HEADER TRANSFERASE/INHIBITOR 11-JAN-16 5HI7 TITLE CO-CRYSTAL STRUCTURE OF HUMAN SMYD3 WITH AN AZA-SAH COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE SMYD3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SET AND MYND DOMAIN-CONTAINING PROTEIN 3,ZINC FINGER MYND COMPND 5 DOMAIN-CONTAINING PROTEIN 1; COMPND 6 EC: 2.1.1.43; 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: SMYD3, ZMYND1, ZNFN3A1; SOURCE 6 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10469; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9 KEYWDS SMYD3, METHYLTRANSFERASE, ONCOLOGY, INHIBITOR, TRANSFERASE-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.A.ELKINS,W.G.BONNETTE REVDAT 4 06-MAR-24 5HI7 1 JRNL REMARK LINK REVDAT 3 18-MAY-16 5HI7 1 JRNL REVDAT 2 27-APR-16 5HI7 1 JRNL REVDAT 1 30-MAR-16 5HI7 0 JRNL AUTH G.S.VAN ALLER,A.P.GRAVES,P.A.ELKINS,W.G.BONNETTE, JRNL AUTH 2 P.J.MCDEVITT,F.ZAPPACOSTA,R.S.ANNAN,T.W.DEAN,D.S.SU, JRNL AUTH 3 C.L.CARPENTER,H.P.MOHAMMAD,R.G.KRUGER JRNL TITL STRUCTURE-BASED DESIGN OF A NOVEL SMYD3 INHIBITOR THAT JRNL TITL 2 BRIDGES THE SAM-AND MEKK2-BINDING POCKETS. JRNL REF STRUCTURE V. 24 774 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27066749 JRNL DOI 10.1016/J.STR.2016.03.010 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1801 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 23433 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1211 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 44.7185 - 4.4710 0.96 2542 130 0.1954 0.2027 REMARK 3 2 4.4710 - 3.5492 0.98 2468 130 0.1663 0.1957 REMARK 3 3 3.5492 - 3.1007 0.99 2464 141 0.1907 0.2015 REMARK 3 4 3.1007 - 2.8172 1.00 2467 140 0.2068 0.2312 REMARK 3 5 2.8172 - 2.6153 1.00 2460 150 0.2147 0.2841 REMARK 3 6 2.6153 - 2.4612 1.00 2448 143 0.2184 0.2357 REMARK 3 7 2.4612 - 2.3379 1.00 2458 118 0.2269 0.2754 REMARK 3 8 2.3379 - 2.2361 1.00 2461 124 0.2226 0.2836 REMARK 3 9 2.2361 - 2.1501 1.00 2454 135 0.2303 0.2717 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.003 3395 REMARK 3 ANGLE : 0.626 4612 REMARK 3 CHIRALITY : 0.037 521 REMARK 3 PLANARITY : 0.004 592 REMARK 3 DIHEDRAL : 11.897 1246 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 3:93) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7044 -3.4687 -5.0462 REMARK 3 T TENSOR REMARK 3 T11: 0.1978 T22: 0.2701 REMARK 3 T33: 0.2804 T12: -0.0032 REMARK 3 T13: 0.0409 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 0.9412 L22: 1.0427 REMARK 3 L33: 6.2003 L12: 0.5447 REMARK 3 L13: 0.9712 L23: 0.4625 REMARK 3 S TENSOR REMARK 3 S11: 0.0258 S12: -0.1029 S13: 0.0942 REMARK 3 S21: 0.2667 S22: -0.0153 S23: 0.0821 REMARK 3 S31: -0.0572 S32: 0.1333 S33: -0.0250 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 94:186) REMARK 3 ORIGIN FOR THE GROUP (A): 13.5955 -17.7629 -5.2762 REMARK 3 T TENSOR REMARK 3 T11: 0.1937 T22: 0.1521 REMARK 3 T33: 0.1899 T12: -0.0384 REMARK 3 