HEADER ONCOPROTEIN 13-JUL-20 6ZRB TITLE CRYSTAL STRUCTURE OF SMYD3 CONJUGATE WITH PIPERIDINE-BASED COVALENT TITLE 2 INHIBITOR EM127 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: 2.1.1.354; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SMYD3, ZMYND1, ZNFN3A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS INHIBITOR, COVALENT INHIBITOR, COMPLEX, METHYLTRANSFERASE, KEYWDS 2 ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.O.TALIBOV,D.ERIKSSON REVDAT 3 31-JAN-24 6ZRB 1 REMARK REVDAT 2 14-SEP-22 6ZRB 1 JRNL REVDAT 1 27-JUL-22 6ZRB 0 JRNL AUTH M.D.PARENTI,M.NALDI,E.MANONI,E.FABINI,D.CEDERFELT, JRNL AUTH 2 V.O.TALIBOV,V.GRESSANI,U.GUVEN,V.GROSSI,C.FASANO,P.SANESE, JRNL AUTH 3 K.DE MARCO,A.A.SHTIL,A.V.KURKIN,A.ALTIERI,U.H.DANIELSON, JRNL AUTH 4 G.CARETTI,C.SIMONE,G.VARCHI,M.BARTOLINI,A.DEL RIO JRNL TITL DISCOVERY OF THE 4-AMINOPIPERIDINE-BASED COMPOUND EM127 FOR JRNL TITL 2 THE SITE-SPECIFIC COVALENT INHIBITION OF SMYD3 JRNL REF EUR.J.MED.CHEM. 14683 2022 JRNL REFN ISSN 0223-5234 JRNL DOI 10.1016/J.EJMECH.2022.114683 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 59518 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3106 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3848 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 189 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3402 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 412 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.14000 REMARK 3 B22 (A**2) : -0.39000 REMARK 3 B33 (A**2) : -0.75000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3540 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3343 ; 0.035 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4777 ; 1.517 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7781 ; 2.316 ; 1.585 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 6.093 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;29.973 ;21.771 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 662 ;13.640 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;15.346 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 449 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3911 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 736 ; 0.011 ; 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): 1711 ; 1.401 ; 2.053 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1710 ; 1.402 ; 2.051 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2136 ; 2.206 ; 3.074 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6ZRB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62691 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 107.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6Z2R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS PRE-INCUBATED WITH THE REMARK 280 COVALENT INHIBITOR, 7 MG/ML AND 0.4 MM, RESPECTIVELY, FOR 8 H AT REMARK 280 RT. CRYSTALLIZATION WAS PERFORMED IN 2 UL HANGING DROPS, 1:1 REMARK 280 PROTEIN TO RESERVOIR RATIO, RESERVOIR: 16% PEG3350, 100 MM TRIS REMARK 280 (PH 8.25), 100 MM MG(OAC)2). PROTEIN CRYSTALS WERE CRYOPROTECTED REMARK 280 IN 20% PEG3350, 100 MM TRIS (PH 8.25), 100 MM MG(OAC)2, 10% DMSO REMARK 280 AND 10% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 30.46750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.65900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.99450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.65900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.46750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.99450 