HEADER TRANSFERASE/TRANSFERASE INHIBITOR 23-OCT-10 3PDN TITLE CRYSTAL STRUCTURE OF SMYD3 IN COMPLEX WITH METHYLTRANSFERASE INHIBITOR TITLE 2 SINEFUNGIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SET AND MYND DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 1; COMPND 5 EC: 2.1.1.43; COMPND 6 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: SMYD3, ZMYND1, ZNFN3A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ROSSMANN FOLD, ZINC FINGER, METHYLTRANSFERASE, TRANSFERASE, KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.SIRINUPONG,J.BRUNZELLE,Z.YANG REVDAT 5 21-FEB-24 3PDN 1 REMARK LINK REVDAT 4 09-FEB-11 3PDN 1 JRNL REVDAT 3 19-JAN-11 3PDN 1 JRNL REVDAT 2 15-DEC-10 3PDN 1 JRNL REVDAT 1 17-NOV-10 3PDN 0 JRNL AUTH N.SIRINUPONG,J.BRUNZELLE,E.DOKO,Z.YANG JRNL TITL STRUCTURAL INSIGHTS INTO THE AUTOINHIBITION AND JRNL TITL 2 POSTTRANSLATIONAL ACTIVATION OF HISTONE METHYLTRANSFERASE JRNL TITL 3 SMYD3. JRNL REF J.MOL.BIOL. V. 406 149 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21167177 JRNL DOI 10.1016/J.JMB.2010.12.014 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 48667 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2467 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3527 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1919 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3352 REMARK 3 BIN R VALUE (WORKING SET) : 0.1899 REMARK 3 BIN FREE R VALUE : 0.2312 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.96 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 175 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3390 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 645 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.67170 REMARK 3 B22 (A**2) : 3.34170 REMARK 3 B33 (A**2) : 1.33000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.171 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3606 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4871 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1737 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 98 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 517 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3606 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.93 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 2:21) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1299 23.0479 25.8451 REMARK 3 T TENSOR REMARK 3 T11: -0.0602 T22: -0.0099 REMARK 3 T33: 0.0117 T12: 0.0102 REMARK 3 T13: -0.0230 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 4.3674 L22: 1.9883 REMARK 3 L33: 2.1325 L12: 0.0799 REMARK 3 L13: -0.4018 L23: 1.5736 REMARK 3 S TENSOR REMARK 3 S11: -0.0300 S12: -0.1867 S13: 0.1810 REMARK 3 S21: -0.0024 S22: 0.1350 S23: -0.4563 REMARK 3 S31: -0.0689 S32: 0.2213 S33: -0.1049 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 22:68) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3844 33.7693 3.3938 REMARK 3 T TENSOR REMARK 3 T11: 0.0146 T22: -0.0344 REMARK 3 T33: -0.0170 T12: 0.0129 REMARK 3 T13: 0.0422 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.2633 L22: 0.5482 REMARK 3 L33: 1.5282 L12: 0.2554 REMARK 3 L13: -0.2524 L23: 0.5867 REMARK 3 S TENSOR REMARK 3 S11: 0.0265 S12: 0.0692 S13: 0.0982 REMARK 3 S21: -0.1764 S22: 0.0784 S23: -0.0689 