T13: -0.0035 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 2.9711 L22: 2.4863 REMARK 3 L33: 3.2539 L12: -0.9539 REMARK 3 L13: -0.5301 L23: -0.0727 REMARK 3 S TENSOR REMARK 3 S11: -0.0363 S12: -0.2268 S13: -0.1225 REMARK 3 S21: 0.2131 S22: 0.0007 S23: -0.0020 REMARK 3 S31: 0.1869 S32: 0.0477 S33: 0.0516 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 187:427) REMARK 3 ORIGIN FOR THE GROUP (A): 21.7708 7.5702 -18.5853 REMARK 3 T TENSOR REMARK 3 T11: 0.2282 T22: 0.1860 REMARK 3 T33: 0.1955 T12: -0.0021 REMARK 3 T13: 0.0211 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.7397 L22: 1.3545 REMARK 3 L33: 0.2434 L12: 0.4704 REMARK 3 L13: -0.0474 L23: -0.2544 REMARK 3 S TENSOR REMARK 3 S11: 0.0023 S12: 0.0116 S13: 0.0416 REMARK 3 S21: 0.0640 S22: 0.0030 S23: -0.0522 REMARK 3 S31: -0.0069 S32: 0.0089 S33: -0.0026 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 5HI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216976. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : NULL 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) : 1.07820 REMARK 200 MONOCHROMATOR : NULL 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46288 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SMYD3 CRYSTALLIZATION AND SOAKING OF REMARK 280 GSK2807: SMYD3 (1-428) EXPRESSED IN BACULOVIRUS AND WITH SAH IN REMARK 280 THE SAM-BINDING SITE WAS CRYSTALLIZED IN SITTING DROPS AT 22C REMARK 280 USING 1UL FRESH PROTEIN AT 8.9MG/ML WITH THE ADDITION OF 1UL REMARK 280 MOTHER LIQUOR (200MM MGOAC TETRAHYDRATE, 20% PEG 3350). CRYSTALS REMARK 280 GREW TO A LARGE SIZE BUT VARIED IN QUANTITY WHEN SET UP IN REMARK 280 REPLICATES. A SEED STOCK WAS FORMED FROM THESE CRYSTALS AND REMARK 280 ADDED AT 20% TO THE MOTHER LIQUOR SOLUTION PRIOR TO PLATE SETUP. REMARK 280 CRYSTALS OF LARGE SIZE WERE THEN CREATED WITH 1.3UL PROTEIN AND REMARK 280 1.3UL OF MOTHER LIQUOR CONTAINING SEEDS IN A SITTING DROP MRC-2 REMARK 280 PLATE (HAMPTON RESEARCH). CRYSTAL NUCLEATION OCCURRED OVERNIGHT REMARK 280 AND REACHED MAXIMUM SIZE IN 4 DAYS, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K 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 30.23500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.42550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.20050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.42550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.23500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.20050 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 PHE A -1 REMARK 465 THR A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 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 PRO A 3 CG CD REMARK 470 LYS A 5 CD CE NZ REMARK 470 ARG A 25 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 42 CG CD CE NZ REMARK 470 LYS A 56 NZ REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 ARG A 61 NH1 NH2 REMARK 470 GLN