HEADER ONCOPROTEIN 14-DEC-20 7B9X TITLE NMR2 STRUCTURE OF TRIM24-BD IN COMPLEX WITH A PRECURSOR OF IACS-9571 CAVEAT 7B9X ASP A 955 HAS WRONG CHIRALITY AT ATOM CA ASP A 983 HAS WRONG CAVEAT 2 7B9X CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INTERMEDIARY FACTOR 1-ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TIF1-ALPHA,E3 UBIQUITIN-PROTEIN LIGASE TRIM24,RING FINGER COMPND 5 PROTEIN 82,RING-TYPE E3 UBIQUITIN TRANSFERASE TIF1-ALPHA,TRIPARTITE COMPND 6 MOTIF-CONTAINING PROTEIN 24; COMPND 7 EC: 2.3.2.27; COMPND 8 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: TRIM24, RNF82, TIF1, TIF1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRIM24, BROMODOMAIN, IACS-9571, NMR2, ONCOPROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.ORTS,F.TORRES,A.G.MILBRADT,R.WALSER REVDAT 3 27-APR-22 7B9X 1 JRNL REVDAT 2 13-APR-22 7B9X 1 JRNL REVDAT 1 12-JAN-22 7B9X 0 JRNL AUTH F.TORRES,R.WALSER,J.KADERLI,E.ROSSI,R.BOBBY,M.J.PACKER, JRNL AUTH 2 S.SARDA,G.WALKER,J.R.HITCHIN,A.G.MILBRADT,J.ORTS JRNL TITL NMR MOLECULAR REPLACEMENT PROVIDES NEW INSIGHTS INTO BINDING JRNL TITL 2 MODES TO BROMODOMAINS OF BRD4 AND TRIM24. JRNL REF J.MED.CHEM. V. 65 5565 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35357834 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01703 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7B9X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292111532. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 1.1 MM [U-13C; U-15N] TRIM24-BD, REMARK 210 50 MM [U-2H] HEPES, 100 MM SODIUM CHLORIDE, 1 MM TCEP, 10 % [U- REMARK 210 2H] D2O, 1.1 MM N-{6-[3-(4-AMINOBUTOXY)-5-PROPOXYPHENOXY]-1,3- REMARK 210 DIMETHYL-2-OXO-2,3-DIHYDRO-1H-1,3-BENZODIAZOL-5-YL}-3,4- REMARK 210 DIMETHOXYBENZENE-1-SULFONAMIDE, 90% H2O/10% D2O; 50 MM [U-2H] REMARK 210 HEPES, 100 MM SODIUM CHLORIDE, 1 MM TCEP, 10 % [U-2H] D2O, 1.1 % REMARK 210 N-{6-[3-(4-AMINOBUTOXY)-5-PROPOXYPHENOXY]-1,3-DIMETHYL-2-OXO-2,3- REMARK 210 DIHYDRO-1H-1,3-BENZODIAZOL-5-YL}-3,4-DIMETHOXYBENZENE-1- REMARK 210 SULFONAMIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-1H COSY; 2D 1H- REMARK 210 1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.9, CARA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OD1 ASP A 926 H38 T52 A 1101 1.49 REMARK 500 HZ2 LYS A 905 OE1 GLU A 909 1.52 REMARK 500 OE2 GLU A 999 HZ2 LYS A 1002 1.55 REMARK 500 H3 THR A 901 OD2 ASP A 904 1.55 REMARK 500 OE2 GLU A 919 HZ3 LYS A 992 1.58 REMARK 500 OD1 ASP A 904 HZ3 LYS A 907 1.58 REMARK 500 HH12 ARG A 951 OD2 ASP A 968 1.60 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 1 ASN A 941 72.14 -112.97 REMARK 500 1 PRO A 942 47.06 -77.19 REMARK 500 1 ASP A 955 79.87 57.41 REMARK 500 1 SER A 957 73.09 60.08 REMARK 500 1 MET A 958 71.63 46.41 REMARK 500 1 ARG A 970 36.00 -88.44 REMARK 500 1 LEU A 971 -43.33 -134.65 REMARK 500 1 PHE A 979 -34.21 -150.94 REMARK 500 1 ASP A 983 14.61 59.86 REMARK 500 2 GLN A 925 -77.17 -116.21 REMARK 500 2 PRO A 927 94.33 -57.54 REMARK 500 2 PRO A 942 48.59 -83.89 REMARK 500 2 ASP A 955 80.33 54.67 REMARK 500 2 SER A 957 84.75 76.20 REMARK 500 2 MET A 958 70.02 47.22 REMARK 500 2 PRO A 962 