HEADER TRANSCRIPTION/TRANSFERASE 07-DEC-16 5U62 TITLE CRYSTAL STRUCTURE OF EED IN COMPLEX WITH H3K27ME3 PEPTIDE AND 6- TITLE 2 (BENZO[D][1,3]DIOXOL-4-YLMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,5- TITLE 3 A]PYRIDIN-3-AMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYCOMB PROTEIN EED; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 76-441; COMPND 5 SYNONYM: HEED,WD PROTEIN ASSOCIATING WITH INTEGRIN CYTOPLASMIC TAILS COMPND 6 1,WAIT-1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE EZH2; COMPND 10 CHAIN: C, D; COMPND 11 FRAGMENT: UNP RESIDUES 39-68; COMPND 12 SYNONYM: ENX-1,ENHANCER OF ZESTE HOMOLOG 2,LYSINE N-METHYLTRANSFERASE COMPND 13 6; COMPND 14 EC: 2.1.1.43; COMPND 15 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: EED; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS EED, FRAGMENT-BASED GENERATION, ONCOLOGY, TRANSCRIPTION-TRANSFERASE KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.BUSSIERE,W.SHU REVDAT 5 06-MAR-24 5U62 1 LINK REVDAT 4 27-SEP-17 5U62 1 REMARK REVDAT 3 25-JAN-17 5U62 1 JRNL REVDAT 2 18-JAN-17 5U62 1 JRNL REVDAT 1 11-JAN-17 5U62 0 JRNL AUTH A.LINGEL,M.SENDZIK,Y.HUANG,M.D.SHULTZ,J.CANTWELL,M.P.DILLON, JRNL AUTH 2 X.FU,J.FULLER,T.GABRIEL,J.GU,X.JIANG,L.LI,F.LIANG,M.MCKENNA, JRNL AUTH 3 W.QI,W.RAO,X.SHENG,W.SHU,J.SUTTON,B.TAFT,L.WANG,J.ZENG, JRNL AUTH 4 H.ZHANG,M.ZHANG,K.ZHAO,M.LINDVALL,D.E.BUSSIERE JRNL TITL STRUCTURE-GUIDED DESIGN OF EED BINDERS ALLOSTERICALLY JRNL TITL 2 INHIBITING THE EPIGENETIC POLYCOMB REPRESSIVE COMPLEX 2 JRNL TITL 3 (PRC2) METHYLTRANSFERASE. JRNL REF J. MED. CHEM. V. 60 415 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 27992714 JRNL DOI 10.1021/ACS.JMEDCHEM.6B01473 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 65103 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 3159 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.95 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.57 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3597 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2310 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3425 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.78 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 172 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6100 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.72020 REMARK 3 B22 (A**2) : 3.14340 REMARK 3 B33 (A**2) : 3.57680 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.200 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.154 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.136 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.139 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.130 