A 64 CG CD OE1 NE2 REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LYS A 74 CD CE NZ REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 84 CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 LYS A 91 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 GLU A 119 CG CD OE1 OE2 REMARK 470 LYS A 122 CD CE NZ REMARK 470 ASP A 139 OD1 REMARK 470 LYS A 141 NZ REMARK 470 GLU A 157 CG CD OE1 OE2 REMARK 470 GLN A 164 CG CD OE1 NE2 REMARK 470 GLU A 192 CG CD OE1 OE2 REMARK 470 ILE A 214 CD1 REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 GLU A 280 CG CD OE1 OE2 REMARK 470 GLN A 281 CG CD OE1 NE2 REMARK 470 LYS A 284 CD CE NZ REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 292 CD CE NZ REMARK 470 LYS A 301 CE NZ REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 ASN A 316 CG OD1 ND2 REMARK 470 SER A 317 OG REMARK 470 GLU A 318 CD OE1 OE2 REMARK 470 LYS A 391 CD CE NZ REMARK 470 ARG A 394 CD NE CZ NH1 NH2 REMARK 470 ARG A 401 CD NE CZ NH1 NH2 REMARK 470 ARG A 406 CD NE CZ NH1 NH2 REMARK 470 GLU A 412 CG CD OE1 OE2 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 VAL A 67 -63.21 -108.43 REMARK 500 MET A 190 -3.59 71.31 REMARK 500 LYS A 271 -5.19 77.07 REMARK 500 ILE A 312 -61.88 -95.28 REMARK 500 PRO A 363 -177.39 -64.05 REMARK 500 HIS A 404 -62.78 -106.44 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 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 52 SG 104.5 REMARK 620 3 CYS A 71 SG 110.5 115.9 REMARK 620 4 CYS A 75 SG 107.1 117.8 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 CYS A 65 SG 104.8 REMARK 620 3 HIS A 83 NE2 110.3 101.1 REMARK 620 4 CYS A 87 SG 109.2 112.8 117.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 261 SG 114.6 REMARK 620 3 CYS A 263 SG 105.8 104.0 REMARK 620 4 CYS A 266 SG 100.0 118.0 114.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 332 OD1 REMARK 620 2 GLN A 372 OE1 75.9 REMARK 620 3 HOH A 605 O 106.6 163.9 REMARK 620 4 HOH A 606 O 86.6 74.0 90.1 REMARK 620 5 HOH A 621 O 160.0 84.3 93.1 90.5 REMARK 620 6 HOH A 713 O 92.3 105.0 90.9 178.6 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 604 O REMARK 620 2 HOH A 612 O 89.6 REMARK 620 3 HOH A 626 O 90.3 179.7 REMARK 620 4 HOH A 677 O 179.8 90.5 89.6 REMARK 620 5 HOH A 695 O 89.9 90.0 90.2 89.9 REMARK 620 6 HOH A 701 O 89.9 89.9 89.8 90.2 179.9 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 ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 62X A 507 DBREF 5HI7 A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 5HI7 GLY A -3 UNP Q9H7B4 EXPRESSION TAG SEQADV 5HI7 SER A -2 UNP Q9H7B4 EXPRESSION TAG SEQADV 5HI7 PHE A -1 UNP Q9H7B4 EXPRESSION TAG SEQADV 5HI7 THR A 0 UNP Q9H7B4 EXPRESSION TAG SEQADV 5HI7 ASN A 13 UNP Q9H7B4 LYS 13 CONFLICT SEQRES 1 A 432 GLY SER PHE THR MET GLU PRO LEU LYS VAL GLU LYS PHE SEQRES 2 A 432 ALA THR ALA ASN ARG GLY ASN GLY LEU ARG ALA VAL THR SEQRES 3 A 