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 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 428 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 329 O HOH A 601 2.02 REMARK 500 O HOH A 904 O HOH A 999 2.08 REMARK 500 O HOH A 798 O HOH A 937 2.08 REMARK 500 O HOH A 879 O HOH A 929 2.12 REMARK 500 O HOH A 874 O HOH A 973 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 13 19.14 -147.61 REMARK 500 LYS A 271 -4.57 78.78 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 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 52 SG 106.7 REMARK 620 3 CYS A 71 SG 114.1 109.2 REMARK 620 4 CYS A 75 SG 107.7 116.9 102.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 CYS A 65 SG 111.1 REMARK 620 3 HIS A 83 NE2 114.3 101.7 REMARK 620 4 CYS A 87 SG 109.3 113.9 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 261 SG 113.1 REMARK 620 3 CYS A 263 SG 105.6 109.7 REMARK 620 4 CYS A 266 SG 98.9 116.0 112.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QON A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 506 DBREF 6ZRB A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 6ZRB GLY A -2 UNP Q9H7B4 EXPRESSION TAG SEQADV 6ZRB SER A -1 UNP Q9H7B4 EXPRESSION TAG SEQADV 6ZRB HIS A 0 UNP Q9H7B4 EXPRESSION TAG SEQADV 6ZRB ASN A 13 UNP Q9H7B4 LYS 13 VARIANT SEQADV 6ZRB ARG A 140 UNP Q9H7B4 LYS 140 VARIANT SEQRES 1 A 431 GLY SER HIS MET GLU PRO LEU LYS VAL GLU LYS PHE ALA SEQRES 2 A 431 THR ALA ASN ARG GLY ASN GLY LEU ARG ALA VAL THR PRO SEQRES 3 A 431 LEU ARG PRO GLY GLU LEU LEU PHE ARG SER ASP PRO LEU SEQRES 4 A 431 ALA TYR THR VAL CYS LYS GLY SER ARG GLY VAL VAL CYS SEQRES 5 A 431 ASP ARG CYS LEU LEU GLY LYS GLU LYS LEU MET ARG CYS SEQRES 6 A 431 SER GLN CYS ARG VAL ALA LYS TYR CYS SER ALA LYS CYS SEQRES 7 A 431 GLN LYS LYS ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS SEQRES 8 A 431 CYS LEU LYS SER CYS LYS PRO ARG TYR PRO PRO ASP SER SEQRES 9 A 431 VAL ARG LEU LEU GLY ARG VAL VAL PHE LYS LEU MET ASP SEQRES 10 A 431 GLY ALA PRO SER GLU SER GLU LYS LEU TYR SER PHE TYR SEQRES 11 A 431 ASP LEU GLU SER ASN ILE ASN LYS LEU THR GLU ASP ARG SEQRES 12 A 431 LYS GLU GLY LEU ARG GLN LEU VAL MET THR PHE GLN HIS SEQRES 13 A 431 PHE MET ARG GLU GLU ILE GLN ASP ALA SER GLN LEU PRO SEQRES 14 A 431 PRO ALA PHE ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE SEQRES 15 A 431 CYS ASN SER PHE THR ILE CYS ASN ALA GLU MET GLN GLU SEQRES 16 A 431 VAL GLY VAL GLY LEU TYR PRO SER ILE SER LEU LEU ASN SEQRES 17 A 431 HIS SER CYS ASP PRO ASN CYS SER ILE VAL PHE ASN GLY SEQRES 18 A 431 PRO HIS LEU LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL SEQRES 19 A 431 GLY GLU GLU LEU THR ILE CYS TYR LEU ASP MET LEU MET SEQRES 20 A 431 THR SER GLU GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR SEQRES 21 A 431 CYS PHE GLU CYS ASP CYS PHE ARG CYS GLN THR GLN ASP SEQRES 22 A 431 LYS ASP ALA ASP MET LEU THR GLY ASP GLU GLN VAL TRP SEQRES 23 A 431 LYS GLU VAL GLN GLU SER LEU LYS LYS ILE GLU GLU LEU SEQRES 24 A 431 LYS ALA HIS TRP LYS TRP GLU GLN VAL LEU ALA MET CYS SEQRES 25 A 431 GLN ALA ILE ILE SER SER ASN SER GLU ARG LEU PRO ASP SEQRES 26 A 431 ILE ASN ILE TYR GLN LEU LYS VAL LEU ASP CYS ALA MET SEQRES 27 A 431 ASP ALA CYS ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU SEQRES 28 A 431 PHE TYR GLY THR ARG THR MET GLU PRO TYR ARG ILE PHE SEQRES 29 A 431 PHE PRO GLY SER HIS PRO VAL ARG GLY VAL GLN VAL MET SEQRES 30 A 431 LYS VAL GLY LYS LEU GLN LEU HIS GLN GLY MET PHE PRO SEQRES 31 A 431 GLN ALA MET LYS ASN LEU ARG LEU ALA PHE ASP ILE MET SEQRES 32 A 431 ARG VAL THR HIS GLY