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6340 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8602 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2213 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 159 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 919 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6340 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 817 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 14 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 7580 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.09 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.69 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.24 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 25.1671 65.6173 0.8577 REMARK 3 T TENSOR REMARK 3 T11: -0.0973 T22: -0.0473 REMARK 3 T33: -0.0629 T12: 0.0075 REMARK 3 T13: -0.0050 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.4852 L22: 1.8193 REMARK 3 L33: 1.3646 L12: -0.1496 REMARK 3 L13: 0.0879 L23: 0.6520 REMARK 3 S TENSOR REMARK 3 S11: -0.0028 S12: -0.0151 S13: -0.0262 REMARK 3 S21: -0.0107 S22: 0.0919 S23: -0.0640 REMARK 3 S31: -0.0038 S32: 0.0723 S33: -0.0891 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 27.7366 19.8731 24.2282 REMARK 3 T TENSOR REMARK 3 T11: -0.0979 T22: -0.0550 REMARK 3 T33: -0.0769 T12: -0.0173 REMARK 3 T13: 0.0134 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.3661 L22: 2.2340 REMARK 3 L33: 1.3813 L12: -0.0202 REMARK 3 L13: -0.1529 L23: 0.8467 REMARK 3 S TENSOR REMARK 3 S11: -0.0094 S12: -0.0065 S13: 0.0168 REMARK 3 S21: -0.0973 S22: 0.1074 S23: -0.0728 REMARK 3 S31: -0.0876 S32: 0.0596 S33: -0.0980 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): 17.2116 56.1214 13.8901 REMARK 3 T TENSOR REMARK 3 T11: 0.0290 T22: -0.0170 REMARK 3 T33: -0.1121 T12: -0.0274 REMARK 3 T13: 0.0573 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 2.5117 L22: 3.1815 REMARK 3 L33: 0.8336 L12: -2.6926 REMARK 3 L13: -1.4181 L23: -1.4991 REMARK 3 S TENSOR REMARK 3 S11: -0.0265 S12: -0.0917 S13: -0.0059 REMARK 3 S21: 0.2529 S22: 0.0784 S23: 0.2984 REMARK 3 S31: 0.2839 S32: 0.0520 S33: -0.0519 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): 16.8241 27.2536 12.2109 REMARK 3 T TENSOR REMARK 3 T11: 0.1101 T22: -0.0592 REMARK 3 T33: -0.1241 T12: 0.0641 REMARK 3 T13: -0.0676 T23: 0.0242 REMARK 3 L TENSOR REMARK 3 L11: 2.8972 L22: 2.1195 REMARK 3 L33: 0.7137 L12: 2.6608 REMARK 3 L13: 0.3200 L23: -0.1305 REMARK 3 S TENSOR REMARK 3 S11: 0.0064 S12: -0.0350 S13: 0.0050 REMARK 3 S21: -0.5452 S22: -0.1474 S23: 0.3353 REMARK 3 S31: -0.3394 S32: -0.0662 S33: 0.1410 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5U62 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225382. