HEADER LIGASE 02-JUN-17 5XPI TITLE STRUCTURE OF UHRF1 TTD IN COMPLEX WITH NV01 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UHRF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 127-283; COMPND 5 SYNONYM: INVERTED CCAAT BOX-BINDING PROTEIN OF 90 KDA,NUCLEAR PROTEIN COMPND 6 95,NUCLEAR ZINC FINGER PROTEIN NP95,HNP95,RING FINGER PROTEIN 106, COMPND 7 RING-TYPE E3 UBIQUITIN TRANSFERASE UHRF1,TRANSCRIPTION FACTOR ICBP90, COMPND 8 UBIQUITIN-LIKE PHD AND RING FINGER DOMAIN-CONTAINING PROTEIN 1, COMPND 9 HUHRF1,UBIQUITIN-LIKE-CONTAINING PHD AND RING FINGER DOMAINS PROTEIN COMPND 10 1; COMPND 11 EC: 2.3.2.27; 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: UHRF1, ICBP90, NP95, RNF106; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TTD DOMAIN, SMALL MOLECULE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR X.LUO,K.ZHAO REVDAT 4 22-NOV-23 5XPI 1 JRNL REVDAT 3 03-OCT-18 5XPI 1 JRNL REVDAT 2 18-JUL-18 5XPI 1 REMARK REVDAT 1 25-APR-18 5XPI 0 JRNL AUTH G.SENISTERRA,H.Y.ZHU,X.LUO,H.ZHANG,G.XUN,C.LU,W.XIAO, JRNL AUTH 2 T.HAJIAN,P.LOPPNAU,I.CHAU,F.LI,A.ALLALI-HASSANI,P.ATADJA, JRNL AUTH 3 C.OYANG,E.LI,P.J.BROWN,C.H.ARROWSMITH,K.ZHAO,Z.YU,M.VEDADI JRNL TITL DISCOVERY OF SMALL-MOLECULE ANTAGONISTS OF THE H3K9ME3 JRNL TITL 2 BINDING TO UHRF1 TANDEM TUDOR DOMAIN JRNL REF SLAS DISCOV V. 23 930 2018 JRNL REFN ESSN 2472-5560 JRNL PMID 29562800 JRNL DOI 10.1177/2472555218766278 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.9.6 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 11900 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 566 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.41 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.63 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2793 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2324 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2664 REMARK 3 BIN R VALUE (WORKING SET) : 0.2307 REMARK 3 BIN FREE R VALUE : 0.2654 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.62 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 129 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 : 1173 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.25790 REMARK 3 B22 (A**2) : 9.25790 REMARK 3 B33 (A**2) : -18.51590 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) : 0.276 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.205 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.163 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.196 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.160 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 : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1224 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1658 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 431 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 48 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 174 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1224 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 147 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL 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 : 1322 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.06 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.63 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5XPI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1300003884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11915 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : 0.21400 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3DB3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.7 M NA FORMATE AND 0.1 M NA ACETATE REMARK 280 PH 5.