HEADER TRANSFERASE 14-MAR-19 6O9O
TITLE CRYSTAL STRUCTURE OF SMYD3 WITH POTENT AND SELECTIVE ISOXAZOLE AMIDE
TITLE 2 INHIBITOR 1
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 HISTONE, MYND, SET, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.A.ELKINS,L.WANG
REVDAT 2 13-MAR-24 6O9O 1 LINK
REVDAT 1 18-MAR-20 6O9O 0
JRNL AUTH D.-S.SU,P.A.ELKINS
JRNL TITL DISCOVERY OF ISOXAZOLE AMIDES AS POTENT AND SELECTIVE SMYD3
JRNL TITL 2 INHIBITORS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.59 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.14_3260)
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.61
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 60111
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.174
REMARK 3 R VALUE (WORKING SET) : 0.172
REMARK 3 FREE R VALUE : 0.200
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940
REMARK 3 FREE R VALUE TEST SET COUNT : 5654
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 56.6500 - 4.9277 0.99 3584 237 0.1740 0.1885
REMARK 3 2 4.9277 - 3.9115 1.00 3618 207 0.1355 0.1492
REMARK 3 3 3.9115 - 3.4171 1.00 3659 175 0.1457 0.1712
REMARK 3 4 3.4171 - 3.1047 1.00 3666 187 0.1596 0.1879
REMARK 3 5 3.1047 - 2.8822 1.00 3626 196 0.1675 0.2092
REMARK 3 6 2.8822 - 2.7123 1.00 3683 170 0.1711 0.1774
REMARK 3 7 2.7123 - 2.5765 1.00 3615 212 0.1738 0.2015
REMARK 3 8 2.5765 - 2.4643 1.00 3668 178 0.1699 0.2066
REMARK 3 9 2.4643 - 2.3694 1.00 3640 194 0.1739 0.1847
REMARK 3 10 2.3694 - 2.2877 1.00 3650 186 0.1723 0.2225
REMARK 3 11 2.2877 - 2.2161 1.00 3645 189 0.1712 0.2237
REMARK 3 12 2.2161 - 2.1528 1.00 3662 194 0.1766 0.2150
REMARK 3 13 2.1528 - 2.0961 1.00 3657 168 0.1768 0.2258
REMARK 3 14 2.0961 - 2.0450 1.00 3639 209 0.1838 0.2072
REMARK 3 15 2.0450 - 1.9985 1.00 3651 196 0.1780 0.2559
REMARK 3 16 1.9985 - 1.9559 1.00 3632 188 0.1904 0.2580
REMARK 3 17 1.9559 - 1.9168 1.00 3664 206 0.1816 0.2047
REMARK 3 18 1.9168 - 1.8806 1.00 3697 149 0.1777 0.2046
REMARK 3 19 1.8806 - 1.8471 1.00 3653 166 0.1830 0.1995
REMARK 3 20 1.8471 - 1.8157 1.00 3622 208 0.1850 0.2090
REMARK 3 21 1.8157 - 1.7865 1.00 3690 195 0.1903 0.2340
REMARK 3 22 1.7865 - 1.7590 1.00 3613 188 0.1887 0.2164
REMARK 3 23 1.7590 - 1.7331 1.00 3666 200 0.1925 0.2528
REMARK 3 24 1.7331 - 1.7087 1.00 3590 200 0.2016 0.2326
REMARK 3 25 1.7087 - 1.6856 1.00 3687 199 0.2151 0.2340
REMARK 3 26 1.6856 - 1.6637 1.00 3609 183 0.2241 0.2287
REMARK 3 27 1.6637 - 1.6429 1.00 3696 167 0.2338 0.2455
REMARK 3 28 1.6429 - 1.6231 0.97 3583 184 0.2605 0.3414
REMARK 3 29 1.6231 - 1.6042 0.94 3472 169 0.2735 0.3225
REMARK 3 30 1.6042 - 1.5862 0.91 3291 154 0.2849 0.3146
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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) : 0.190
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.900
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.71
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
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 6O9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-19.
REMARK 100 THE DEPOSITION ID IS D_1000240272.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-JUL-16
REMARK 200 TEMPERATURE (KELVIN) : 100
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 : 22-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60184
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.586
REMARK 200 RESOLUTION RANGE LOW (A) : 66.640
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 200 DATA REDUNDANCY : 6.900
REMARK 200 R MERGE (I) : 0.07100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6
REMARK 200 DATA REDUNDANCY IN SHELL : 5.50
REMARK 200 R MERGE FOR SHELL (I) : 0.57200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.53
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: LIBRO 24 WELL SITTING DROP TRAY.