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 270 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65168 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: USING A PEG/SALT COMBINATION AS A REMARK 280 PRECIPITANT. BRIEFLY, EED WAS INCUBATED WITH 10 MM B- REMARK 280 NICOTINAMIDE ADENINE DINUCLEOTIDE HYDRATE, 2 MM OF A TIGHTLY REMARK 280 BINDING PROPRIETARY COMPOUND, AND 0.5 MM OF A SYNTHESIZED REMARK 280 PEPTIDE WHICH COMPRISES THE HELIX ON EZH2 WHICH INTERACTS WITH REMARK 280 EED. THE CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION METHOD. REMARK 280 ONE UL OF THE PROTEIN MIXTURE WAS COMBINED WITH 1 UL OF A REMARK 280 PRECIPITANT COMPRISED OF 20% (W/V) PEG3350, 0.2 M POTASSIUM REMARK 280 IODIDE, AND 0.1M TRIS-HCL, PH 8.5, ON A COVER SLIP WHICH WAS REMARK 280 SUSPENDED OVER A RESERVOIR COMPRISED OF 0.5 ML OF PRECIPITANT AT REMARK 280 18 CELSIUS AND SEALED. THE CRYSTALS GREW IN 4-6 DAYS AT 18 REMARK 280 CELSIUS AND THEN HARVESTED AND SOAKED IN DEFINED DROPS REMARK 280 CONSISTING OF 30 UL OF PRECIPITANT AND 2 MM OF COMPOUND FOR 24 REMARK 280 H. CRYSTALS WERE CRYOPRESERVED FOR DATA COLLECTION USING A REMARK 280 CRYOSOLUTION CONSISTING OF 30% PEG 400 (V/V), 20% (W/V) PEG 3350, REMARK 280 0.2 M POTASSIUM IODIDE, AND 0.1M TRIS-HCL, PH 8.5., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 46.44050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 89.05650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.44050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 89.05650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 75 REMARK 465 LYS A 76 REMARK 465 LYS A 77 REMARK 465 CYS A 78 REMARK 465 ASN A 281 REMARK 465 PRO A 282 REMARK 465 ASN A 283 REMARK 465 LYS A 284 REMARK 465 THR A 285 REMARK 465 ASN A 286 REMARK 465 GLU A 394 REMARK 465 ASP A 395 REMARK 465 PRO A 396 REMARK 465 HIS A 397 REMARK 465 LYS A 398 REMARK 465 ALA A 399 REMARK 465 LYS A 400 REMARK 465 ARG A 441 REMARK 465 GLY B 75 REMARK 465 LYS B 76 REMARK 465 LYS B 77 REMARK 465 CYS B 78 REMARK 465 LYS B 79 REMARK 465 GLU B 394 REMARK 465 ASP B 395 REMARK 465 PRO B 396 REMARK 465 HIS B 397 REMARK 465 LYS B 398 REMARK 465 ALA B 399 REMARK 465 LYS B 400 REMARK 465 ARG B 441 REMARK 465 LYS C 39 REMARK 465 SER C 40 REMARK 465 MET C 41 REMARK 465 PHE C 42 REMARK 465 LYS D 39 REMARK 465 SER D 40 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 GLU A 107 CG CD OE1 OE2 REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 ARG A 287 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 ARG A 302 NE CZ NH1 NH2 REMARK 470 ARG A 306 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 344 CG CD CE NZ REMARK 470 VAL A 393 CG1 CG2 REMARK 470 LYS B 