ARG GLU HIS SER LEU ILE GLU ASP SEQRES 33 A 431 LEU ILE LEU LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG SEQRES 34 A 431 ALA SER HET SAM A 501 27 HET QON A 502 20 HET ACT A 503 4 HET ZN A 504 1 HET ZN A 505 1 HET ZN A 506 1 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM QON N-[1-(2-CHLOROACETYL)PIPERIDIN-4-YL]-5-CYCLOPROPYL-1,2- HETNAM 2 QON OXAZOLE-3-CARBOXAMIDE HETNAM ACT ACETATE ION HETNAM ZN ZINC ION HETSYN QON ~{N}-[1-(2-CHLORANYLETHANOYL)PIPERIDIN-4-YL]-5- HETSYN 2 QON CYCLOPROPYL-1,2-OXAZOLE-3-CARBOXAMIDE FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 QON C14 H18 CL N3 O3 FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 ZN 3(ZN 2+) FORMUL 8 HOH *412(H2 O) HELIX 1 AA1 LYS A 42 ARG A 45 5 4 HELIX 2 AA2 SER A 72 CYS A 93 1 22 HELIX 3 AA3 PRO A 99 GLY A 115 1 17 HELIX 4 AA4 SER A 118 LYS A 122 5 5 HELIX 5 AA5 SER A 125 LEU A 129 5 5 HELIX 6 AA6 ASN A 132 LEU A 136 5 5 HELIX 7 AA7 THR A 137 MET A 155 1 19 HELIX 8 AA8 ASP A 161 LEU A 165 5 5 HELIX 9 AA9 ASP A 170 SER A 182 1 13 HELIX 10 AB1 SER A 200 LEU A 204 5 5 HELIX 11 AB2 THR A 245 CYS A 258 1 14 HELIX 12 AB3 CYS A 263 GLN A 269 1 7 HELIX 13 AB4 LYS A 271 LEU A 276 1 6 HELIX 14 AB5 ASP A 279 HIS A 299 1 21 HELIX 15 AB6 LYS A 301 SER A 314 1 14 HELIX 16 AB7 ASN A 324 GLY A 342 1 19 HELIX 17 AB8 LEU A 343 PHE A 362 1 20 HELIX 18 AB9 HIS A 366 GLN A 383 1 18 HELIX 19 AC1 MET A 385 HIS A 404 1 20 HELIX 20 AC2 HIS A 408 ALA A 427 1 20 SHEET 1 AA1 4 VAL A 6 ALA A 10 0 SHEET 2 AA1 4 ASN A 16 ALA A 20 -1 O GLY A 17 N PHE A 9 SHEET 3 AA1 4 GLU A 234 ILE A 237 -1 O LEU A 235 N LEU A 18 SHEET 4 AA1 4 ASN A 205 HIS A 206 1 N ASN A 205 O ILE A 237 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 221 N SER A 33 SHEET 3 AA2 3 CYS A 212 ASN A 217 -1 N VAL A 215 O LEU A 222 SHEET 1 AA3 3 ALA A 37 VAL A 40 0 SHEET 2 AA3 3 GLU A 192 LEU A 197 -1 O VAL A 195 N THR A 39 SHEET 3 AA3 3 PHE A 183 CYS A 186 -1 N ILE A 185 O VAL A 193 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 LINK SG CYS A 186 C01 QON A 502 1555 1555 1.75 LINK SG CYS A 49 ZN ZN A 505 1555 1555 2.38 LINK SG CYS A 52 ZN ZN A 505 1555 1555 2.28 LINK SG CYS A 62 ZN ZN A 506 1555 1555 2.28 LINK SG CYS A 65 ZN ZN A 506 1555 1555 2.32 LINK SG CYS A 71 ZN ZN A 505 1555 1555 2.29 LINK SG CYS A 75 ZN ZN A 505 1555 1555 2.32 LINK NE2 HIS A 83 ZN ZN A 506 1555 1555 2.10 LINK SG CYS A 87 ZN ZN A 506 1555 1555 2.35 LINK SG CYS A 208 ZN ZN A 504 1555 1555 2.40 LINK SG CYS A 261 ZN ZN A 504 1555 1555 2.33 LINK SG CYS A 263 ZN ZN A 504 1555 1555 2.30 LINK SG CYS A 266 ZN ZN A 504 1555 1555 2.32 CISPEP 1 LYS A 94 PRO A 95 0 1.65 SITE 1 AC1 22 ARG A 14 ASN A 16 TYR A 124 GLU A 130 SITE 2 AC1 22 ASN A 132 CYS A 180 ASN A 181 SER A 202 SITE 3 AC1 22 LEU A 203 LEU A 204 ASN A 205 HIS A 206 SITE 4 AC1 22 TYR A 239 TYR A 257 PHE A 259 HOH A 663 SITE 5 AC1 22 HOH A 675 HOH A 707 HOH A 715 HOH A 836 SITE 6 AC1 22 HOH A 853 HOH A 881 SITE 1 AC2 15 CYS A 180 SER A 182 PHE A 183 THR A 184 SITE 2 AC2 15 CYS A 186 MET A 190 PHE A 216 ILE A 237 SITE 3 AC2 15 TYR A 239 TYR A 257 HOH A 710 HOH A 724 SITE 4 AC2 15 HOH A 727 HOH A 744 HOH A 780 SITE 1 AC3 4 PRO A 99 MET A 113 THR A 150 HOH A 924 SITE 1 AC4 4 CYS A 208 CYS A 261 CYS A 263 CYS A 266 SITE 1 AC5 4 CYS A 49 CYS A 52 CYS A 71 CYS A 75 SITE 1 AC6 4 CYS A 62 CYS A 65 HIS A 83 CYS A 87 CRYST1 60.935 65.989 107.318 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 0.016411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015154 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009318 0.00000