51.85 -63.88 REMARK 500 2 ARG A 970 38.60 -98.34 REMARK 500 2 LEU A 971 -44.63 -134.65 REMARK 500 2 PHE A 979 -43.74 -151.22 REMARK 500 3 GLN A 925 -65.57 -121.59 REMARK 500 3 PRO A 927 92.04 -58.21 REMARK 500 3 ASP A 955 83.55 58.78 REMARK 500 3 SER A 957 85.03 76.82 REMARK 500 3 MET A 958 73.12 47.61 REMARK 500 3 ARG A 970 47.40 -86.39 REMARK 500 3 LEU A 971 -30.55 -133.22 REMARK 500 3 GLU A 978 32.54 -88.03 REMARK 500 3 PHE A 979 -35.63 -151.01 REMARK 500 3 TYR A1005 75.11 -118.80 REMARK 500 4 GLN A 925 -68.75 -129.17 REMARK 500 4 PRO A 927 95.57 -47.53 REMARK 500 4 PRO A 942 46.58 -76.07 REMARK 500 4 ASP A 955 80.29 53.46 REMARK 500 4 SER A 957 85.52 68.06 REMARK 500 4 MET A 958 70.60 46.61 REMARK 500 4 PRO A 962 65.03 -69.99 REMARK 500 4 ARG A 970 47.64 -98.51 REMARK 500 4 LEU A 971 -30.52 -131.97 REMARK 500 4 PHE A 979 -43.59 -150.10 REMARK 500 5 PRO A 927 89.52 -69.31 REMARK 500 5 ASN A 941 72.17 -114.08 REMARK 500 5 PRO A 942 60.33 -68.35 REMARK 500 5 ASP A 955 80.36 55.31 REMARK 500 5 SER A 957 73.37 67.75 REMARK 500 5 MET A 958 67.68 34.86 REMARK 500 5 PRO A 962 65.52 -50.60 REMARK 500 5 ARG A 970 32.67 -99.36 REMARK 500 5 LEU A 971 -37.16 -135.86 REMARK 500 5 PHE A 979 -47.73 -150.79 REMARK 500 6 GLN A 925 -77.77 -118.20 REMARK 500 REMARK 500 THIS ENTRY HAS 103 RAMACHANDRAN OUTLIERS. 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 3 ARG A 970 0.09 SIDE CHAIN REMARK 500 10 ARG A 906 0.08 SIDE CHAIN 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 T52 A 1101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34583 RELATED DB: BMRB REMARK 900 NMR2 STRUCTURE OF TRIM24-BD IN COMPLEX WITH A PRECURSOR OF IACS-9571 DBREF 7B9X A 901 1006 UNP O15164 TIF1A_HUMAN 901 1006 SEQRES 1 A 106 THR PRO ILE ASP LYS ARG LYS CYS GLU ARG LEU LEU LEU SEQRES 2 A 106 PHE LEU TYR CYS HIS GLU MET SER LEU ALA PHE GLN ASP SEQRES 3 A 106 PRO VAL PRO LEU THR VAL PRO ASP TYR TYR LYS ILE ILE SEQRES 4 A 106 LYS ASN PRO MET ASP LEU SER THR ILE LYS LYS ARG LEU SEQRES 5 A 106 GLN GLU ASP TYR SER MET TYR SER LYS PRO GLU ASP PHE SEQRES 6 A 106 VAL ALA ASP PHE ARG LEU ILE PHE GLN ASN CYS ALA GLU SEQRES 7 A 106 PHE ASN GLU PRO ASP SER GLU VAL ALA ASN ALA GLY ILE SEQRES 8 A 106 LYS LEU GLU ASN TYR PHE GLU GLU LEU LEU LYS ASN LEU SEQRES 9 A 106 TYR PRO HET T52 A1101 82 HETNAM T52 N-{6-[3-(4-AMINOBUTOXY)-5-PROPOXYPHENOXY]-1,3-DIMETHYL- HETNAM 2 T52 2-OXO-2,3-DIHYDRO-1H-1,3-BENZODIAZOL-5-YL}-3,4- HETNAM 3 T52 DIMETHOXYBENZENE-1-SULFONAMIDE HETSYN T52 ~{N}-[6-[3-(4-AZANYLBUTOXY)-5-PROPOXY-PHENOXY]-1,3- HETSYN 2 T52 DIMETHYL-2-OXIDANYLIDENE-BENZIMIDAZOL-5-YL]-3,4- HETSYN 3 T52 DIMETHOXY-BENZENESULFONAMIDE FORMUL 2 T52 C30 H39 N4 O8 S 1+ HELIX 1 AA1 THR A 901 HIS A 918 1 18 HELIX 2 AA2 SER A 921 GLN A 925 5 5 HELIX 3 AA3 ASP A 934 ILE A 938 5 5 HELIX 4 AA4 LEU A 945 ARG A 951 1 7 HELIX 5 AA5 PRO A 962 PHE A 973 1 12 HELIX 6 AA6 PHE A 973 GLU A 978 1 6 HELIX 7 AA7 SER A 984 TYR A 1005 1 22 SITE 1 AC1 12 MET A 920 LEU A 922 ALA A 923 ASP A 926 SITE 2 AC1 12 VAL A 928 PRO A 929 THR A 931 VAL A 932 SITE 3 AC1 12 ASN A 980 GLU A 985 VAL A 986 ALA A 989 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1