83 CG CD CE NZ REMARK 470 LYS B 106 CG CD CE NZ REMARK 470 GLU B 107 CG CD OE1 OE2 REMARK 470 LYS B 275 CG CD CE NZ REMARK 470 LYS B 284 CG CD CE NZ REMARK 470 ASN B 286 CG OD1 ND2 REMARK 470 LYS B 293 CG CD CE NZ REMARK 470 LYS B 344 CG CD CE NZ REMARK 470 VAL B 393 CG1 CG2 REMARK 470 GLN C 47 CG CD OE1 NE2 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 SER A 118 -139.11 52.17 REMARK 500 ASN A 191 -164.67 -165.01 REMARK 500 PHE A 299 146.58 -172.20 REMARK 500 SER A 323 -153.75 -122.74 REMARK 500 CYS A 361 55.97 -140.74 REMARK 500 TYR A 365 63.14 73.72 REMARK 500 SER B 118 -140.22 53.16 REMARK 500 LEU B 135 -81.51 -93.70 REMARK 500 HIS B 213 9.60 81.19 REMARK 500 PHE B 299 148.51 -173.16 REMARK 500 SER B 323 -151.88 -122.91 REMARK 500 CYS B 361 49.88 -141.85 REMARK 500 TYR B 365 63.84 75.57 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 A 973 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH A 974 DISTANCE = 8.84 ANGSTROMS REMARK 525 HOH B 965 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH B 966 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH B 967 DISTANCE = 7.54 ANGSTROMS REMARK 525 HOH B 968 DISTANCE = 7.68 ANGSTROMS REMARK 525 HOH B 969 DISTANCE = 7.95 ANGSTROMS REMARK 525 HOH B 970 DISTANCE = 10.04 ANGSTROMS REMARK 525 HOH B 971 DISTANCE = 11.52 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 YT3 A 502 Y REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 637 O REMARK 620 2 ARG B 269 NH1 42.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YT3 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YT3 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7WD A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7WD B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U5H RELATED DB: PDB REMARK 900 RELATED ID: 5U5K RELATED DB: PDB REMARK 900 RELATED ID: 5U5T RELATED DB: PDB DBREF 5U62 A 76 441 UNP O75530 EED_HUMAN 76 441 DBREF 5U62 B 76 441 UNP O75530 EED_HUMAN 76 441 DBREF 5U62 C 39 68 UNP Q15910 EZH2_HUMAN 39 68 DBREF 5U62 D 39 68 UNP Q15910 EZH2_HUMAN 39 68 SEQADV 5U62 GLY A 75 UNP O75530 EXPRESSION TAG SEQADV 5U62 GLY B 75 UNP O75530 EXPRESSION TAG SEQRES 1 A 367 GLY LYS LYS CYS LYS TYR SER PHE LYS CYS VAL ASN SER SEQRES 2 A 367 LEU LYS GLU ASP HIS ASN GLN PRO LEU PHE GLY VAL GLN SEQRES 3 A 367 PHE ASN TRP HIS SER LYS GLU GLY ASP PRO LEU VAL PHE SEQRES 4 A 367 ALA THR VAL GLY SER ASN ARG VAL THR LEU TYR GLU CYS SEQRES 5 A 367 HIS SER GLN GLY GLU ILE ARG LEU LEU GLN SER TYR VAL SEQRES 6 A 367 ASP ALA ASP ALA ASP GLU ASN PHE TYR THR CYS ALA TRP SEQRES 7 A 367 THR TYR ASP SER ASN THR SER HIS PRO LEU LEU ALA VAL SEQRES 8 A 367 ALA GLY SER ARG GLY ILE ILE ARG ILE ILE ASN PRO ILE SEQRES 9 A 367 THR MET GLN