REMARK 280 RESERVOIR SOLUTION: 10% PEG 3350, 0.2M MGOAC DROPS COMPOSED OF
REMARK 280 2UL PROTEIN + 2 UL RESERVOIR. FROZEN SEED STOCK ADDED TO ENSURE
REMARK 280 NUCLEATION. CRYSTALS SHOULD GROW OVERNIGHT AT 22C AND FULLY
REMARK 280 MATURE WITHIN 3 DAYS APO CRYSTALS WERE SOAKED WITH INHIBITOR AS
REMARK 280 FOLLOWS: 1UL 100MM COMPOUND + 1UL WELL BUFFER ADD 0.3UL TO THE
REMARK 280 DROP INCUBATE AT ROOM TEMPERATURE, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 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 30.71650
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.67000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.31800
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.67000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.71650
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.31800
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 ARG A 25 CD NE CZ NH1 NH2
REMARK 470 LYS A 42 CD CE NZ
REMARK 470 LYS A 56 CG CD CE NZ
REMARK 470 GLU A 57 CG CD OE1 OE2
REMARK 470 LYS A 58 CG CD CE NZ
REMARK 470 GLN A 64 CG CD OE1 NE2
REMARK 470 LYS A 77 CE NZ
REMARK 470 LYS A 78 CE NZ
REMARK 470 LYS A 84 CE NZ
REMARK 470 LYS A 88 CG CD CE NZ
REMARK 470 LYS A 91 CG CD CE NZ
REMARK 470 CYS A 93 SG
REMARK 470 LYS A 94 CG CD CE NZ
REMARK 470 ARG A 96 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 111 NZ
REMARK 470 LYS A 284 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 GLN A 383 CD OE1 NE2
REMARK 470 LYS A 391 CE NZ
REMARK 470 ARG A 401 CZ NH1 NH2
REMARK 470 ARG A 406 CD NE CZ NH1 NH2
REMARK 470 ARG A 426 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 19.55 -148.37
REMARK 500 TYR A 124 137.98 -173.71
REMARK 500 LYS A 271 -3.09 76.30
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 106.3
REMARK 620 3 CYS A 71 SG 113.4 111.8
REMARK 620 4 CYS A 75 SG 106.5 118.2 100.7
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 62 SG
REMARK 620 2 CYS A 65 SG 111.6
REMARK 620 3 HIS A 83 NE2 112.9 99.3
REMARK 620 4 CYS A 87 SG 112.0 112.3 108.1
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 111.0
REMARK 620 3 CYS A 263 SG 106.1 110.8
REMARK 620 4 CYS A 266 SG 98.2 115.6 114.0
REMARK 620 N 1 2 3
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 696 O
REMARK 620 2 HOH A 741 O 88.0
REMARK 620 3 HOH A 786 O 97.4 91.8
REMARK 620 4 HOH A 811 O 88.0 172.2 82.0
REMARK 620 5 HOH A 966 O 94.6 97.2 165.3 89.9
REMARK 620 6 HOH A 969 O 168.1 100.1 73.8 82.8 93.0
REMARK 620 N 1 2 3 4 5
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 HOH A 632 O
REMARK 620 2 HOH A 643 O 86.1
REMARK 620 3 HOH A 653 O 170.7 92.4
REMARK 620 4 HOH A 670 O 95.4 178.2 86.4
REMARK 620 5 HOH A 681 O 78.2 89.8 92.7 91.5
REMARK 620 6 HOH A 871 O 93.8 91.0 95.4 87.8 171.8
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 GOL A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 508
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SAH A 509
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue LUP A 510
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6NTQ RELATED DB: PDB
DBREF 6O9O A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428
SEQADV 6O9O GLY A -3 UNP Q9H7B4 EXPRESSION TAG
SEQADV 6O9O SER A -2 UNP Q9H7B4 EXPRESSION TAG
SEQADV 6O9O PHE A -1 UNP Q9H7B4 EXPRESSION TAG
