HEADER TRANSFERASE 08-JUL-24 9CKC TITLE CRYSTAL STRUCTURE OF SMYD2 IN COMPLEX WITH TWO PARP1 PEPTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-LYSINE METHYLTRANSFERASE SMYD2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HSKM-B,HISTONE METHYLTRANSFERASE SMYD2,LYSINE N- COMPND 5 METHYLTRANSFERASE 3C,SET AND MYND DOMAIN-CONTAINING PROTEIN 2; COMPND 6 EC: 2.1.1.-,2.1.1.43; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: POLY [ADP-RIBOSE] POLYMERASE 1, PROCESSED C-TERMINUS; COMPND 10 CHAIN: C, D, E, F; COMPND 11 SYNONYM: POLY [ADP-RIBOSE] POLYMERASE 1,89-KDA FORM; COMPND 12 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: SMYD2, KMT3C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCDF-SUMO; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS SMYD2, PARP1, METHYLTRANSFERASE, SET AND MYND-CONTAINING PROTEIN, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,E.ALSHAMMARI,N.SPELLMON,J.BRUNZELLE,Z.YANG REVDAT 1 15-JAN-25 9CKC 0 JRNL AUTH Y.ZHANG,E.ALSHAMMARI,J.SOBOTA,N.SPELLMON,E.PERRY,T.CAO, JRNL AUTH 2 T.MUGUNAMALWATHTHA,S.SMITH,J.BRUNZELLE,G.WU,T.STEMMLER, JRNL AUTH 3 J.JIN,C.LI,Z.YANG JRNL TITL STRUCTURE OF THE SMYD2-PARP1 COMPLEX REVEALS BOTH PRODUCTIVE JRNL TITL 2 AND ALLOSTERIC MODES OF PEPTIDE BINDING. JRNL REF BIORXIV 2024 JRNL REFN ISSN 2692-8205 JRNL PMID 39677743 JRNL DOI 10.1101/2024.12.03.626679 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 3 NUMBER OF REFLECTIONS : 51079 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2578 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 66.5800 - 5.5100 1.00 3172 170 0.1649 0.1782 REMARK 3 2 5.5100 - 4.3700 1.00 3083 175 0.1356 0.1625 REMARK 3 3 4.3700 - 3.8200 0.98 3025 159 0.1411 0.1550 REMARK 3 4 3.8200 - 3.4700 0.94 2863 149 0.1595 0.1767 REMARK 3 5 3.4700 - 3.2200 0.88 2693 141 0.1817 0.2105 REMARK 3 6 3.2200 - 3.0300 1.00 3034 155 0.2103 0.2197 REMARK 3 7 3.0300 - 2.8800 1.00 3030 171 0.2153 0.2686 REMARK 3 8 2.8800 - 2.7500 1.00 3046 162 0.2139 0.2464 REMARK 3 9 2.7500 - 2.6500 0.70 2120 102 0.2262 0.2435 REMARK 3 10 2.6500 - 2.5600 1.00 3039 164 0.2196 0.2552 REMARK 3 11 2.5600 - 2.4800 1.00 2992 179 0.2170 0.2530 REMARK 3 12 2.4800 - 2.4100 1.00 3047 155 0.2188 0.2244 REMARK 3 13 2.4100 - 2.3400 1.00 2987 176 0.2179 0.2368 REMARK 3 14 2.3400 - 2.2800 0.93 2719 140 0.2315 0.2866 REMARK 3 15 2.2300 - 2.1900 0.92 1642 79 0.2594 0.2629 REMARK 3 16 2.1900 - 2.1400 1.00 3041 161 0.2520 0.3100 REMARK 3 17 2.1400 - 2.1000 1.00 2968 140 0.2649 0.2696 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) : 0.217 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.753 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.37 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 : 0.004 7303 REMARK 3 ANGLE : 0.718 9842 