CYS ILE LYS HIS TYR VAL GLY HIS GLY ASN SEQRES 10 A 367 ALA ILE ASN GLU LEU LYS PHE HIS PRO ARG ASP PRO ASN SEQRES 11 A 367 LEU LEU LEU SER VAL SER LYS ASP HIS ALA LEU ARG LEU SEQRES 12 A 367 TRP ASN ILE GLN THR ASP THR LEU VAL ALA ILE PHE GLY SEQRES 13 A 367 GLY VAL GLU GLY HIS ARG ASP GLU VAL LEU SER ALA ASP SEQRES 14 A 367 TYR ASP LEU LEU GLY GLU LYS ILE MET SER CYS GLY MET SEQRES 15 A 367 ASP HIS SER LEU LYS LEU TRP ARG ILE ASN SER LYS ARG SEQRES 16 A 367 MET MET ASN ALA ILE LYS GLU SER TYR ASP TYR ASN PRO SEQRES 17 A 367 ASN LYS THR ASN ARG PRO PHE ILE SER GLN LYS ILE HIS SEQRES 18 A 367 PHE PRO ASP PHE SER THR ARG ASP ILE HIS ARG ASN TYR SEQRES 19 A 367 VAL ASP CYS VAL ARG TRP LEU GLY ASP LEU ILE LEU SER SEQRES 20 A 367 LYS SER CYS GLU ASN ALA ILE VAL CYS TRP LYS PRO GLY SEQRES 21 A 367 LYS MET GLU ASP ASP ILE ASP LYS ILE LYS PRO SER GLU SEQRES 22 A 367 SER ASN VAL THR ILE LEU GLY ARG PHE ASP TYR SER GLN SEQRES 23 A 367 CYS ASP ILE TRP TYR MET ARG PHE SER MET ASP PHE TRP SEQRES 24 A 367 GLN LYS MET LEU ALA LEU GLY ASN GLN VAL GLY LYS LEU SEQRES 25 A 367 TYR VAL TRP ASP LEU GLU VAL GLU ASP PRO HIS LYS ALA SEQRES 26 A 367 LYS CYS THR THR LEU THR HIS HIS LYS CYS GLY ALA ALA SEQRES 27 A 367 ILE ARG GLN THR SER PHE SER ARG ASP SER SER ILE LEU SEQRES 28 A 367 ILE ALA VAL CYS ASP ASP ALA SER ILE TRP ARG TRP ASP SEQRES 29 A 367 ARG LEU ARG SEQRES 1 B 367 GLY LYS LYS CYS LYS TYR SER PHE LYS CYS VAL ASN SER SEQRES 2 B 367 LEU LYS GLU ASP HIS ASN GLN PRO LEU PHE GLY VAL GLN SEQRES 3 B 367 PHE ASN TRP HIS SER LYS GLU GLY ASP PRO LEU VAL PHE SEQRES 4 B 367 ALA THR VAL GLY SER ASN ARG VAL THR LEU TYR GLU CYS SEQRES 5 B 367 HIS SER GLN GLY GLU ILE ARG LEU LEU GLN SER TYR VAL SEQRES 6 B 367 ASP ALA ASP ALA ASP GLU ASN PHE TYR THR CYS ALA TRP SEQRES 7 B 367 THR TYR ASP SER ASN THR SER HIS PRO LEU LEU ALA VAL SEQRES 8 B 367 ALA GLY SER ARG GLY ILE ILE ARG ILE ILE ASN PRO ILE SEQRES 9 B 367 THR MET GLN CYS ILE LYS HIS TYR VAL GLY HIS GLY ASN SEQRES 10 B 367 ALA ILE ASN GLU LEU LYS PHE HIS PRO ARG ASP PRO ASN SEQRES 11 B 367 LEU LEU LEU SER VAL SER LYS ASP HIS ALA LEU ARG LEU SEQRES 12 B 367 TRP ASN ILE GLN THR ASP THR LEU VAL ALA ILE PHE GLY SEQRES 13 B 367 GLY VAL GLU GLY HIS ARG ASP GLU VAL LEU SER ALA ASP SEQRES 14 B 367 TYR ASP LEU LEU GLY GLU LYS ILE MET SER CYS GLY MET SEQRES 15 B 367 ASP HIS SER LEU LYS LEU TRP ARG ILE ASN SER LYS ARG SEQRES 16 B 367 MET MET ASN ALA ILE LYS GLU SER TYR ASP TYR ASN PRO SEQRES 17 B 367 ASN LYS THR ASN ARG PRO PHE ILE SER GLN LYS ILE HIS SEQRES 18 B 367 PHE PRO ASP PHE SER THR ARG ASP ILE HIS ARG ASN TYR SEQRES 19 B 367 VAL ASP CYS VAL ARG TRP LEU GLY ASP LEU ILE LEU SER SEQRES 20 B 367 LYS SER CYS GLU ASN ALA ILE VAL CYS TRP LYS