HEADER TRANSFERASE/TRANSFERASE INHIBITOR 02-JUL-15 5CCL TITLE CRYSTAL STRUCTURE OF SMYD3 WITH SAM AND OXINDOLE 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-INHIBITOR COMPLEX, METHYLTRANSFERASE, EPIGENETICS, DRUG KEYWDS 2 DISCOVERY, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.A.BORIACK-SJODIN REVDAT 3 06-MAR-24 5CCL 1 REMARK REVDAT 2 30-MAR-16 5CCL 1 JRNL REVDAT 1 09-SEP-15 5CCL 0 JRNL AUTH L.H.MITCHELL,P.A.BORIACK-SJODIN,S.SMITH,M.THOMENIUS,N.RIOUX, JRNL AUTH 2 M.MUNCHHOF,J.E.MILLS,C.KLAUS,J.TOTMAN,T.V.RIERA,A.RAIMONDI, JRNL AUTH 3 S.L.JACQUES,K.WEST,M.FOLEY,N.J.WATERS,K.W.KUNTZ,T.J.WIGLE, JRNL AUTH 4 M.P.SCOTT,R.A.COPELAND,J.J.SMITH,R.CHESWORTH JRNL TITL NOVEL OXINDOLE SULFONAMIDES AND SULFAMIDES: EPZ031686, THE JRNL TITL 2 FIRST ORALLY BIOAVAILABLE SMALL MOLECULE SMYD3 INHIBITOR. JRNL REF ACS MED.CHEM.LETT. V. 7 134 2016 JRNL REFN ISSN 1948-5875 JRNL PMID 26985287 JRNL DOI 10.1021/ACSMEDCHEMLETT.5B00272 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 59053 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) : 0.116 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3081 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4464 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.1150 REMARK 3 BIN FREE R VALUE SET COUNT : 215 REMARK 3 BIN FREE R VALUE : 0.1830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3400 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 449 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61000 REMARK 3 B22 (A**2) : -0.56000 REMARK 3 B33 (A**2) : -0.05000 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): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.113 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3816 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3680 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5146 ; 1.732 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8506 ; 0.913 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 468 ; 6.110 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;32.614 ;23.873 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 719 ;14.196 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;19.865 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 555 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4280 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 859 ; 0.002 ; 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): 1839 ; 3.367 ; 1.950 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1839 ; 3.367 ; 1.950 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2318 ; 3.787 ; 2.925 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): 7496 ; 3.323 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 90 ;23.573 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7760 ;11.646 ; 5.000 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 5CCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211372. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-14 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97907 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62186 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 55.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.22600 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: NULL 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 (%): 40.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.10 M MAGNESIUM FORMATE, 0.1M TRIS REMARK 280 8.0, 14% W/V PEG 3350. CRYSTALS OF SMYD3-SAM WERE PRODUCED AND REMARK 280 COMPOUND WAS SOAKED INTO THE PRE-FORMED CRYSTALS, PH 8.0, VAPOR REMARK 280 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 29.29700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.98300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.61600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.98300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.29700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.61600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 428 REMARK 465 PHE A 429 REMARK 