REMARK 3 S31: -0.2833 S32: -0.0658 S33: -0.1050 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 69:96) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3233 27.6623 -9.2425 REMARK 3 T TENSOR REMARK 3 T11: 0.0082 T22: 0.0204 REMARK 3 T33: -0.0373 T12: -0.0113 REMARK 3 T13: 0.0252 T23: 0.0257 REMARK 3 L TENSOR REMARK 3 L11: 0.6937 L22: 7.0625 REMARK 3 L33: 4.2959 L12: 2.1517 REMARK 3 L13: -0.3066 L23: -2.8098 REMARK 3 S TENSOR REMARK 3 S11: -0.0216 S12: 0.0933 S13: 0.0519 REMARK 3 S21: -0.3449 S22: 0.2759 S23: 0.0225 REMARK 3 S31: 0.0386 S32: -0.2666 S33: -0.2543 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 97:175) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4333 14.5196 4.8679 REMARK 3 T TENSOR REMARK 3 T11: -0.0325 T22: -0.0305 REMARK 3 T33: -0.0471 T12: 0.0012 REMARK 3 T13: 0.0110 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.6727 L22: 0.8565 REMARK 3 L33: 1.2120 L12: 0.4255 REMARK 3 L13: -0.3152 L23: -0.3263 REMARK 3 S TENSOR REMARK 3 S11: -0.0438 S12: 0.0538 S13: 0.0224 REMARK 3 S21: -0.1262 S22: 0.0565 S23: -0.0229 REMARK 3 S31: 0.1096 S32: 0.0129 S33: -0.0126 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 176:278) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9479 29.3928 21.8237 REMARK 3 T TENSOR REMARK 3 T11: -0.0234 T22: -0.0176 REMARK 3 T33: -0.0130 T12: -0.0022 REMARK 3 T13: 0.0025 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.1503 L22: 0.5972 REMARK 3 L33: 0.6702 L12: -0.1738 REMARK 3 L13: -0.3284 L23: 0.3071 REMARK 3 S TENSOR REMARK 3 S11: 0.0362 S12: -0.0129 S13: 0.0342 REMARK 3 S21: -0.0025 S22: -0.0013 S23: -0.0462 REMARK 3 S31: -0.0378 S32: 0.0332 S33: -0.0349 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 279:303) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7832 36.5863 12.6950 REMARK 3 T TENSOR REMARK 3 T11: 0.0058 T22: 0.0069 REMARK 3 T33: -0.0088 T12: 0.0226 REMARK 3 T13: -0.0245 T23: -0.0343 REMARK 3 L TENSOR REMARK 3 L11: 1.5885 L22: 1.6883 REMARK 3 L33: 3.1235 L12: -0.1412 REMARK 3 L13: -1.5822 L23: -0.5570 REMARK 3 S TENSOR REMARK 3 S11: 0.0406 S12: 0.1469 S13: -0.1335 REMARK 3 S21: -0.2301 S22: -0.1417 S23: 0.0340 REMARK 3 S31: 0.1635 S32: -0.0723 S33: 0.1011 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 304:380) REMARK 3 ORIGIN FOR THE GROUP (A): 0.8880 46.8557 17.2920 REMARK 3 T TENSOR REMARK 3 T11: 0.0048 T22: -0.0630 REMARK 3 T33: -0.0560 T12: 0.0170 REMARK 3 T13: 0.0323 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.2777 L22: 1.0991 REMARK 3 L33: 0.7193 L12: -0.3370 REMARK 3 L13: -0.1973 L23: 0.1005 REMARK 3 S TENSOR REMARK 3 S11: 0.1394 S12: 0.0596 S13: 0.0491 REMARK 3 S21: -0.1918 S22: -0.0268 S23: -0.0293 REMARK 3 S31: -0.1275 S32: -0.0442 S33: -0.1127 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 381:428) REMARK 3 ORIGIN FOR THE GROUP (A): 18.5473 55.7122 17.1912 REMARK 3 T TENSOR REMARK 3 T11: -0.0090 T22: -0.0773 REMARK 3 T33: 0.1305 T12: -0.0304 REMARK 3 T13: 0.1099 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 0.4675 L22: 3.4512 REMARK 3 L33: 0.4185 L12: -0.9445 REMARK 3 L13: -0.0167 L23: -0.2161 REMARK 3 S TENSOR REMARK 3 S11: 0.1551 S12: -0.0371 S13: 0.4156 REMARK 3 S21: -0.1890 S22: -0.0065 S23: -0.4331 REMARK 3 S31: -0.1732 S32: 0.0042 S33: -0.1486 