REMARK 3 CHIRALITY : 0.046 1052 REMARK 3 PLANARITY : 0.005 1263 REMARK 3 DIHEDRAL : 14.148 2794 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 4.6503 -11.6365 31.9171 REMARK 3 T TENSOR REMARK 3 T11: 0.1731 T22: 0.1643 REMARK 3 T33: 0.1768 T12: -0.0322 REMARK 3 T13: -0.0119 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.2111 L22: 0.1851 REMARK 3 L33: 0.2732 L12: -0.1553 REMARK 3 L13: -0.2078 L23: 0.2247 REMARK 3 S TENSOR REMARK 3 S11: -0.0089 S12: 0.0186 S13: -0.0288 REMARK 3 S21: -0.0097 S22: -0.0171 S23: 0.0260 REMARK 3 S31: -0.0054 S32: 0.0226 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND (RESID 5 THROUGH 34 OR REMARK 3 RESID 36 THROUGH 250 OR RESID 252 THROUGH REMARK 3 306 OR RESID 308 THROUGH 323 OR RESID 325 REMARK 3 THROUGH 433)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 5 THROUGH 34 OR REMARK 3 RESID 36 THROUGH 250 OR RESID 252 THROUGH REMARK 3 306 OR RESID 308 THROUGH 323 OR RESID 325 REMARK 3 THROUGH 433)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9CKC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000285686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57685 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 133.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.86200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 (%): 48.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 100 MM TRIS PH 7.5, 5% REMARK 280 ETHANOL, 1 MM PARP1 PEPTIDE, 0.6 MM ADOHCY, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 71.39600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.09250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.39600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.09250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, F 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 ARG A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 4 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 ALA B 3 REMARK 465 ARG C 522 REMARK 465 MET C 523 REMARK 465 LYS C 524 REMARK 465 LEU C 525 REMARK 465 ALA C 532 REMARK 465 VAL C 533 REMARK 465 ASP C 534 REMARK 465 ARG D 522 REMARK 465 MET D 523 REMARK 465 LYS D 524 REMARK 465 LEU D 525 REMARK 465 GLY D 530 REMARK 465 ALA D 531 REMARK 465 ALA D 532 REMARK 465 VAL D 533 REMARK 465 ASP D 534 REMARK 465 THR E 526 REMARK 465 LEU E 527 REMARK 465 LYS E 528 REMARK 465 GLY E 529 REMARK 465 GLY E 530 REMARK 465 ALA E 531 REMARK 465 ALA E 532 REMARK 465 VAL E 533 REMARK 465 ASP E 534 REMARK 465 LYS F 528 REMARK 465 GLY F 529 REMARK 465 GLY F 530 REMARK 465 ALA F 531 REMARK 465 ALA F 532 REMARK 465 VAL F 533 REMARK 465 ASP F 534 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 101 51.85 -149.13 REMARK 500 HIS A 119 74.68 -119.83 REMARK 500 PRO A 167 -178.13 -67.70 REMARK 500 VAL A 277 52.34 -112.61 REMARK 500 TYR A 377 56.97 -112.37 REMARK 500 GLU A 431 44.84 -102.87 REMARK 500 SER A 432 -53.65 -127.57 REMARK 500 ASN B 101 51.81 -149.16 REMARK 500 ASP B 142 44.63 -99.19 REMARK 500 ASN B 143 -48.17 61.89 REMARK 500 HIS B 163 -30.46 85.62 REMARK 500 PRO B 167 -177.09 -67.39 REMARK 500 VAL B 277 53.71 -111.29 REMARK 500 TYR B 377 54.29 -111.58 REMARK 500 GLU B 431 51.93 -106.09 REMARK 500 SER B 432 -54.82 -127.74 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 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 52 SG REMARK 620 2 CYS A 55 SG 107.2 REMARK 620 3 CYS A 74 SG 99.8 100.5 REMARK 620 4 CYS A 78 SG 106.4 119.7 120.9 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 65 SG REMARK 620 2 CYS A 68 SG 108.7 REMARK 620 3 HIS A 86 NE2 112.4 103.4 REMARK 620 4 CYS A 90 SG 116.5 109.4 105.7 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 209 SG REMARK 620 2 CYS A 262 SG 113.1 REMARK 620 3 CYS A 264 SG 110.1 106.4 REMARK 620 4 CYS A 267 SG 99.2 114.1 113.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 52 SG REMARK 620 2 CYS B 55 SG 105.9 REMARK 620 3 CYS B 74 SG 106.2 94.9 REMARK 620 4 CYS B 78 SG 111.8 118.4 117.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 65 SG REMARK 620 2 CYS B 68 SG 113.4 REMARK 620 3 HIS B 86 NE2 99.4 106.9 REMARK 620 4 CYS B 90 SG 111.0 126.1 94.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 209 SG REMARK 620 2 CYS B 262 SG 115.8 REMARK 620 3 CYS B 264 SG 111.9 101.4 REMARK 620 4 CYS B 267 SG 97.1 115.8 115.7 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6N3G RELATED DB: PDB DBREF 9CKC A 1 433 UNP Q9NRG4 SMYD2_HUMAN 1 433 DBREF 9CKC B 1 433 UNP Q9NRG4 SMYD2_HUMAN 1 433 DBREF 9CKC C 522 534 UNP P09874 PARP1_HUMAN 522 534 DBREF 9CKC D 522 534 UNP P09874 PARP1_HUMAN 522 534 DBREF 9CKC E 522 534 UNP P09874 PARP1_HUMAN 522 534 DBREF 9CKC F 522 534 UNP P09874 PARP1_HUMAN 522 534 SEQADV 9CKC GLU A 165 UNP Q9NRG4 GLY 165 CONFLICT SEQADV 9CKC GLU B 165 UNP Q9NRG4 GLY 165 CONFLICT SEQRES 1 A 433 MET ARG ALA GLU GLY LEU GLY GLY LEU GLU ARG PHE CYS SEQRES 2 A 433 SER PRO GLY LYS GLY ARG GLY LEU ARG ALA LEU GLN PRO SEQRES 3 A 433 PHE GLN VAL GLY ASP LEU LEU PHE SER CYS PRO ALA TYR SEQRES 4 A 433 ALA TYR VAL LEU THR VAL ASN GLU ARG GLY ASN HIS CYS SEQRES 5 A 433 GLU TYR CYS PHE THR ARG LYS GLU GLY LEU SER LYS CYS SEQRES 6 A 433 GLY ARG CYS LYS GLN ALA PHE TYR CYS ASN VAL GLU CYS SEQRES 7 A 433 GLN LYS GLU ASP TRP PRO MET HIS LYS LEU GLU CYS SER SEQRES 8 A 433 PRO MET VAL VAL PHE GLY GLU ASN TRP ASN PRO SER GLU SEQRES 9 A 433 THR VAL ARG LEU THR ALA ARG ILE LEU ALA LYS GLN LYS SEQRES 10 A 433 ILE HIS PRO GLU ARG THR PRO SER GLU LYS LEU LEU ALA SEQRES 11 A 433 VAL LYS GLU PHE GLU SER HIS LEU ASP LYS LEU ASP ASN SEQRES 12 A 433 GLU LYS LYS ASP LEU