432 PRO LEU ARG PRO GLY GLU LEU LEU PHE ARG SER ASP PRO SEQRES 4 A 432 LEU ALA TYR THR VAL CYS LYS GLY SER ARG GLY VAL VAL SEQRES 5 A 432 CYS ASP ARG CYS LEU LEU GLY LYS GLU LYS LEU MET ARG SEQRES 6 A 432 CYS SER GLN CYS ARG VAL ALA LYS TYR CYS SER ALA LYS SEQRES 7 A 432 CYS GLN LYS LYS ALA TRP PRO ASP HIS LYS ARG GLU CYS SEQRES 8 A 432 LYS CYS LEU LYS SER CYS LYS PRO ARG TYR PRO PRO ASP SEQRES 9 A 432 SER VAL ARG LEU LEU GLY ARG VAL VAL PHE LYS LEU MET SEQRES 10 A 432 ASP GLY ALA PRO SER GLU SER GLU LYS LEU TYR SER PHE SEQRES 11 A 432 TYR ASP LEU GLU SER ASN ILE ASN LYS LEU THR GLU ASP SEQRES 12 A 432 LYS LYS GLU GLY LEU ARG GLN LEU VAL MET THR PHE GLN SEQRES 13 A 432 HIS PHE MET ARG GLU GLU ILE GLN ASP ALA SER GLN LEU SEQRES 14 A 432 PRO PRO ALA PHE ASP LEU PHE GLU ALA PHE ALA LYS VAL SEQRES 15 A 432 ILE CYS ASN SER PHE THR ILE CYS ASN ALA GLU MET GLN SEQRES 16 A 432 GLU VAL GLY VAL GLY LEU TYR PRO SER ILE SER LEU LEU SEQRES 17 A 432 ASN HIS SER CYS ASP PRO ASN CYS SER ILE VAL PHE ASN SEQRES 18 A 432 GLY PRO HIS LEU LEU LEU ARG ALA VAL ARG ASP ILE GLU SEQRES 19 A 432 VAL GLY GLU GLU LEU THR ILE CYS TYR LEU ASP MET LEU SEQRES 20 A 432 MET THR SER GLU GLU ARG ARG LYS GLN LEU ARG ASP GLN SEQRES 21 A 432 TYR CYS PHE GLU CYS ASP CYS PHE ARG CYS GLN THR GLN SEQRES 22 A 432 ASP LYS ASP ALA ASP MET LEU THR GLY ASP GLU GLN VAL SEQRES 23 A 432 TRP LYS GLU VAL GLN GLU SER LEU LYS LYS ILE GLU GLU SEQRES 24 A 432 LEU LYS ALA HIS TRP LYS TRP GLU GLN VAL LEU ALA MET SEQRES 25 A 432 CYS GLN ALA ILE ILE SER SER ASN SER GLU ARG LEU PRO SEQRES 26 A 432 ASP ILE ASN ILE TYR GLN LEU LYS VAL LEU ASP CYS ALA SEQRES 27 A 432 MET ASP ALA CYS ILE ASN LEU GLY LEU LEU GLU GLU ALA SEQRES 28 A 432 LEU PHE TYR GLY THR ARG THR MET GLU PRO TYR ARG ILE SEQRES 29 A 432 PHE PHE PRO GLY SER HIS PRO VAL ARG GLY VAL GLN VAL SEQRES 30 A 432 MET LYS VAL GLY LYS LEU GLN LEU HIS GLN GLY MET PHE SEQRES 31 A 432 PRO GLN ALA MET LYS ASN LEU ARG LEU ALA PHE ASP ILE SEQRES 32 A 432 MET ARG VAL THR HIS GLY ARG GLU HIS SER LEU ILE GLU SEQRES 33 A 432 ASP LEU ILE LEU LEU LEU GLU GLU CYS ASP ALA ASN ILE SEQRES 34 A 432 ARG ALA SER HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET MG A 504 1 HET MG A 505 1 HET DMS A 506 10 HET 62X A 507 32 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM 62X 5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL][3-(DIMETHYLAMINO) HETNAM 2 62X PROPYL]AMINO}-5'-DEOXYADENOSINE FORMUL 2 ZN 3(ZN 2+) FORMUL 5 MG 2(MG 2+) FORMUL 7 DMS C2 H6 O S FORMUL 8 62X C19 H32 N8 O5 FORMUL 9 HOH *119(H2 O) HELIX 1 AA1 SER A 72 LYS A 94 1 23 HELIX 2 AA2 PRO A 99 GLY A 115 1 17 HELIX 3 AA3 SER A 118 LYS A 122 5 5 HELIX 4 AA4 ASN A 132 LEU A 136 5 5 HELIX 5 AA5 THR A 137 MET A 155 1 19 HELIX 6 AA6 ASP A 161 LEU A 165 5 5 HELIX 7 AA7 ASP A 170 SER A 182 1 13 HELIX 8 AA8 SER A 200 LEU A 204 5 5 HELIX 9 AA9 THR A 245 GLN A 256 1 12 HELIX 10 AB1 CYS A 263 GLN