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.27823, 1.28268 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48766 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.51900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 3350, 50 MM NA FORMATE, 100 MM REMARK 280 TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, 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 30.62000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.69200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.12300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.69200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.62000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.12300 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 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 GLU A 2 CG CD OE1 OE2 REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ARG A 96 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 426 CG CD NE CZ NH1 NH2 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 ASN A 13 18.38 -144.09 REMARK 500 LYS A 271 -6.92 78.54 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 ZN A 437 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 52 SG 106.1 REMARK 620 3 CYS A 71 SG 112.3 107.9 REMARK 620 4 CYS A 75 SG 108.4 118.7 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 436 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 CYS A 65 SG 110.2 REMARK 620 3 HIS A 83 NE2 113.9 103.0 REMARK 620 4 CYS A 87 SG 109.2 113.0 107.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 438 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 261 SG 117.0 REMARK 620 3 CYS A 263 SG 110.9 103.7 REMARK 620 4 CYS A 266 SG 101.4 113.3 110.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 439 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 751 O REMARK 620 2 HOH A 791 O 86.9 REMARK 620 3 HOH A 875 O 86.5 93.1 REMARK 620 4 HOH A 932 O 95.1 176.8 89.5 REMARK 620 5 HOH A1002 O 175.9 89.9 91.2 88.2 REMARK 620 6 HOH A1003 O 90.9 95.7 170.6 81.8 91.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 440 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 869 O REMARK 620 2 HOH A 896 O 94.9 REMARK 620 3 HOH A1004 O 83.4 175.8 REMARK 620 4 HOH A1005 O 86.2 92.6 91.1 REMARK 620 5 HOH A1006 O 96.7 86.6 89.8 177.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFG A 429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 431 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 432 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 434 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 435 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 436 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 437 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 438 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 439 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 440 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS SEQUENCE CORRESPONDS TO GENBANK ENTRY BC031010. DBREF 3PDN A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 3PDN ASN A 13 UNP Q9H7B4 LYS 13 SEE REMARK 999 SEQADV 3PDN ARG A 140 UNP Q9H7B4 LYS 140 SEE REMARK 999 SEQRES 1 A 428 MET GLU PRO LEU LYS VAL GLU LYS PHE ALA THR ALA ASN SEQRES 2 A 428 ARG GLY ASN GLY LEU ARG ALA VAL THR PRO LEU ARG PRO SEQRES 3 A 428 GLY GLU LEU