465 SEC A 430 REMARK 465 LEU A 431 REMARK 465 LEU A 432 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 O HOH A 937 O HOH A 940 1.85 REMARK 500 NZ LYS A 140 O HOH A 601 1.93 REMARK 500 O HOH A 846 O HOH A 939 1.96 REMARK 500 NH1 ARG A 66 O HOH A 602 1.96 REMARK 500 OD1 ASP A 398 O HOH A 603 2.05 REMARK 500 OG1 THR A 137 OD1 ASP A 139 2.14 REMARK 500 O HOH A 630 O HOH A 789 2.16 REMARK 500 OE2 GLU A 247 O HOH A 604 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 64 O HOH A 702 2554 2.14 REMARK 500 NH2 ARG A 96 O HOH A 892 4555 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 247 CD GLU A 247 OE2 0.074 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 50 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 241 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 394 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES 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 15.49 -148.18 REMARK 500 VAL A 67 -53.17 -123.58 REMARK 500 SER A 92 -86.53 -19.73 REMARK 500 LYS A 94 154.99 -47.31 REMARK 500 PRO A 95 65.38 -68.36 REMARK 500 LYS A 271 -6.52 79.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1049 DISTANCE = 6.76 ANGSTROMS 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 52 SG 107.4 REMARK 620 3 CYS A 71 SG 113.3 110.7 REMARK 620 4 CYS A 75 SG 107.7 114.0 103.9 REMARK 620 N 1 2 3 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 62 SG REMARK 620 2 CYS A 65 SG 109.0 REMARK 620 3 HIS A 83 NE2 112.7 104.9 REMARK 620 4 CYS A 87 SG 111.5 110.5 108.1 REMARK 620 N 1 2 3 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 62 SG REMARK 620 2 CYS A 65 SG 104.6 REMARK 620 3 HIS A 83 NE2 120.7 78.1 REMARK 620 4 CYS A 87 SG 114.7 104.8 121.7 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 208 SG REMARK 620 2 CYS A 261 SG 113.4 REMARK 620 3 CYS A 263 SG 106.5 108.3 REMARK 620 4 CYS A 266 SG 98.8 115.5 113.8 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 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 SAM A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4ZW A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4ZW A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CCM RELATED DB: PDB DBREF 5CCL A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 5CCL ASN A 13 UNP Q9H7B4 LYS 13 CONFLICT SEQADV 5CCL PHE A 429 UNP Q9H7B4 EXPRESSION TAG SEQADV 5CCL SEC A 430 UNP Q9H7B4 EXPRESSION TAG SEQADV 5CCL LEU A 431 UNP Q9H7B4 EXPRESSION TAG SEQADV 5CCL LEU A 432 UNP Q9H7B4 EXPRESSION TAG SEQRES 1 A 432 MET GLU PRO LEU LYS VAL GLU LYS PHE ALA THR ALA ASN SEQRES 2 A 432 ARG GLY ASN GLY LEU ARG ALA VAL THR PRO LEU ARG PRO SEQRES 3 A 432 GLY GLU LEU LEU PHE ARG SER ASP PRO LEU ALA TYR THR SEQRES 4 A 432 VAL CYS LYS GLY SER ARG GLY VAL VAL CYS ASP ARG CYS SEQRES 5 A 432 LEU LEU GLY LYS GLU LYS LEU MET ARG CYS SER GLN CYS SEQRES 6 A 432 ARG VAL ALA LYS TYR CYS SER ALA LYS CYS GLN LYS LYS SEQRES 7 A 432 ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS CYS LEU LYS SEQRES 8 A 432 SER CYS LYS PRO ARG TYR PRO PRO ASP SER VAL ARG LEU SEQRES 9 A 432 LEU GLY ARG VAL VAL PHE LYS LEU MET ASP GLY ALA PRO SEQRES 10 A 432 SER GLU SER GLU LYS LEU TYR SER PHE TYR ASP LEU GLU SEQRES 11 A 432 SER ASN ILE ASN LYS LEU THR GLU ASP LYS LYS GLU GLY SEQRES 12 A 432 LEU ARG GLN LEU VAL MET THR PHE GLN HIS PHE MET ARG SEQRES 13 A 432 GLU GLU ILE GLN ASP ALA SER GLN LEU PRO PRO ALA PHE SEQRES 14 A 432 ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE CYS ASN SER SEQRES 15 A 432 PHE THR ILE CYS ASN ALA GLU MET GLN GLU VAL GLY VAL SEQRES 16 A 432 GLY LEU TYR PRO SER ILE SER LEU LEU ASN HIS SER CYS SEQRES 17 A 432 ASP PRO ASN CYS SER ILE VAL PHE ASN GLY PRO HIS LEU SEQRES 18 A 432 LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL GLY GLU GLU SEQRES 19 A 432 LEU THR ILE CYS TYR LEU ASP MET LEU MET THR SER GLU SEQRES 20 A 432 GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR CYS PHE GLU SEQRES 21 A 432 CYS ASP CYS PHE ARG CYS GLN THR GLN ASP LYS ASP ALA SEQRES 22 A 432 ASP MET LEU THR GLY ASP GLU GLN VAL TRP LYS