4657 T12: 0.0663 REMARK 3 T13: -0.0963 T23: 0.0773 REMARK 3 L TENSOR REMARK 3 L11: 1.1435 L22: 1.3373 REMARK 3 L33: 13.3944 L12: -1.2255 REMARK 3 L13: 2.4987 L23: -3.0279 REMARK 3 S TENSOR REMARK 3 S11: 0.2393 S12: 0.2517 S13: 0.3364 REMARK 3 S21: -0.2317 S22: -0.3413 S23: -0.3633 REMARK 3 S31: 0.0698 S32: 0.8071 S33: 0.1020 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 443 A 507 REMARK 3 ORIGIN FOR THE GROUP (A): 30.1530 38.1940 53.2250 REMARK 3 T TENSOR REMARK 3 T11: 0.0412 T22: 0.0933 REMARK 3 T33: 0.2533 T12: -0.0013 REMARK 3 T13: -0.0195 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 6.1823 L22: 1.5125 REMARK 3 L33: 3.2233 L12: -1.8772 REMARK 3 L13: -1.4193 L23: 0.9113 REMARK 3 S TENSOR REMARK 3 S11: -0.0088 S12: 0.1723 S13: 0.2273 REMARK 3 S21: 0.0855 S22: 0.0467 S23: 0.0799 REMARK 3 S31: -0.2122 S32: -0.0135 S33: -0.0379 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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. U VALUES: WITH TLS ADDED
REMARK 4 REMARK 4 3V51 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-11. REMARK 100 THE RCSB ID CODE IS RCSB069603.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I REMARK 200 -BEAM SINGLE CRYSTAL; ASYMMETRIC REMARK 200 CUT 4.965 DEGS. REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32294 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.948 REMARK 200 RESOLUTION RANGE LOW (A) : 39.398 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.67300 REMARK 200 R SYM FOR SHELL (I) : 0.67300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 3350, 0.250 M AMMONIUM REMARK 280 CITRATE, 5 MM DTT, 2.3 MM RM-1-176, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K
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 36.30950 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: 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 GLY A 24 REMARK 465 PRO A 25 REMARK 465 GLY A 26 REMARK 465 SER A 27 REMARK 465 MET A 28 REMARK 465 MET A 29 REMARK 465 ASP A 30 REMARK 465 HIS A 31 REMARK 465 LEU A 32 REMARK 465 HIS A 33 REMARK 465 ALA A 34 REMARK 465 THR A 35 REMARK 465 PRO A 36 REMARK 465 GLY A 37 REMARK 465 MET A 38 REMARK 465 PHE A 39 REMARK 465 VAL A 40 REMARK 465 GLN A 41 REMARK 465 HIS A 42 REMARK 465 GLU A 314 REMARK 465 GLN A 315 REMARK 465 ILE A 316 REMARK 465 SER A 317 REMARK 465 VAL A 318 REMARK 465 ASN A 488
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 LYS A 93 CG CD CE NZ REMARK 470 LYS A 144 CG CD CE NZ REMARK 470 ARG A 145 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 ASP A 319 CG OD1 OD2 REMARK 470 LYS A 369 CG CD CE NZ REMARK 470 ASN A 487 CG OD1 ND2