LEU PHE ARG SER ASP PRO LEU ALA TYR THR SEQRES 4 A 428 VAL CYS LYS GLY SER ARG GLY VAL VAL CYS ASP ARG CYS SEQRES 5 A 428 LEU LEU GLY LYS GLU LYS LEU MET ARG CYS SER GLN CYS SEQRES 6 A 428 ARG VAL ALA LYS TYR CYS SER ALA LYS CYS GLN LYS LYS SEQRES 7 A 428 ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS CYS LEU LYS SEQRES 8 A 428 SER CYS LYS PRO ARG TYR PRO PRO ASP SER VAL ARG LEU SEQRES 9 A 428 LEU GLY ARG VAL VAL PHE LYS LEU MET ASP GLY ALA PRO SEQRES 10 A 428 SER GLU SER GLU LYS LEU TYR SER PHE TYR ASP LEU GLU SEQRES 11 A 428 SER ASN ILE ASN LYS LEU THR GLU ASP ARG LYS GLU GLY SEQRES 12 A 428 LEU ARG GLN LEU VAL MET THR PHE GLN HIS PHE MET ARG SEQRES 13 A 428 GLU GLU ILE GLN ASP ALA SER GLN LEU PRO PRO ALA PHE SEQRES 14 A 428 ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE CYS ASN SER SEQRES 15 A 428 PHE THR ILE CYS ASN ALA GLU MET GLN GLU VAL GLY VAL SEQRES 16 A 428 GLY LEU TYR PRO SER ILE SER LEU LEU ASN HIS SER CYS SEQRES 17 A 428 ASP PRO ASN CYS SER ILE VAL PHE ASN GLY PRO HIS LEU SEQRES 18 A 428 LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL GLY GLU GLU SEQRES 19 A 428 LEU THR ILE CYS TYR LEU ASP MET LEU MET THR SER GLU SEQRES 20 A 428 GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR CYS PHE GLU SEQRES 21 A 428 CYS ASP CYS PHE ARG CYS GLN THR GLN ASP LYS ASP ALA SEQRES 22 A 428 ASP MET LEU THR GLY ASP GLU GLN VAL TRP LYS GLU VAL SEQRES 23 A 428 GLN GLU SER LEU LYS LYS ILE GLU GLU LEU LYS ALA HIS SEQRES 24 A 428 TRP LYS TRP GLU GLN VAL LEU ALA MET CYS GLN ALA ILE SEQRES 25 A 428 ILE SER SER ASN SER GLU ARG LEU PRO ASP ILE ASN ILE SEQRES 26 A 428 TYR GLN LEU LYS VAL LEU ASP CYS ALA MET ASP ALA CYS SEQRES 27 A 428 ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU PHE TYR GLY SEQRES 28 A 428 THR ARG THR MET GLU PRO TYR ARG ILE PHE PHE PRO GLY SEQRES 29 A 428 SER HIS PRO VAL ARG GLY VAL GLN VAL MET LYS VAL GLY SEQRES 30 A 428 LYS LEU GLN LEU HIS GLN GLY MET PHE PRO GLN ALA MET SEQRES 31 A 428 LYS ASN LEU ARG LEU ALA PHE ASP ILE MET ARG VAL THR SEQRES 32 A 428 HIS GLY ARG GLU HIS SER LEU ILE GLU ASP LEU ILE LEU SEQRES 33 A 428 LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG ALA SER HET SFG A 429 27 HET GOL A 430 6 HET GOL A 431 6 HET GOL A 432 6 HET GOL A 433 6 HET GOL A 434 6 HET GOL A 435 6 HET ZN A 436 1 HET ZN A 437 1 HET ZN A 438 1 HET MG A 439 1 HET MG A 440 1 HETNAM SFG SINEFUNGIN HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETSYN SFG ADENOSYL-ORNITHINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SFG C15 H23 N7 O5 FORMUL 3 GOL 6(C3 H8 O3) FORMUL 9 ZN 3(ZN 2+) FORMUL 12 MG 2(MG 2+) FORMUL 14 HOH *645(H2 O) HELIX 1 1 SER A 72 CYS A 93 1 22 HELIX 2 2 PRO A 99 GLY A 115 1 17 HELIX 3 3 SER A 118 LYS A 122 5 5 HELIX 4 4 SER A 125 LEU A 129 5 5 HELIX 5 5 ASN A 132 LEU A 136 5 5 HELIX 6 6 THR A 137 MET A 155 1 19 HELIX 7 7 ASP A 161 LEU A 165 5 5 HELIX 8 8 ASP A 170 SER A 182 1 13 HELIX 9 9 SER A 200 LEU A 204 5 5 HELIX 10 10 THR A 245 CYS A 258 1 14 HELIX 11 11 CYS A 263 GLN A 269 1 7 HELIX 12 12 LYS A 271 LEU A 276 1 6 HELIX 13 13 ASP A 279 HIS A 299 1 21 HELIX 14 14 LYS A 301 SER A 314 1 14 HELIX 15 15 ASN A 324 GLY A 342 1 19 HELIX 16 16 LEU A 343 PHE A 362 1 20 HELIX 17 17 HIS A 366 GLN A 383 1 18 HELIX 18 18 MET A 385 HIS A 404 1 20 HELIX 19 19 HIS