ILE GLN SER ASP ILE ALA ALA LEU SEQRES 13 A 433 HIS HIS PHE TYR SER LYS HIS LEU GLU PHE PRO ASP ASN SEQRES 14 A 433 ASP SER LEU VAL VAL LEU PHE ALA GLN VAL ASN CYS ASN SEQRES 15 A 433 GLY PHE THR ILE GLU ASP GLU GLU LEU SER HIS LEU GLY SEQRES 16 A 433 SER ALA ILE PHE PRO ASP VAL ALA LEU MET ASN HIS SER SEQRES 17 A 433 CYS CYS PRO ASN VAL ILE VAL THR TYR LYS GLY THR LEU SEQRES 18 A 433 ALA GLU VAL ARG ALA VAL GLN GLU ILE LYS PRO GLY GLU SEQRES 19 A 433 GLU VAL PHE THR SER TYR ILE ASP LEU LEU TYR PRO THR SEQRES 20 A 433 GLU ASP ARG ASN ASP ARG LEU ARG ASP SER TYR PHE PHE SEQRES 21 A 433 THR CYS GLU CYS GLN GLU CYS THR THR LYS ASP LYS ASP SEQRES 22 A 433 LYS ALA LYS VAL GLU ILE ARG LYS LEU SER ASP PRO PRO SEQRES 23 A 433 LYS ALA GLU ALA ILE ARG ASP MET VAL ARG TYR ALA ARG SEQRES 24 A 433 ASN VAL ILE GLU GLU PHE ARG ARG ALA LYS HIS TYR LYS SEQRES 25 A 433 SER PRO SER GLU LEU LEU GLU ILE CYS GLU LEU SER GLN SEQRES 26 A 433 GLU LYS MET SER SER VAL PHE GLU ASP SER ASN VAL TYR SEQRES 27 A 433 MET LEU HIS MET MET TYR GLN ALA MET GLY VAL CYS LEU SEQRES 28 A 433 TYR MET GLN ASP TRP GLU GLY ALA LEU GLN TYR GLY GLN SEQRES 29 A 433 LYS ILE ILE LYS PRO TYR SER LYS HIS TYR PRO LEU TYR SEQRES 30 A 433 SER LEU ASN VAL ALA SER MET TRP LEU LYS LEU GLY ARG SEQRES 31 A 433 LEU TYR MET GLY LEU GLU HIS LYS ALA ALA GLY GLU LYS SEQRES 32 A 433 ALA LEU LYS LYS ALA ILE ALA ILE MET GLU VAL ALA HIS SEQRES 33 A 433 GLY LYS ASP HIS PRO TYR ILE SER GLU ILE LYS GLN GLU SEQRES 34 A 433 ILE GLU SER HIS SEQRES 1 B 433 MET ARG ALA GLU GLY LEU GLY GLY LEU GLU ARG PHE CYS SEQRES 2 B 433 SER PRO GLY LYS GLY ARG GLY LEU ARG ALA LEU GLN PRO SEQRES 3 B 433 PHE GLN VAL GLY ASP LEU LEU PHE SER CYS PRO ALA TYR SEQRES 4 B 433 ALA TYR VAL LEU THR VAL ASN GLU ARG GLY ASN HIS CYS SEQRES 5 B 433 GLU TYR CYS PHE THR ARG LYS GLU GLY LEU SER LYS CYS SEQRES 6 B 433 GLY ARG CYS LYS GLN ALA PHE TYR CYS ASN VAL GLU CYS SEQRES 7 B 433 GLN LYS GLU ASP TRP PRO MET HIS LYS LEU GLU CYS SER SEQRES 8 B 433 PRO MET VAL VAL PHE GLY GLU ASN TRP ASN PRO SER GLU SEQRES 9 B 433 THR VAL ARG LEU THR ALA ARG ILE LEU ALA LYS GLN LYS SEQRES 10 B 433 ILE HIS PRO GLU ARG THR PRO SER GLU LYS LEU LEU ALA SEQRES 11 B 433 VAL LYS GLU PHE GLU SER HIS LEU ASP LYS LEU ASP ASN SEQRES 12 B 433 GLU LYS LYS ASP LEU ILE GLN SER ASP ILE ALA ALA LEU SEQRES 13 B 433 HIS HIS PHE TYR SER LYS HIS LEU GLU PHE PRO ASP ASN SEQRES 14 B 433 ASP SER LEU VAL VAL LEU PHE ALA GLN VAL ASN CYS ASN SEQRES 15 B 433 GLY PHE THR ILE GLU ASP GLU GLU LEU SER HIS LEU GLY SEQRES 16 B 433 SER ALA ILE PHE PRO ASP VAL ALA LEU MET ASN HIS SER SEQRES 17 B 433 CYS CYS PRO ASN VAL ILE VAL THR TYR LYS GLY THR LEU SEQRES 18 B 433 ALA GLU VAL ARG ALA VAL GLN GLU ILE LYS PRO GLY GLU SEQRES 19 B 433 GLU VAL PHE THR SER TYR ILE ASP LEU LEU