A 269 1 7 HELIX 11 AB2 LYS A 271 LEU A 276 1 6 HELIX 12 AB3 ASP A 279 HIS A 299 1 21 HELIX 13 AB4 LYS A 301 SER A 314 1 14 HELIX 14 AB5 ASN A 324 LEU A 341 1 18 HELIX 15 AB6 LEU A 343 THR A 354 1 12 HELIX 16 AB7 THR A 354 PHE A 362 1 9 HELIX 17 AB8 HIS A 366 GLN A 383 1 18 HELIX 18 AB9 MET A 385 HIS A 404 1 20 HELIX 19 AC1 HIS A 408 ALA A 427 1 20 SHEET 1 AA1 2 VAL A 6 ALA A 10 0 SHEET 2 AA1 2 ASN A 16 ALA A 20 -1 O GLY A 17 N PHE A 9 SHEET 1 AA2 3 LEU A 29 SER A 33 0 SHEET 2 AA2 3 HIS A 220 ALA A 225 -1 O LEU A 223 N PHE A 31 SHEET 3 AA2 3 CYS A 212 ASN A 217 -1 N ASN A 217 O HIS A 220 SHEET 1 AA3 3 ALA A 37 VAL A 40 0 SHEET 2 AA3 3 GLU A 192 LEU A 197 -1 O LEU A 197 N ALA A 37 SHEET 3 AA3 3 PHE A 183 CYS A 186 -1 N ILE A 185 O GLY A 194 SHEET 1 AA4 2 MET A 60 ARG A 61 0 SHEET 2 AA4 2 LYS A 69 TYR A 70 -1 O TYR A 70 N MET A 60 SHEET 1 AA5 2 ASN A 205 HIS A 206 0 SHEET 2 AA5 2 THR A 236 ILE A 237 1 O ILE A 237 N ASN A 205 LINK SG CYS A 49 ZN ZN A 503 1555 1555 2.34 LINK SG CYS A 52 ZN ZN A 503 1555 1555 2.34 LINK SG CYS A 62 ZN ZN A 502 1555 1555 2.55 LINK SG CYS A 65 ZN ZN A 502 1555 1555 2.35 LINK SG CYS A 71 ZN ZN A 503 1555 1555 2.31 LINK SG CYS A 75 ZN ZN A 503 1555 1555 2.25 LINK NE2 HIS A 83 ZN ZN A 502 1555 1555 2.04 LINK SG CYS A 87 ZN ZN A 502 1555 1555 2.30 LINK SG CYS A 208 ZN ZN A 501 1555 1555 2.41 LINK SG CYS A 261 ZN ZN A 501 1555 1555 2.25 LINK SG CYS A 263 ZN ZN A 501 1555 1555 2.29 LINK SG CYS A 266 ZN ZN A 501 1555 1555 2.35 LINK OD1 ASP A 332 MG MG A 505 1555 1555 2.75 LINK OE1 GLN A 372 MG MG A 505 1555 1555 2.76 LINK MG MG A 504 O HOH A 604 1555 1555 2.18 LINK MG MG A 504 O HOH A 612 1555 1555 2.18 LINK MG MG A 504 O HOH A 626 1555 1555 2.18 LINK MG MG A 504 O HOH A 677 1555 3644 2.18 LINK MG MG A 504 O HOH A 695 1555 1555 2.18 LINK MG MG A 504 O HOH A 701 1555 3644 2.18 LINK MG MG A 505 O HOH A 605 1555 1555 2.18 LINK MG MG A 505 O HOH A 606 1555 1555 2.18 LINK MG MG A 505 O HOH A 621 1555 1555 2.18 LINK MG MG A 505 O HOH A 713 1555 1555 2.18 CISPEP 1 LYS A 94 PRO A 95 0 1.32 SITE 1 AC1 4 CYS A 208 CYS A 261 CYS A 263 CYS A 266 SITE 1 AC2 4 CYS A 62 CYS A 65 HIS A 83 CYS A 87 SITE 1 AC3 4 CYS A 49 CYS A 52 CYS A 71 CYS A 75 SITE 1 AC4 6 HOH A 604 HOH A 612 HOH A 626 HOH A 677 SITE 2 AC4 6 HOH A 695 HOH A 701 SITE 1 AC5 6 ASP A 332 GLN A 372 HOH A 605 HOH A 606 SITE 2 AC5 6 HOH A 621 HOH A 713 SITE 1 AC6 5 ASN A 187 MET A 190 PRO A 367 VAL A 368 SITE 2 AC6 5 HOH A 669 SITE 1 AC7 21 ARG A 14 ASN A 16 TYR A 124 GLU A 130 SITE 2 AC7 21 ASN A 132 LYS A 135 CYS A 180 ASN A 181 SITE 3 AC7 21 SER A 182 PHE A 183 SER A 202 ASN A 205 SITE 4 AC7 21 HIS A 206 TYR A 239 TYR A 257 PHE A 259 SITE 5 AC7 21 HOH A 609 HOH A 623 HOH A 644 HOH A 667 SITE 6 AC7 21 HOH A 670 CRYST1 60.470 66.401 104.851 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 0.016537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009537 0.00000