HEADER TRANSCRIPTION 29-APR-22 7UUU TITLE FIRST BROMODOMAIN OF BRDT LIGANDED WITH COMPOUND 2C COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN TESTIS-SPECIFIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CANCER/TESTIS ANTIGEN 9,CT9,RING3-LIKE PROTEIN; COMPND 5 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: BRDT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, ACETYL-LYSINE, TRANSCRIPTION REGULATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.SCHONBRUNN,A.CHAN REVDAT 3 18-OCT-23 7UUU 1 REMARK REVDAT 2 09-NOV-22 7UUU 1 JRNL REVDAT 1 24-AUG-22 7UUU 0 JRNL AUTH J.JIANG,P.L.ZHAO,L.H.SIGUA,A.CHAN,E.SCHONBRUNN,J.QI, JRNL AUTH 2 G.I.GEORG JRNL TITL 1,4-DIHYDROPYRIDINEBUTYROLACTONE-DERIVED RING-OPENED ESTER JRNL TITL 2 AND AMIDE ANALOGS TARGETING BET BROMODOMAINS. JRNL REF ARCH PHARM V. 355 00288 2022 JRNL REFN ESSN 1521-4184 JRNL PMID 35941525 JRNL DOI 10.1002/ARDP.202200288 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20740 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1182 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 35.9300 - 3.0400 1.00 2642 159 0.1582 0.1788 REMARK 3 2 3.0400 - 2.4100 1.00 2467 149 0.1535 0.1869 REMARK 3 3 2.4100 - 2.1100 1.00 2441 148 0.1411 0.1708 REMARK 3 4 2.1100 - 1.9100 1.00 2426 147 0.1458 0.1640 REMARK 3 5 1.9100 - 1.7800 1.00 2417 146 0.1573 0.2014 REMARK 3 6 1.7800 - 1.6700 1.00 2388 144 0.1494 0.1784 REMARK 3 7 1.6700 - 1.5900 1.00 2378 144 0.1532 0.1826 REMARK 3 8 1.5900 - 1.5200 1.00 2399 145 0.1665 0.1832 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.39 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.4428 -15.6557 -19.7152 REMARK 3 T TENSOR REMARK 3 T11: 0.0700 T22: 0.0484 REMARK 3 T33: 0.1002 T12: 0.0046 REMARK 3 T13: -0.0007 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.9469 L22: 1.0146 REMARK 3 L33: 2.3950 L12: 0.0696 REMARK 3 L13: 0.1931 L23: 0.3001 REMARK 3 S TENSOR REMARK 3 S11: -0.0202 S12: -0.0023 S13: 0.0543 REMARK 3 S21: -0.0226 S22: 0.0341 S23: -0.0157 REMARK 3 S31: -0.1326 S32: 0.0149 S33: -0.0176 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 7UUU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20743 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 35.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5VBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M BIS-TRIS PH 6.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 25.40500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.54500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.40500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.40500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.54500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.40500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.40500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 49.54500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.40500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.40500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.54500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 327 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 329 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 349 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 375 LIES ON A SPECIAL POSITION. 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 137 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 348 O HOH A 396 2.17 REMARK 500 O HOH A 412 O HOH A 419 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 389 O HOH A 397 2545 2.17 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 429 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 430 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 431 DISTANCE = 6.24 ANGSTROMS DBREF 7UUU A 29 137 UNP Q58F21 BRDT_HUMAN 29 137 SEQADV 7UUU GLY A 25 UNP Q58F21 EXPRESSION TAG SEQADV 7UUU ALA A 26 UNP Q58F21 EXPRESSION TAG SEQADV 7UUU ALA A 27 UNP Q58F21 EXPRESSION TAG SEQADV 7UUU SER A 28 UNP Q58F21 EXPRESSION TAG SEQRES 1 A 113 GLY ALA ALA SER THR ASN GLN LEU GLN TYR LEU GLN LYS SEQRES 2 A 113 VAL VAL LEU LYS ASP LEU TRP LYS HIS SER PHE SER TRP SEQRES 3 A 113 PRO PHE GLN ARG PRO VAL ASP ALA VAL LYS LEU GLN LEU SEQRES 4 A 113 PRO ASP TYR TYR THR ILE ILE LYS ASN PRO MET ASP LEU SEQRES 5 A 113 ASN THR ILE LYS LYS ARG LEU GLU ASN LYS TYR TYR ALA SEQRES 6 A 113 LYS ALA SER GLU CYS ILE GLU ASP PHE ASN THR MET PHE SEQRES 7 A 113 SER ASN CYS TYR LEU TYR ASN LYS PRO GLY ASP ASP ILE SEQRES 8 A 113 VAL LEU MET ALA GLN ALA LEU GLU LYS LEU PHE MET GLN SEQRES 9 A 113 LYS LEU SER GLN MET PRO GLN GLU GLU HET OFR A 201 51 HET EDO A 202 10 HET EDO A 203 10 HET EDO A 204 10 HET EDO A 205 10 HETNAM OFR PROP-2-EN-1-YL (5S)-1-ETHYL-7-METHYL-5-(4- HETNAM 2 OFR METHYLPHENYL)-2,4-DIOXO-1,2,3,4,5,8-HEXAHYDROPYRIDO[2, HETNAM 3 OFR 3-D]PYRIMIDINE-6-CARBOXYLATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 OFR C21 H23 N3 O4 FORMUL 3 EDO 4(C2 H6 O2) FORMUL 7 HOH *131(H2 O) HELIX 1 AA1 THR A 29 VAL A 38 1 10 HELIX 2 AA2 VAL A 38 HIS A 46 1 9 HELIX 3 AA3 SER A 49 GLN A 53 5 5 HELIX 4 AA4 ASP A 65 ILE A 70 1 6 HELIX 5 AA5 ASP A 75 ASN A 85 1 11 HELIX 6 AA6 LYS A 90 ASN A 109 1 20 HELIX 7 AA7 ASP A 113 GLN A 132 1 20 CRYST1 50.810 50.810 99.090 90.00 90.00 90.00 P 42 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 0.019681 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010092 0.00000