HEADER TRANSFERASE 16-NOV-21 7QA6 OBSLTE 30-AUG-23 7QA6 8OWO TITLE SMYD3 IN COMPLEX WITH FRAGMENT FL01507 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 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 METHYLTRANSFERASE, EPIGENETIC, ONCOGEN, HISTONE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.A.LUND,D.CEDERFELT,D.DOBRITZSCH REVDAT 3 14-FEB-24 7QA6 1 REMARK REVDAT 2 30-AUG-23 7QA6 1 OBSLTE REVDAT 1 30-NOV-22 7QA6 0 JRNL AUTH B.A.LUND,D.CEDERFELT,D.DOBRITZSCH JRNL TITL SMYD3 IN COMPLEX WITH FRAGMENTS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 40359 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1938 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 53.0800 - 4.3400 1.00 2992 131 0.1679 0.1867 REMARK 3 2 4.3400 - 3.4400 1.00 2839 162 0.1396 0.1574 REMARK 3 3 3.4400 - 3.0100 1.00 2787 153 0.1575 0.1746 REMARK 3 4 3.0100 - 2.7300 1.00 2821 130 0.1599 0.1689 REMARK 3 5 2.7300 - 2.5400 1.00 2781 145 0.1638 0.1976 REMARK 3 6 2.5400 - 2.3900 1.00 2782 142 0.1573 0.1856 REMARK 3 7 2.3900 - 2.2700 1.00 2758 154 0.1471 0.1823 REMARK 3 8 2.2700 - 2.1700 1.00 2767 128 0.1471 0.1989 REMARK 3 9 2.1700 - 2.0900 1.00 2759 133 0.1514 0.1826 REMARK 3 10 2.0900 - 2.0100 1.00 2777 129 0.1577 0.2009 REMARK 3 11 2.0100 - 1.9500 1.00 2742 135 0.1518 0.2103 REMARK 3 12 1.9500 - 1.8900 0.99 2693 159 0.1589 0.2087 REMARK 3 13 1.8900 - 1.8500 0.94 2568 122 0.1578 0.1792 REMARK 3 14 1.8500 - 1.8000 0.86 2355 115 0.1690 0.2079 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) : 0.122 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.891 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.02 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 : 0.012 3562 REMARK 3 ANGLE : 1.348 4808 REMARK 3 CHIRALITY : 0.056 528 REMARK 3 PLANARITY : 0.007 635 REMARK 3 DIHEDRAL : 22.187 507 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 10.0909 1.9818 8.4761 REMARK 3 T TENSOR REMARK 3 T11: 0.1545 T22: 0.1617 REMARK 3 T33: 0.2048 T12: -0.0082 REMARK 3 T13: -0.0578 T23: 0.0151 REMARK 3 L TENSOR REMARK 3 L11: 0.9239 L22: 1.3348 REMARK 3 L33: 2.5890 L12: -0.0610 REMARK 3 L13: 0.1411 L23: -0.0680 REMARK 3 S TENSOR REMARK 3 S11: 0.0087 S12: 0.0911 S13: -0.0815 REMARK 3 S21: -0.2164 S22: 0.0503 S23: 0.1216 REMARK 3 S31: 0.2765 S32: 0.0734 S33: -0.0323 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 13.0680 9.7998 -5.5893 REMARK 3 T TENSOR REMARK 3 T11: 0.3031 T22: 0.2537 REMARK 3 T33: 0.1927 T12: -0.0469 REMARK 3 T13: 0.0091 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.9138 L22: 3.2968 REMARK 3 L33: 2.2244 L12: -0.3083 REMARK 3 L13: 1.2011 L23: 0.9939 REMARK 3 S TENSOR REMARK 3 S11: -0.0884 S12: 0.2215 S13: 0.0559 REMARK 3 S21: -0.6077 S22: 0.0938 S23: -0.0217 REMARK 3 S31: -0.1678 S32: 0.1555 S33: 0.0195 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 14.1534 20.2494 5.8917 REMARK 3 T TENSOR REMARK 3 T11: 0.1826 T22: 0.1696 REMARK 3 T33: 0.1958 T12: 0.0009 REMARK 3 T13: -0.0267 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 1.7442 L22: 1.3272 REMARK 3 L33: 1.9010 L12: 0.4645 REMARK 3 L13: -0.0923 L23: -0.0415 REMARK 3 S TENSOR REMARK 3 S11: -0.1217 S12: 0.1412 S13: 0.0728 REMARK 3 S21: -0.1875 S22: 0.1006 S23: 0.0818 REMARK 3 S31: -0.1402 S32: -0.0623 S33: 0.0363 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 22.0990 -6.7577 18.2954 REMARK 3 T TENSOR REMARK 3 T11: 0.1764 T22: 0.1585 REMARK 3 T33: 0.1706 T12: -0.0032 REMARK 3 T13: -0.0202 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.6514 L22: 1.0689 REMARK 3 L33: 0.6062 L12: -0.5066 REMARK 3 L13: 0.3331 L23: -0.2161 REMARK 3 S TENSOR REMARK 3 S11: 0.0993 S12: 0.0299 S13: -0.1103 REMARK 3 S21: -0.0803 S22: -0.0356 S23: 0.0845 REMARK 3 S31: 0.1556 S32: 0.0195 S33: -0.0445 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 7QA6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119122. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.25-8.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97628 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 516903 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 53.