PRO GLY SEQRES 21 B 367 LYS MET GLU ASP ASP ILE ASP LYS ILE LYS PRO SER GLU SEQRES 22 B 367 SER ASN VAL THR ILE LEU GLY ARG PHE ASP TYR SER GLN SEQRES 23 B 367 CYS ASP ILE TRP TYR MET ARG PHE SER MET ASP PHE TRP SEQRES 24 B 367 GLN LYS MET LEU ALA LEU GLY ASN GLN VAL GLY LYS LEU SEQRES 25 B 367 TYR VAL TRP ASP LEU GLU VAL GLU ASP PRO HIS LYS ALA SEQRES 26 B 367 LYS CYS THR THR LEU THR HIS HIS LYS CYS GLY ALA ALA SEQRES 27 B 367 ILE ARG GLN THR SER PHE SER ARG ASP SER SER ILE LEU SEQRES 28 B 367 ILE ALA VAL CYS ASP ASP ALA SER ILE TRP ARG TRP ASP SEQRES 29 B 367 ARG LEU ARG SEQRES 1 C 30 LYS SER MET PHE SER SER ASN ARG GLN LYS ILE LEU GLU SEQRES 2 C 30 ARG THR GLU ILE LEU ASN GLN GLU TRP LYS GLN ARG ARG SEQRES 3 C 30 ILE GLN PRO VAL SEQRES 1 D 30 LYS SER MET PHE SER SER ASN ARG GLN LYS ILE LEU GLU SEQRES 2 D 30 ARG THR GLU ILE LEU ASN GLN GLU TRP LYS GLN ARG ARG SEQRES 3 D 30 ILE GLN PRO VAL HET GOL A 501 6 HET YT3 A 502 1 HET YT3 A 503 1 HET 7WD A 504 20 HET 7WD B 501 20 HETNAM GOL GLYCEROL HETNAM YT3 YTTRIUM (III) ION HETNAM 7WD (6S)-6-[(2H-1,3-BENZODIOXOL-4-YL)METHYL]-5,6,7,8- HETNAM 2 7WD TETRAHYDROIMIDAZO[1,5-A]PYRIDIN-3-AMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 YT3 2(Y 3+) FORMUL 8 7WD 2(C15 H17 N3 O2) FORMUL 10 HOH *800(H2 O) HELIX 1 AA1 SER A 267 TYR A 280 1 14 HELIX 2 AA2 ASP A 339 ILE A 343 5 5 HELIX 3 AA3 SER B 267 TYR B 280 1 14 HELIX 4 AA4 SER C 44 ARG C 63 1 20 HELIX 5 AA5 PHE D 42 ARG D 63 1 22 SHEET 1 AA1 4 PHE A 82 LYS A 89 0 SHEET 2 AA1 4 SER A 433 ARG A 439 -1 O ARG A 436 N ASN A 86 SHEET 3 AA1 4 ILE A 424 CYS A 429 -1 N LEU A 425 O TRP A 437 SHEET 4 AA1 4 ILE A 413 PHE A 418 -1 N SER A 417 O ILE A 426 SHEET 1 AA2 4 LEU A 96 PHE A 101 0 SHEET 2 AA2 4 LEU A 111 GLY A 117 -1 O ALA A 114 N GLN A 100 SHEET 3 AA2 4 ARG A 120 CYS A 126 -1 O CYS A 126 N LEU A 111 SHEET 4 AA2 4 ILE A 132 VAL A 139 -1 O TYR A 138 N VAL A 121 SHEET 1 AA3 4 PHE A 147 TYR A 154 0 SHEET 2 AA3 4 PRO A 161 GLY A 167 -1 O ALA A 164 N ALA A 151 SHEET 3 AA3 4 ILE A 172 ASN A 176 -1 O ILE A 175 N LEU A 163 SHEET 4 AA3 4 GLN A 181 TYR A 186 -1 O ILE A 183 N ILE A 174 SHEET 1 AA4 5 ILE A 193 PHE A 198 0 SHEET 2 AA4 5 LEU A 205 SER A 210 -1 O LEU A 207 N LYS A 197 SHEET 3 AA4 5 LEU A 215 ASN A 219 -1 O TRP A 218 N LEU A 206 SHEET 4 AA4 5 THR A 224 PHE A 229 -1 O PHE A 229 N LEU A 215 SHEET 5 AA4 5 GLN A 292 ILE A 294 1 O ILE A 294 N ILE A 228 SHEET 1 AA5 4 VAL A 239 TYR A 244 0 SHEET 2 AA5 4 LYS A 250 GLY A 255 -1 O CYS A 254 N SER A 241 SHEET 3 AA5 4 LEU A 260 ARG A 264 -1 O TRP A 263 N ILE A 251 SHEET 4 AA5 4 PHE A 299 THR A 301 -1 O PHE A 299 N LEU A 262 SHEET 1 AA6 4 CYS A 311 LEU A 315 0 SHEET 2 AA6 4 LEU A 318 LYS A 322 -1 O LEU A 318 N LEU A 315 SHEET 3 