TYR PRO THR SEQRES 20 B 433 GLU ASP ARG ASN ASP ARG LEU ARG ASP SER TYR PHE PHE SEQRES 21 B 433 THR CYS GLU CYS GLN GLU CYS THR THR LYS ASP LYS ASP SEQRES 22 B 433 LYS ALA LYS VAL GLU ILE ARG LYS LEU SER ASP PRO PRO SEQRES 23 B 433 LYS ALA GLU ALA ILE ARG ASP MET VAL ARG TYR ALA ARG SEQRES 24 B 433 ASN VAL ILE GLU GLU PHE ARG ARG ALA LYS HIS TYR LYS SEQRES 25 B 433 SER PRO SER GLU LEU LEU GLU ILE CYS GLU LEU SER GLN SEQRES 26 B 433 GLU LYS MET SER SER VAL PHE GLU ASP SER ASN VAL TYR SEQRES 27 B 433 MET LEU HIS MET MET TYR GLN ALA MET GLY VAL CYS LEU SEQRES 28 B 433 TYR MET GLN ASP TRP GLU GLY ALA LEU GLN TYR GLY GLN SEQRES 29 B 433 LYS ILE ILE LYS PRO TYR SER LYS HIS TYR PRO LEU TYR SEQRES 30 B 433 SER LEU ASN VAL ALA SER MET TRP LEU LYS LEU GLY ARG SEQRES 31 B 433 LEU TYR MET GLY LEU GLU HIS LYS ALA ALA GLY GLU LYS SEQRES 32 B 433 ALA LEU LYS LYS ALA ILE ALA ILE MET GLU VAL ALA HIS SEQRES 33 B 433 GLY LYS ASP HIS PRO TYR ILE SER GLU ILE LYS GLN GLU SEQRES 34 B 433 ILE GLU SER HIS SEQRES 1 C 13 ARG MET LYS LEU THR LEU LYS GLY GLY ALA ALA VAL ASP SEQRES 1 D 13 ARG MET LYS LEU THR LEU LYS GLY GLY ALA ALA VAL ASP SEQRES 1 E 13 ARG MET LYS LEU THR LEU LYS GLY GLY ALA ALA VAL ASP SEQRES 1 F 13 ARG MET LYS LEU THR LEU LYS GLY GLY ALA ALA VAL ASP HET SAH A 501 26 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET SAH B 501 26 HET ZN B 502 1 HET ZN B 503 1 HET ZN B 504 1 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION FORMUL 7 SAH 2(C14 H20 N6 O5 S) FORMUL 8 ZN 6(ZN 2+) FORMUL 15 HOH *420(H2 O) HELIX 1 AA1 VAL A 45 ARG A 48 5 4 HELIX 2 AA2 ASN A 75 LYS A 87 1 13 HELIX 3 AA3 GLU A 89 GLY A 97 1 9 HELIX 4 AA4 GLU A 98 TRP A 100 5 3 HELIX 5 AA5 SER A 103 HIS A 119 1 17 HELIX 6 AA6 ALA A 130 PHE A 134 5 5 HELIX 7 AA7 HIS A 137 LEU A 141 5 5 HELIX 8 AA8 ASP A 142 SER A 161 1 20 HELIX 9 AA9 ASP A 168 GLY A 183 1 16 HELIX 10 AB1 PHE A 199 LEU A 204 1 6 HELIX 11 AB2 PRO A 246 PHE A 259 1 14 HELIX 12 AB3 CYS A 264 LYS A 270 1 7 HELIX 13 AB4 LYS A 272 VAL A 277 1 6 HELIX 14 AB5 LYS A 287 LYS A 309 1 23 HELIX 15 AB6 SER A 313 SER A 330 1 18 HELIX 16 AB7 ASN A 336 MET A 353 1 18 HELIX 17 AB8 ASP A 355 TYR A 374 1 20 HELIX 18 AB9 SER A 378 LEU A 395 1 18 HELIX 19 AC1 HIS A 397 GLY A 417 1 21 HELIX 20 AC2 HIS A 420 GLU A 431 1 12 HELIX 21 AC3 VAL B 45 ARG B 48 5 4 HELIX 22 AC4 ASN B 75 LYS B 87 1 13 HELIX 23 AC5 GLU B 89 GLY B 97 1 9 HELIX 24 AC6 GLU B 98 TRP B 100 5 3 HELIX 25 AC7 SER B 103 HIS B 119 1 17 HELIX 26 AC8 THR B 123 LYS B 127 5 5 HELIX 27 AC9 ALA B 130 PHE B 134 5 5 HELIX 28 AD1 HIS B 137 LEU B 141 5 5 HELIX 29 AD2 ASN B 143 SER B 161 1 19 HELIX 30 AD3 ASP B 168 GLY B 183 1 16 HELIX 31 AD4 PHE B 199 LEU B 204 1 6 HELIX 32 AD5 PRO B 246 PHE B 259 1 14 HELIX 33 AD6 CYS B 264 LYS B 270 1 7 HELIX 34 AD7 LYS B 272 