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.05034 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26950 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.470 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: NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.25-8.75 0.1M MAGNESIUM REMARK 280 ACETATE 15-18 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 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 30.54000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.64000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.64000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.54000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.07000 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 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 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 H TYR A 97 O HOH A 603 1.13 REMARK 500 HE21 GLN A 267 O HOH A 601 1.30 REMARK 500 O HOH A 609 O HOH A 615 1.77 REMARK 500 O ASP A 262 O HOH A 601 1.89 REMARK 500 O HOH A 1001 O HOH A 1067 1.91 REMARK 500 OE1 GLU A 119 O HOH A 602 1.95 REMARK 500 N TYR A 97 O HOH A 603 1.97 REMARK 500 SD SAM A 501 O HOH A 668 2.02 REMARK 500 O HOH A 943 O HOH A 1010 2.02 REMARK 500 O HOH A 649 O HOH A 1017 2.05 REMARK 500 O HOH A 890 O HOH A 1056 2.10 REMARK 500 O HOH A 915 O HOH A 940 2.10 REMARK 500 OD2 ASP A 336 O HOH A 604 2.14 REMARK 500 OE2 GLU A 173 O HOH A 605 2.14 REMARK 500 NE2 GLN A 267 O HOH A 601 2.15 REMARK 500 O HOH A 714 O HOH A 1017 2.17 REMARK 500 O HOH A 973 O HOH A 1015 2.18 REMARK 500 O HOH A 797 O HOH A 928 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 O HOH A 927 O HOH A 1017 3645 1.48 REMARK 500 O HOH A 641 O HOH A 1017 1545 1.93 REMARK 500 O HOH A 615 O HOH A 1024 1545 1.96 REMARK 500 O HOH A 677 O HOH A 971 2555 2.03 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 LEU A 4 CG LEU A 4 CD2 0.239 REMARK 500 LYS A 84 CB LYS A 84 CG -0.172 REMARK 500 LYS A 84 CD LYS A 84 CE -0.275 REMARK 500 LYS A 84 CE LYS A 84 NZ -0.178 REMARK 500 GLU A 295 CG GLU A 295 CD 0.229 REMARK 500 GLU A 295 CD GLU A 295 OE1 0.137 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 25 CB - CG - CD ANGL. DEV. = -21.1 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 GLU A 295 OE1 - CD - OE2 ANGL. DEV. = -25.3 DEGREES REMARK 500 GLU A 295 CG - CD - OE1 ANGL. DEV. = 41.0 DEGREES REMARK 500 GLU A 295 CG - CD - OE2 ANGL. DEV. = -22.6 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 20.84 -146.62 REMARK 500 TYR A 124 134.30 -170.32 REMARK 500 LYS A 271 -5.95 78.04 REMARK 500 ALA A 427 43.23 -73.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 295 0.08 SIDE CHAIN 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 107.7 REMARK 620 3 CYS A 71 SG 111.5 108.9 REMARK 620 4 CYS A 75 SG 108.9 116.0 103.9 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 62 SG REMARK 620 2 CYS A 65 SG 109.0 REMARK 620 3 HIS A 83 NE2 113.7 105.5 REMARK 620 4 CYS A 87 SG 109.5 113.4 105.7 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 115.1 REMARK 620 3 CYS A 263 SG 107.7 106.1 REMARK 620 4 CYS A 266 SG 102.0 114.0 112.0 REMARK 620 N 1 2 3 DBREF 7QA6 A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 7QA6 GLY A -2 UNP Q9H7B4 EXPRESSION TAG SEQADV 7QA6 SER A -1 UNP Q9H7B4 EXPRESSION TAG SEQADV 7QA6 HIS A 0 UNP Q9H7B4 EXPRESSION TAG SEQADV 7QA6 ASN A 13 UNP Q9H7B4 LYS 13 ENGINEERED MUTATION SEQADV 7QA6 ARG A 140 UNP Q9H7B4 LYS 140 ENGINEERED MUTATION 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 46 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET 9W9 A 505 14 HET 9W9 A 506 14 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM ZN ZINC ION HETNAM 9W9 3-OXIDANYLBENZENECARBONITRILE HETSYN 9W9 DARUNAVIR; TMC114; UIC-94017 FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 ZN 3(ZN 2+) FORMUL 6 9W9 2(C7 H5 N O) FORMUL 8 HOH *482(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 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 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 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 2.36 LINK SG CYS A 52 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 62 ZN ZN A 504 1555 1555 2.31 LINK SG CYS A 65 ZN ZN A 504 1555 1555 2.33 LINK SG CYS A 71 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 75 ZN ZN A 503 1555 1555 2.32 LINK NE2 HIS A 83 ZN ZN A 504 1555 1555 2.06 LINK SG CYS A 87 ZN ZN A 504 1555 1555 2.31 LINK SG CYS A 208 ZN ZN A 502 1555 1555 2.33 LINK SG CYS A 261 ZN ZN A 502 1555 1555 2.35 LINK SG CYS A 263 ZN ZN A 502 1555 1555 2.33 LINK SG CYS A 266 ZN ZN A 502 1555 1555 2.32 CRYST1 61.080 66.140 107.280 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 0.016372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015119 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009321 0.00000