AA6 4 ALA A 327 PRO A 333 -1 O VAL A 329 N SER A 321 SHEET 4 AA6 4 VAL A 350 ASP A 357 -1 O LEU A 353 N CYS A 330 SHEET 1 AA7 4 PHE A 368 MET A 370 0 SHEET 2 AA7 4 MET A 376 GLY A 380 -1 O ALA A 378 N SER A 369 SHEET 3 AA7 4 LEU A 386 ASP A 390 -1 O TYR A 387 N LEU A 379 SHEET 4 AA7 4 THR A 402 LEU A 404 -1 O LEU A 404 N LEU A 386 SHEET 1 AA8 4 SER B 81 LYS B 89 0 SHEET 2 AA8 4 SER B 433 LEU B 440 -1 O LEU B 440 N SER B 81 SHEET 3 AA8 4 ILE B 424 CYS B 429 -1 N LEU B 425 O TRP B 437 SHEET 4 AA8 4 ILE B 413 PHE B 418 -1 N SER B 417 O ILE B 426 SHEET 1 AA9 4 LEU B 96 PHE B 101 0 SHEET 2 AA9 4 LEU B 111 GLY B 117 -1 O ALA B 114 N GLN B 100 SHEET 3 AA9 4 ARG B 120 CYS B 126 -1 O CYS B 126 N LEU B 111 SHEET 4 AA9 4 ILE B 132 VAL B 139 -1 O ARG B 133 N GLU B 125 SHEET 1 AB1 4 PHE B 147 TYR B 154 0 SHEET 2 AB1 4 PRO B 161 GLY B 167 -1 O LEU B 162 N THR B 153 SHEET 3 AB1 4 ILE B 172 ASN B 176 -1 O ILE B 175 N LEU B 163 SHEET 4 AB1 4 GLN B 181 TYR B 186 -1 O LYS B 184 N ILE B 174 SHEET 1 AB2 5 ILE B 193 PHE B 198 0 SHEET 2 AB2 5 LEU B 205 SER B 210 -1 O LEU B 207 N LYS B 197 SHEET 3 AB2 5 LEU B 215 ASN B 219 -1 O TRP B 218 N LEU B 206 SHEET 4 AB2 5 THR B 224 PHE B 229 -1 O PHE B 229 N LEU B 215 SHEET 5 AB2 5 GLN B 292 ILE B 294 1 O ILE B 294 N ILE B 228 SHEET 1 AB3 4 VAL B 239 TYR B 244 0 SHEET 2 AB3 4 LYS B 250 GLY B 255 -1 O CYS B 254 N SER B 241 SHEET 3 AB3 4 LEU B 260 ARG B 264 -1 O TRP B 263 N ILE B 251 SHEET 4 AB3 4 PHE B 299 THR B 301 -1 O PHE B 299 N LEU B 262 SHEET 1 AB4 4 CYS B 311 LEU B 315 0 SHEET 2 AB4 4 LEU B 318 LYS B 322 -1 O LEU B 318 N LEU B 315 SHEET 3 AB4 4 ALA B 327 PRO B 333 -1 O TRP B 331 N ILE B 319 SHEET 4 AB4 4 VAL B 350 ASP B 357 -1 O GLY B 354 N CYS B 330 SHEET 1 AB5 4 PHE B 368 MET B 370 0 SHEET 2 AB5 4 MET B 376 GLY B 380 -1 O ALA B 378 N SER B 369 SHEET 3 AB5 4 LEU B 386 ASP B 390 -1 O TYR B 387 N LEU B 379 SHEET 4 AB5 4 THR B 402 LEU B 404 -1 O LEU B 404 N LEU B 386 LINK NH1 ARG A 269 Y YT3 A 503 1555 1555 3.39 LINK Y YT3 A 502 O HOH A 637 1555 1555 3.48 LINK Y YT3 A 502 NH1 ARG B 269 1556 1555 3.41 SITE 1 AC1 5 ASN A 326 SER A 359 GLN A 360 ASP A 362 SITE 2 AC1 5 HOH A 725 SITE 1 AC2 2 ARG B 269 HIS B 295 SITE 1 AC3 3 ARG A 269 LYS A 293 HIS A 295 SITE 1 AC4 11 PHE A 97 TYR A 148 ASN A 194 GLU A 238 SITE 2 AC4 11 ASP A 310 TYR A 365 MET A 366 ARG A 367 SITE 3 AC4 11 ARG A 414 HOH A 604 HOH A 613 SITE 1 AC5 11 PHE B 97 ASN B 194 GLU B 238 ASP B 310 SITE 2 AC5 11 TYR B 365 MET B 366 ARG B 367 ARG B 414 SITE 3 AC5 11 HOH B 635 HOH B 645 HOH B 784 CRYST1 92.881 178.113 50.480 90.00 90.00 90.00 P 21 21 2 8 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 0.010766 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019810 0.00000