SEQADV 6O9O THR A 0 UNP Q9H7B4 EXPRESSION TAG
SEQADV 6O9O 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 GOL A 506 6
HET GOL A 507 6
HET GOL A 508 6
HET SAH A 509 26
HET LUP A 510 37
HETNAM ZN ZINC ION
HETNAM MG MAGNESIUM ION
HETNAM GOL GLYCEROL
HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE
HETNAM LUP 5-CYCLOPROPYL-N-{1-[({TRANS-4-[(4,4,4-TRIFLUOROBUTYL)
HETNAM 2 LUP AMINO]CYCLOHEXYL}METHYL)SULFONYL]PIPERIDIN-4-YL}-1,2-
HETNAM 3 LUP OXAZOLE-3-CARBOXAMIDE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 ZN 3(ZN 2+)
FORMUL 5 MG 2(MG 2+)
FORMUL 7 GOL 3(C3 H8 O3)
FORMUL 10 SAH C14 H20 N6 O5 S
FORMUL 11 LUP C23 H35 F3 N4 O4 S
FORMUL 12 HOH *391(H2 O)
HELIX 1 AA1 SER A 72 ALA A 79 1 8
HELIX 2 AA2 ALA A 79 LYS A 94 1 16
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 LEU A 341 1 18
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 LEU A 30
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 503 1555 1555 2.45
LINK SG CYS A 52 ZN ZN A 503 1555 1555 2.26
LINK SG CYS A 62 ZN ZN A 502 1555 1555 2.25
LINK SG CYS A 65 ZN ZN A 502 1555 1555 2.40
LINK SG CYS A 71 ZN ZN A 503 1555 1555 2.27
LINK SG CYS A 75 ZN ZN A 503 1555 1555 2.23
LINK NE2 HIS A 83 ZN ZN A 502 1555 1555 2.09
LINK SG CYS A 87 ZN ZN A 502 1555 1555 2.29
LINK SG CYS A 208 ZN ZN A 501 1555 1555 2.43
LINK SG CYS A 261 ZN ZN A 501 1555 1555 2.26
LINK SG CYS A 263 ZN ZN A 501 1555 1555 2.30
LINK SG CYS A 266 ZN ZN A 501 1555 1555 2.31
LINK MG MG A 504 O HOH A 696 1555 1555 2.12
LINK MG MG A 504 O HOH A 741 1555 1555 2.25
LINK MG MG A 504 O HOH A 786 1555 1555 2.09
LINK MG MG A 504 O HOH A 811 1555 1545 2.25
LINK MG MG A 504 O HOH A 966 1555 1555 2.11
LINK MG MG A 504 O HOH A 969 1555 1545 2.23
LINK MG MG A 505 O HOH A 632 1555 1555 2.08
LINK MG MG A 505 O HOH A 643 1555 3644 2.18
LINK MG MG A 505 O HOH A 653 1555 1555 2.17
LINK MG MG A 505 O HOH A 670 1555 1555 2.11
LINK MG MG A 505 O HOH A 681 1555 3644 2.17
LINK MG MG A 505 O HOH A 871 1555 1555 2.02
CISPEP 1 LYS A 94 PRO A 95 0 3.56
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 696 HOH A 741 HOH A 786 HOH A 811
SITE 2 AC4 6 HOH A 966 HOH A 969
SITE 1 AC5 6 HOH A 632 HOH A 643 HOH A 653 HOH A 670
SITE 2 AC5 6 HOH A 681 HOH A 871
SITE 1 AC6 7 ASP A 332 ASP A 336 GLN A 372 LYS A 375
SITE 2 AC6 7 HOH A 684 HOH A 808 HOH A 823
SITE 1 AC7 9 SER A 213 ILE A 214 CYS A 238 HIS A 366
SITE 2 AC7 9 PRO A 367 LUP A 510 HOH A 648 HOH A 691
SITE 3 AC7 9 HOH A 701
SITE 1 AC8 6 PRO A 99 MET A 113 GLY A 115 GLN A 146
SITE 2 AC8 6 THR A 150 HOH A 715
SITE 1 AC9 21 ARG A 14 ASN A 16 TYR A 124 GLU A 130
SITE 2 AC9 21 ASN A 132 CYS A 180 ASN A 181 SER A 202
SITE 3 AC9 21 LEU A 204 ASN A 205 HIS A 206 TYR A 239
SITE 4 AC9 21 TYR A 257 PHE A 259 HOH A 639 HOH A 647
SITE 5 AC9 21 HOH A 680 HOH A 719 HOH A 771 HOH A 774
SITE 6 AC9 21 HOH A 793
SITE 1 AD1 20 CYS A 180 ASN A 181 SER A 182 PHE A 183
SITE 2 AD1 20 THR A 184 CYS A 186 GLU A 192 ILE A 237
SITE 3 AD1 20 TYR A 239 ASP A 241 TYR A 257 LEU A 290
SITE 4 AD1 20 GLU A 294 LYS A 329 CYS A 333 VAL A 368
SITE 5 AD1 20 GOL A 507 HOH A 602 HOH A 759 HOH A 810
CRYST1 61.433 66.636 107.340 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 0.016278 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015007 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009316 0.00000