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 PHE A 62 -13.68 77.87 REMARK 500 ASP A 120 -168.77 -128.76 REMARK 500 ARG A 173 -30.08 77.91 REMARK 500 ASP A 195 11.08 80.51 REMARK 500 LEU A 323 71.11 -101.38 REMARK 500 LEU A 398 42.99 -102.03 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 I76 A 701
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UPX RELATED DB: PDB REMARK 900 RELATED ID: 3UPZ RELATED DB: PDB REMARK 900 RELATED ID: 3UQF RELATED DB: PDB REMARK 900 RELATED ID: 3UQG RELATED DB: PDB REMARK 900 RELATED ID: 3V5P RELATED DB: PDB REMARK 900 RELATED ID: 3V5T RELATED DB: PDB
DBREF 3V51 A 30 507 UNP Q9BJF5 Q9BJF5_TOXGO 30 507
SEQADV 3V51 GLY A 24 UNP Q9BJF5 EXPRESSION TAG SEQADV 3V51 PRO A 25 UNP Q9BJF5 EXPRESSION TAG SEQADV 3V51 GLY A 26 UNP Q9BJF5 EXPRESSION TAG SEQADV 3V51 SER A 27 UNP Q9BJF5 EXPRESSION TAG SEQADV 3V51 MET A 28 UNP Q9BJF5 EXPRESSION TAG SEQADV 3V51 MET A 29 UNP Q9BJF5 EXPRESSION TAG
SEQRES 1 A 484 GLY PRO GLY SER MET MET ASP HIS LEU HIS ALA THR PRO SEQRES 2 A 484 GLY MET PHE VAL GLN HIS SER THR ALA ILE PHE SER ASP SEQRES 3 A 484 ARG TYR LYS GLY GLN ARG VAL LEU GLY LYS GLY SER PHE SEQRES 4 A 484 GLY GLU VAL ILE LEU CYS LYS ASP LYS ILE THR GLY GLN SEQRES 5 A 484 GLU CYS ALA VAL LYS VAL ILE SER LYS ARG GLN VAL LYS SEQRES 6 A 484 GLN LYS THR ASP LYS GLU SER LEU LEU ARG GLU VAL GLN SEQRES 7 A 484 LEU LEU LYS GLN LEU ASP HIS PRO ASN ILE MET LYS LEU SEQRES 8 A 484 TYR GLU PHE PHE GLU ASP LYS GLY TYR PHE TYR LEU VAL SEQRES 9 A 484 GLY GLU VAL TYR THR GLY GLY GLU LEU PHE ASP GLU ILE SEQRES 10 A 484 ILE SER ARG LYS ARG PHE SER GLU VAL ASP ALA ALA ARG SEQRES 11 A 484 ILE ILE ARG GLN VAL LEU SER GLY ILE THR TYR MET HIS SEQRES 12 A 484 LYS ASN LYS ILE VAL HIS ARG ASP LEU LYS PRO GLU ASN SEQRES 13 A 484 LEU LEU LEU GLU SER LYS SER LYS ASP ALA ASN ILE ARG SEQRES 14 A 484 ILE ILE ASP PHE GLY LEU SER THR HIS PHE GLU ALA SER SEQRES 15 A 484 LYS LYS MET LYS ASP LYS ILE GLY THR ALA TYR TYR ILE SEQRES 16 A 484 ALA PRO GLU VAL LEU HIS GLY THR TYR ASP GLU LYS CYS SEQRES 17 A 484 ASP VAL TRP SER THR GLY VAL ILE LEU TYR ILE LEU LEU SEQRES 18 A 484 SER GLY CYS PRO PRO PHE ASN GLY ALA ASN GLU TYR ASP SEQRES 19 A 484 ILE LEU LYS LYS VAL GLU LYS GLY LYS TYR THR PHE GLU SEQRES 20 A 484 LEU PRO GLN TRP LYS LYS VAL SER GLU SER ALA LYS ASP SEQRES 21 A 484 LEU ILE ARG LYS MET LEU THR TYR VAL PRO SER MET ARG SEQRES 22 A 484 ILE SER ALA ARG ASP ALA LEU ASP HIS GLU TRP ILE GLN SEQRES 23 A 484 THR TYR THR LYS GLU GLN ILE SER VAL ASP VAL PRO SER SEQRES 24 A 484 LEU ASP ASN ALA ILE LEU ASN ILE ARG GLN PHE GLN GLY SEQRES 25 A 484 THR GLN LYS LEU ALA GLN ALA ALA LEU LEU TYR MET GLY SEQRES 26 A 484 SER LYS LEU THR SER GLN ASP GLU THR LYS GLU LEU THR SEQRES 27 A 484 ALA ILE PHE HIS LYS MET ASP LYS ASN GLY ASP GLY GLN