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.54333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.77167 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.54333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.77167 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 ALA A 163 REMARK 465 PRO A 164 REMARK 465 SER A 165 REMARK 465 ARG A 166 REMARK 465 ASP A 167 REMARK 465 GLU A 168 REMARK 465 PRO A 169 REMARK 465 CYS A 170 REMARK 465 SER A 171 REMARK 465 SER A 172 REMARK 465 THR A 173 REMARK 465 SER A 174 REMARK 465 ARG A 175 REMARK 465 PRO A 176 REMARK 465 ALA A 177 REMARK 465 LEU A 178 REMARK 465 GLU A 179 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 138 -7.54 82.23 REMARK 500 ASP A 181 53.57 -117.86 REMARK 500 THR A 249 -167.70 -116.23 REMARK 500 LEU A 261 -147.70 -100.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8C3 A 301 DBREF 5XPI A 127 283 UNP Q96T88 UHRF1_HUMAN 127 283 SEQRES 1 A 157 TRP ASP GLU THR GLU LEU GLY LEU TYR LYS VAL ASN GLU SEQRES 2 A 157 TYR VAL ASP ALA ARG ASP THR ASN MET GLY ALA TRP PHE SEQRES 3 A 157 GLU ALA GLN VAL VAL ARG VAL THR ARG LYS ALA PRO SER SEQRES 4 A 157 ARG ASP GLU PRO CYS SER SER THR SER ARG PRO ALA LEU SEQRES 5 A 157 GLU GLU ASP VAL ILE TYR HIS VAL LYS TYR ASP ASP TYR SEQRES 6 A 157 PRO GLU ASN GLY VAL VAL GLN MET ASN SER ARG ASP VAL SEQRES 7 A 157 ARG ALA ARG ALA ARG THR ILE ILE LYS TRP GLN ASP LEU SEQRES 8 A 157 GLU VAL GLY GLN VAL VAL MET LEU ASN TYR ASN PRO ASP SEQRES 9 A 157 ASN PRO LYS GLU ARG GLY PHE TRP TYR ASP ALA GLU ILE SEQRES 10 A 157 SER ARG LYS ARG GLU THR ARG THR ALA ARG GLU LEU TYR SEQRES 11 A 157 ALA ASN VAL VAL LEU GLY ASP ASP SER LEU ASN ASP CYS SEQRES 12 A 157 ARG ILE ILE PHE VAL ASP GLU VAL PHE LYS ILE GLU ARG SEQRES 13 A 157 PRO HET 8C3 A 301 26 HETNAM 8C3 N-[3-(DIETHYLAMINO)PROPYL]-2-(12-METHYL-9- HETNAM 2 8C3 OXIDANYLIDENE-5-THIA-1,10,11-TRIAZATRICYCLO[6.4.0.0^2, HETNAM 3 8C3 6]DODECA-2(6),3,7,11-TETRAEN-10-YL)ETHANAMIDE FORMUL 2 8C3 C18 H25 N5 O2 S FORMUL 3 HOH *116(H2 O) HELIX 1 AA1 TYR A 191 GLY A 195 5 5 HELIX 2 AA2 LYS A 213 LEU A 217 5 5 SHEET 1 AA1 4 ASP A 128 GLU A 129 0 SHEET 2 AA1 4 TRP A 151 ARG A 161 -1 O ARG A 161 N ASP A 128 SHEET 3 AA1 4 VAL A 182 TYR A 188 -1 O HIS A 185 N ARG A 158 SHEET 4 AA1 4 VAL A 197 ASN A 200 -1 O MET A 199 N TYR A 184 SHEET 1 AA2 4 ASP A 128 GLU A 129 0 SHEET 2 AA2 4 TRP A 151 ARG A 161 -1 O ARG A 161 N ASP A 128 SHEET 3 AA2 4 TYR A 140 ARG A 144 -1 N VAL A 141 O ALA A 154 SHEET 4 AA2 4 VAL A 204 ALA A 206 -1 O ARG A 205 N ASP A 142 SHEET 1 AA3 4 VAL A 222 TYR A 227 0 SHEET 2 AA3 4 PHE A 237 GLU A 248 -1 O ALA A 241 N VAL A 223 SHEET 3 AA3 4 ARG A 253 VAL A 260 -1 O ASN A 258 N GLU A 242 SHEET 4 AA3 4 SER A 265 ARG A 270 -1 O CYS A 269 N ALA A 257 SITE 1 AC1 9 GLU A 131 ASP A 145 MET A 148 PHE A 152 SITE 2 AC1 9 TYR A 188 TYR A 191 ASN A 194 PHE A 237 SITE 3 AC1 9 HOH A 420 CRYST1 99.001 99.001 41.315 90.00 90.00 120.00 P 62 6 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 0.010101 0.005832 0.000000 0.00000 SCALE2 0.000000 0.011664 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024204 0.00000