VAL B 277 1 6 HELIX 35 AD8 LYS B 287 LYS B 309 1 23 HELIX 36 AD9 SER B 313 SER B 329 1 17 HELIX 37 AE1 ASN B 336 MET B 353 1 18 HELIX 38 AE2 ASP B 355 TYR B 374 1 20 HELIX 39 AE3 SER B 378 LEU B 395 1 18 HELIX 40 AE4 HIS B 397 GLY B 417 1 21 HELIX 41 AE5 HIS B 420 GLU B 431 1 12 SHEET 1 AA1 2 LEU A 9 SER A 14 0 SHEET 2 AA1 2 GLY A 18 ALA A 23 -1 O ARG A 22 N GLU A 10 SHEET 1 AA2 3 LEU A 32 PRO A 37 0 SHEET 2 AA2 3 LEU A 221 ALA A 226 -1 O VAL A 224 N LEU A 33 SHEET 3 AA2 3 VAL A 213 LYS A 218 -1 N THR A 216 O GLU A 223 SHEET 1 AA3 3 ALA A 40 LEU A 43 0 SHEET 2 AA3 3 HIS A 193 ILE A 198 -1 O ILE A 198 N ALA A 40 SHEET 3 AA3 3 PHE A 184 GLU A 187 -1 N ILE A 186 O LEU A 194 SHEET 1 AA4 2 SER A 63 LYS A 64 0 SHEET 2 AA4 2 PHE A 72 TYR A 73 -1 O TYR A 73 N SER A 63 SHEET 1 AA5 2 ASN A 206 HIS A 207 0 SHEET 2 AA5 2 PHE A 237 THR A 238 1 O THR A 238 N ASN A 206 SHEET 1 AA6 2 LEU B 9 SER B 14 0 SHEET 2 AA6 2 GLY B 18 ALA B 23 -1 O ARG B 22 N GLU B 10 SHEET 1 AA7 3 LEU B 32 PRO B 37 0 SHEET 2 AA7 3 LEU B 221 ALA B 226 -1 O VAL B 224 N LEU B 33 SHEET 3 AA7 3 VAL B 213 LYS B 218 -1 N LYS B 218 O LEU B 221 SHEET 1 AA8 3 ALA B 40 LEU B 43 0 SHEET 2 AA8 3 HIS B 193 ILE B 198 -1 O ILE B 198 N ALA B 40 SHEET 3 AA8 3 PHE B 184 GLU B 187 -1 N PHE B 184 O ALA B 197 SHEET 1 AA9 2 SER B 63 LYS B 64 0 SHEET 2 AA9 2 PHE B 72 TYR B 73 -1 O TYR B 73 N SER B 63 SHEET 1 AB1 2 ASN B 206 HIS B 207 0 SHEET 2 AB1 2 PHE B 237 THR B 238 1 O THR B 238 N ASN B 206 LINK SG CYS A 52 ZN ZN A 504 1555 1555 2.46 LINK SG CYS A 55 ZN ZN A 504 1555 1555 2.35 LINK SG CYS A 65 ZN ZN A 502 1555 1555 2.43 LINK SG CYS A 68 ZN ZN A 502 1555 1555 2.29 LINK SG CYS A 74 ZN ZN A 504 1555 1555 2.37 LINK SG CYS A 78 ZN ZN A 504 1555 1555 2.38 LINK NE2 HIS A 86 ZN ZN A 502 1555 1555 2.07 LINK SG CYS A 90 ZN ZN A 502 1555 1555 2.31 LINK SG CYS A 209 ZN ZN A 503 1555 1555 2.31 LINK SG CYS A 262 ZN ZN A 503 1555 1555 2.34 LINK SG CYS A 264 ZN ZN A 503 1555 1555 2.39 LINK SG CYS A 267 ZN ZN A 503 1555 1555 2.31 LINK SG CYS B 52 ZN ZN B 504 1555 1555 2.43 LINK SG CYS B 55 ZN ZN B 504 1555 1555 2.56 LINK SG CYS B 65 ZN ZN B 502 1555 1555 2.28 LINK SG CYS B 68 ZN ZN B 502 1555 1555 2.40 LINK SG CYS B 74 ZN ZN B 504 1555 1555 2.32 LINK SG CYS B 78 ZN ZN B 504 1555 1555 2.35 LINK NE2 HIS B 86 ZN ZN B 502 1555 1555 2.29 LINK SG CYS B 90 ZN ZN B 502 1555 1555 2.66 LINK SG CYS B 209 ZN ZN B 503 1555 1555 2.38 LINK SG CYS B 262 ZN ZN B 503 1555 1555 2.34 LINK SG CYS B 264 ZN ZN B 503 1555 1555 2.42 LINK SG CYS B 267 ZN ZN B 503 1555 1555 2.31 CRYST1 142.792 52.185 144.916 90.00 113.24 90.00 C 1 2 1 16 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 0.007003 0.000000 0.003008 0.00000 SCALE2 0.000000 0.019163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007510 0.00000