SEQRES 28 A 484 LEU ASP ARG ALA GLU LEU ILE GLU GLY TYR LYS GLU LEU SEQRES 29 A 484 MET ARG MET LYS GLY GLN ASP ALA SER MET LEU ASP ALA SEQRES 30 A 484 SER ALA VAL GLU HIS GLU VAL ASP GLN VAL LEU ASP ALA SEQRES 31 A 484 VAL ASP PHE ASP LYS ASN GLY TYR ILE GLU TYR SER GLU SEQRES 32 A 484 PHE VAL THR VAL ALA MET ASP ARG LYS THR LEU LEU SER SEQRES 33 A 484 ARG GLU ARG LEU GLU ARG ALA PHE ARG MET PHE ASP SER SEQRES 34 A 484 ASP ASN SER GLY LYS ILE SER SER THR GLU LEU ALA THR SEQRES 35 A 484 ILE PHE GLY VAL SER ASP VAL ASP SER GLU THR TRP LYS SEQRES 36 A 484 SER VAL LEU SER GLU VAL ASP LYS ASN ASN ASP GLY GLU SEQRES 37 A 484 VAL ASP PHE ASP GLU PHE GLN GLN MET LEU LEU LYS LEU SEQRES 38 A 484 CYS GLY ASN
HET I76 A 701 32
HETNAM I76 3-{6-[(3-CHLOROBENZYL)OXY]NAPHTHALEN-2-YL}-1-(PROPAN-2- HETNAM 2 I76 YL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-AMINE
FORMUL 2 I76 C25 H22 CL N5 O FORMUL 3 HOH *76(H2 O)
HELIX 1 1 ILE A 46 ARG A 50 1 5 HELIX 2 2 ASP A 92 LEU A 106 1 15 HELIX 3 3 GLU A 135 ARG A 143 1 9 HELIX 4 4 SER A 147 ASN A 168 1 22 HELIX 5 5 LYS A 176 GLU A 178 5 3 HELIX 6 6 GLY A 197 PHE A 202 1 6 HELIX 7 7 LYS A 207 ILE A 212 1 6 HELIX 8 8 ALA A 219 GLY A 225 1 7 HELIX 9 9 LYS A 230 GLY A 246 1 17 HELIX 10 10 ASN A 254 GLY A 265 1 12 HELIX 11 11 LEU A 271 LYS A 275 5 5 HELIX 12 12 SER A 278 LEU A 289 1 12 HELIX 13 13 VAL A 292 ARG A 296 5 5 HELIX 14 14 SER A 298 ASP A 304 1 7 HELIX 15 15 HIS A 305 THR A 312 1 8 HELIX 16 16 LEU A 323 ASP A 368 1 46 HELIX 17 17 ARG A 377 LYS A 391 1 15 HELIX 18 18 ASP A 394 LEU A 398 5 5 HELIX 19 19 ASP A 399 ASP A 415 1 17 HELIX 20 20 TYR A 424 ASP A 451 1 28 HELIX 21 21 SER A 460 SER A 470 1 11 HELIX 22 22 ASP A 473 ASP A 485 1 13 HELIX 23 23 PHE A 494 LEU A 504 1 11
SHEET 1 A 5 TYR A 51 GLY A 60 0 SHEET 2 A 5 GLY A 63 ASP A 70 -1 O LEU A 67 N GLN A 54 SHEET 3 A 5 GLU A 76 SER A 83 -1 O CYS A 77 N CYS A 68 SHEET 4 A 5 TYR A 123 GLY A 128 -1 O LEU A 126 N LYS A 80 SHEET 5 A 5 LEU A 114 GLU A 119 -1 N TYR A 115 O VAL A 127 SHEET 1 B 2 LEU A 180 LEU A 182 0 SHEET 2 B 2 ILE A 191 ILE A 193 -1 O ARG A 192 N LEU A 181 SHEET 1 C 2 GLN A 374 ASP A 376 0 SHEET 2 C 2 TYR A 421 GLU A 423 -1 O ILE A 422 N LEU A 375 SHEET 1 D 2 LYS A 457 SER A 459 0 SHEET 2 D 2 GLU A 491 ASP A 493 -1 O VAL A 492 N ILE A 458
SITE 1 AC1 14 GLY A 58 VAL A 65 ALA A 78 LYS A 80 SITE 2 AC1 14 LEU A 103 MET A 112 LEU A 126 GLU A 129 SITE 3 AC1 14 VAL A 130 TYR A 131 ASP A 195 GLY A 197 SITE 4 AC1 14 LEU A 198 HIS A 201
CRYST1 48.317 72.619 67.356 90.00 103.90 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 0.020697 0.000000 0.005124 0.00000
SCALE2 0.000000 0.013771 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015295 0.00000