A 408 ALA A 427 1 20 SHEET 1 A 4 VAL A 6 ALA A 10 0 SHEET 2 A 4 ASN A 16 ALA A 20 -1 O GLY A 17 N PHE A 9 SHEET 3 A 4 GLU A 234 ILE A 237 -1 O LEU A 235 N LEU A 18 SHEET 4 A 4 ASN A 205 HIS A 206 1 N ASN A 205 O ILE A 237 SHEET 1 B 3 LEU A 29 SER A 33 0 SHEET 2 B 3 HIS A 220 ALA A 225 -1 O LEU A 223 N PHE A 31 SHEET 3 B 3 CYS A 212 ASN A 217 -1 N VAL A 215 O LEU A 222 SHEET 1 C 3 ALA A 37 VAL A 40 0 SHEET 2 C 3 GLU A 192 LEU A 197 -1 O VAL A 195 N THR A 39 SHEET 3 C 3 PHE A 183 CYS A 186 -1 N ILE A 185 O VAL A 193 SHEET 1 D 2 MET A 60 ARG A 61 0 SHEET 2 D 2 LYS A 69 TYR A 70 -1 O TYR A 70 N MET A 60 LINK SG CYS A 49 ZN ZN A 437 1555 1555 2.44 LINK SG CYS A 52 ZN ZN A 437 1555 1555 2.29 LINK SG CYS A 62 ZN ZN A 436 1555 1555 2.31 LINK SG CYS A 65 ZN ZN A 436 1555 1555 2.41 LINK SG CYS A 71 ZN ZN A 437 1555 1555 2.34 LINK SG CYS A 75 ZN ZN A 437 1555 1555 2.29 LINK NE2 HIS A 83 ZN ZN A 436 1555 1555 2.06 LINK SG CYS A 87 ZN ZN A 436 1555 1555 2.29 LINK SG CYS A 208 ZN ZN A 438 1555 1555 2.32 LINK SG CYS A 261 ZN ZN A 438 1555 1555 2.33 LINK SG CYS A 263 ZN ZN A 438 1555 1555 2.38 LINK SG CYS A 266 ZN ZN A 438 1555 1555 2.37 LINK MG MG A 439 O HOH A 751 1555 1555 2.13 LINK MG MG A 439 O HOH A 791 1555 1555 2.14 LINK MG MG A 439 O HOH A 875 1555 1555 2.09 LINK MG MG A 439 O HOH A 932 1555 1555 2.12 LINK MG MG A 439 O HOH A1002 1555 1555 2.11 LINK MG MG A 439 O HOH A1003 1555 1555 2.17 LINK MG MG A 440 O HOH A 869 1555 1555 1.96 LINK MG MG A 440 O HOH A 896 1555 1555 2.26 LINK MG MG A 440 O HOH A1004 1555 1555 2.18 LINK MG MG A 440 O HOH A1005 1555 1555 2.05 LINK MG MG A 440 O HOH A1006 1555 1555 1.98 CISPEP 1 LYS A 94 PRO A 95 0 8.42 SITE 1 AC1 23 ARG A 14 ASN A 16 TYR A 124 GLU A 130 SITE 2 AC1 23 ASN A 132 CYS A 180 ASN A 181 SER A 202 SITE 3 AC1 23 LEU A 203 LEU A 204 ASN A 205 HIS A 206 SITE 4 AC1 23 TYR A 239 TYR A 257 PHE A 259 GOL A 431 SITE 5 AC1 23 HOH A 655 HOH A 670 HOH A 674 HOH A 697 SITE 6 AC1 23 HOH A 725 HOH A 766 HOH A 827 SITE 1 AC2 8 CYS A 238 LEU A 240 MET A 242 HIS A 366 SITE 2 AC2 8 GOL A 432 HOH A 669 HOH A 678 HOH A 837 SITE 1 AC3 10 ASN A 181 SER A 182 PHE A 183 SER A 202 SITE 2 AC3 10 ILE A 237 TYR A 239 TYR A 257 SFG A 429 SITE 3 AC3 10 HOH A 702 HOH A 938 SITE 1 AC4 9 ILE A 214 VAL A 215 HIS A 366 PRO A 367 SITE 2 AC4 9 VAL A 368 GOL A 430 HOH A 652 HOH A 693 SITE 3 AC4 9 HOH A 779 SITE 1 AC5 9 PRO A 81 ASP A 82 LYS A 111 GLY A 115 SITE 2 AC5 9 GLU A 142 GLN A 146 HOH A 536 HOH A 738 SITE 3 AC5 9 HOH A1015 SITE 1 AC6 6 PHE A 151 GLN A 152 ILE A 159 LEU A 171 SITE 2 AC6 6 HOH A 602 HOH A 817 SITE 1 AC7 11 PHE A 126 ALA A 168 PHE A 169 ASP A 170 SITE 2 AC7 11 GLU A 173 ALA A 174 LYS A 177 HOH A 461 SITE 3 AC7 11 HOH A 528 HOH A 853 HOH A1036 SITE 1 AC8 4 CYS A 62 CYS A 65 HIS A 83 CYS A 87 SITE 1 AC9 4 CYS A 49 CYS A 52 CYS A 71 CYS A 75 SITE 1 BC1 4 CYS A 208 CYS A 261 CYS A 263 CYS A 266 SITE 1 BC2 6 HOH A 751 HOH A 791 HOH A 875 HOH A 932 SITE 2 BC2 6 HOH A1002 HOH A1003 SITE 1 BC3 5 HOH A 869 HOH A 896 HOH A1004 HOH A1005 SITE 2 BC3 5 HOH A1006 CRYST1 61.240 66.246 107.384 90.00 90.00 90.00 P 21 21 21 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 0.016329 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015095 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009312 0.00000