GLU VAL SEQRES 23 A 432 GLN GLU SER LEU LYS LYS ILE GLU GLU LEU LYS ALA HIS SEQRES 24 A 432 TRP LYS TRP GLU GLN VAL LEU ALA MET CYS GLN ALA ILE SEQRES 25 A 432 ILE SER SER ASN SER GLU ARG LEU PRO ASP ILE ASN ILE SEQRES 26 A 432 TYR GLN LEU LYS VAL LEU ASP CYS ALA MET ASP ALA CYS SEQRES 27 A 432 ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU PHE TYR GLY SEQRES 28 A 432 THR ARG THR MET GLU PRO TYR ARG ILE PHE PHE PRO GLY SEQRES 29 A 432 SER HIS PRO VAL ARG GLY VAL GLN VAL MET LYS VAL GLY SEQRES 30 A 432 LYS LEU GLN LEU HIS GLN GLY MET PHE PRO GLN ALA MET SEQRES 31 A 432 LYS ASN LEU ARG LEU ALA PHE ASP ILE MET ARG VAL THR SEQRES 32 A 432 HIS GLY ARG GLU HIS SER LEU ILE GLU ASP LEU ILE LEU SEQRES 33 A 432 LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG ALA SER PHE SEQRES 34 A 432 SEC LEU LEU HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 2 HET SAM A 504 27 HET 4ZW A 505 19 HET 4ZW A 506 19 HET EDO A 507 4 HETNAM ZN ZINC ION HETNAM SAM S-ADENOSYLMETHIONINE HETNAM 4ZW 2-OXIDANYLIDENE-N-PIPERIDIN-4-YL-1,3-DIHYDROINDOLE-5- HETNAM 2 4ZW CARBOXAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 3(ZN 2+) FORMUL 5 SAM C15 H22 N6 O5 S FORMUL 6 4ZW 2(C14 H17 N3 O2) FORMUL 8 EDO C2 H6 O2 FORMUL 9 HOH *449(H2 O) HELIX 1 AA1 LYS A 42 ARG A 45 5 4 HELIX 2 AA2 SER A 72 LYS A 84 1 13 HELIX 3 AA3 GLU A 86 LYS A 94 1 9 HELIX 4 AA4 PRO A 99 GLY A 115 1 17 HELIX 5 AA5 SER A 118 LYS A 122 5 5 HELIX 6 AA6 SER A 125 LEU A 129 5 5 HELIX 7 AA7 ASN A 132 LEU A 136 5 5 HELIX 8 AA8 THR A 137 MET A 155 1 19 HELIX 9 AA9 ASP A 161 LEU A 165 5 5 HELIX 10 AB1 ASP A 170 SER A 182 1 13 HELIX 11 AB2 SER A 200 LEU A 204 5 5 HELIX 12 AB3 THR A 245 CYS A 258 1 14 HELIX 13 AB4 CYS A 263 GLN A 269 1 7 HELIX 14 AB5 LYS A 271 LEU A 276 1 6 HELIX 15 AB6 ASP A 279 HIS A 299 1 21 HELIX 16 AB7 LYS A 301 SER A 314 1 14 HELIX 17 AB8 ASN A 324 LEU A 341 1 18 HELIX 18 AB9 LEU A 343 PHE A 362 1 20 HELIX 19 AC1 HIS A 366 GLN A 383 1 18 HELIX 20 AC2 MET A 385 HIS A 404 1 20 HELIX 21 AC3 HIS A 408 ARG A 426 1 19 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 221 N SER A 33 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 PHE A 183 O GLY A 196 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 501 1555 1555 2.34 LINK SG CYS A 52 ZN ZN A 501 1555 1555 2.31 LINK SG ACYS A 62 ZN A ZN A 503 1555 1555 2.30 LINK SG BCYS A 62 ZN B ZN A 503 1555 1555 2.29 LINK SG ACYS A 65 ZN A ZN A 503 1555 1555 2.36 LINK SG BCYS A 65 ZN B ZN A 503 1555 1555 2.40 LINK SG CYS A 71 ZN ZN A 501 1555 1555 2.32 LINK SG CYS A 75 ZN ZN A 501 1555 1555 2.32 LINK NE2 HIS A 83 ZN B ZN A 503 1555 1555 1.96 LINK NE2 HIS A 83 ZN A ZN A 503 1555 1555 2.18 LINK SG ACYS A 87 ZN A ZN A 503 1555 1555 2.25 LINK SG BCYS A 87 ZN B ZN A 503 1555 1555 2.29 LINK SG CYS A 208 ZN ZN A 502 1555 1555 2.38 LINK SG CYS A 261 ZN ZN A 502 1555 1555 2.34 LINK SG CYS A 263 ZN ZN A 502 1555 1555 2.32 LINK SG CYS A 266 ZN ZN A 502 1555 1555 2.31 CISPEP 1 LYS A 94 PRO A 95 0 -0.98 CISPEP 2 LYS A 94 PRO A 95 0 -2.37 SITE 1 AC1 4 CYS A 49 CYS A 52 CYS A 71 CYS A 75 SITE 1 AC2 4 CYS A 208 CYS A 261 CYS A 263 CYS A 266 SITE 1 AC3 5 CYS A 62 CYS A 65 TRP A 80 HIS A 83 SITE 2 AC3 5 CYS A 87 SITE 1 AC4 24 ARG A 14 GLY A 15 ASN A 16 TYR A 124 SITE 2 AC4 24 GLU A 130 ASN A 132 CYS A 180 ASN A 181 SITE 3 AC4 24 SER A 202 LEU A 203 LEU A 204 ASN A 205 SITE 4 AC4 24 HIS A 206 TYR A 239 TYR A 257 PHE A 259 SITE 5 AC4 24 4ZW A 505 HOH A 673 HOH A 692 HOH A 723 SITE 6 AC4 24 HOH A 738 HOH A 750 HOH A 805 HOH A 809 SITE 1 AC5 13 ASN A 181 SER A 182 PHE A 183 THR A 184 SITE 2 AC5 13 GLU A 192 SER A 202 TYR A 239 ASP A 241 SITE 3 AC5 13 TYR A 257 SAM A 504 HOH A 605 HOH A 725 SITE 4 AC5 13 HOH A 760 SITE 1 AC6 8 ARG A 19 VAL A 21 GLY A 232 MET A 390 SITE 2 AC6 8 ARG A 394 ILE A 415 GLU A 419 HOH A 831 SITE 1 AC7 5 LEU A 344 HIS A 382 GLN A 383 HOH A 683 SITE 2 AC7 5 HOH A 818 CRYST1 58.594 65.232 105.966 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 0.017067 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009437 0.00000