HEADER TRANSCRIPTION 06-MAR-26 24KJ TITLE CRYSTAL STRUCTURE OF SECOND BROMODOMAIN (BD2) OF HUMAN BRD2 IN COMPLEX TITLE 2 WITH 2PE AND P6G COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1; 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS INHIBITOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR B.PADMANABHAN,S.ASHOK REVDAT 1 29-JUL-26 24KJ 0 JRNL AUTH A.SRIDHAR,N.KANDHASAMI,S.MATHUR,G.KRISHNAPPA,S.THIYAGARAJAN, JRNL AUTH 2 B.PADMANABHAN JRNL TITL BET BROMODOMAIN TARGETING BY NSAIDS: STRUCTURAL, JRNL TITL 2 BIOPHYSICAL, AND COMPUTATIONAL INSIGHTS. JRNL REF PROTEINS 2026 JRNL REFN ESSN 1097-0134 JRNL PMID 42458221 JRNL DOI 10.1002/PROT.70154 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.17.1_3660: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 11602 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 580 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 25.5100 - 2.8600 0.99 2854 150 0.1602 0.1995 REMARK 3 2 2.8600 - 2.2700 1.00 2748 144 0.1696 0.1971 REMARK 3 3 2.2700 - 1.9800 1.00 2719 143 0.1524 0.1824 REMARK 3 4 1.9800 - 1.8000 1.00 2701 143 0.1715 0.2272 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 996 REMARK 3 ANGLE : 0.789 1331 REMARK 3 CHIRALITY : 0.046 130 REMARK 3 PLANARITY : 0.004 170 REMARK 3 DIHEDRAL : 13.239 161 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): 0.4902 10.2605 2.6881 REMARK 3 T TENSOR REMARK 3 T11: 0.0629 T22: 0.0715 REMARK 3 T33: 0.0807 T12: 0.0021 REMARK 3 T13: -0.0168 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.8003 L22: 1.6672 REMARK 3 L33: 2.2735 L12: 0.0045 REMARK 3 L13: -0.0264 L23: -0.3879 REMARK 3 S TENSOR REMARK 3 S11: -0.0209 S12: -0.0118 S13: 0.0377 REMARK 3 S21: 0.0052 S22: 0.0033 S23: 0.0091 REMARK 3 S31: -0.0215 S32: -0.0371 S33: -0.0005 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 24KJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1300068362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 300 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16374 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 25.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50900 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: PHENIX REMARK 200 STARTING MODEL: 7VRM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG MME 2000, 50MM TRIS, 50MM NACL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.23050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.64400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.23050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.64400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 886 LIES ON A SPECIAL POSITION. 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 927 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A 928 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 929 DISTANCE = 6.51 ANGSTROMS DBREF 24KJ A 348 455 UNP P25440 BRD2_HUMAN 348 455 SEQADV 24KJ ALA A 345 UNP P25440 EXPRESSION TAG SEQADV 24KJ ASN A 346 UNP P25440 EXPRESSION TAG SEQADV 24KJ PRO A 347 UNP P25440 EXPRESSION TAG SEQADV 24KJ SER A 358 UNP P25440 LYS 358 ENGINEERED MUTATION SEQADV 24KJ SER A 363 UNP P25440 LYS 363 ENGINEERED MUTATION SEQRES 1 A 111 ALA ASN PRO GLU GLN LEU LYS HIS CYS ASN GLY ILE LEU SEQRES 2 A 111 SER GLU LEU LEU SER SER LYS HIS ALA ALA TYR ALA TRP SEQRES 3 A 111 PRO PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY LEU SEQRES 4 A 111 HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP LEU SEQRES 5 A 111 SER THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR ARG SEQRES 6 A 111 ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET PHE SEQRES 7 A 111 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP VAL SEQRES 8 A 111 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU PHE SEQRES 9 A 111 ARG TYR ALA LYS MET PRO ASP HET 2PE A 701 28 HET P6G A 702 19 HETNAM 2PE NONAETHYLENE GLYCOL HETNAM P6G HEXAETHYLENE GLYCOL HETSYN P6G POLYETHYLENE GLYCOL PEG400 FORMUL 2 2PE C18 H38 O10 FORMUL 3 P6G C12 H26 O7 FORMUL 4 HOH *129(H2 O) HELIX 1 AA1 ALA A 345 LEU A 361 1 17 HELIX 2 AA2 SER A 362 LYS A 364 5 3 HELIX 3 AA3 HIS A 365 TRP A 370 1 6 HELIX 4 AA4 PRO A 371 TYR A 373 5 3 HELIX 5 AA5 ASP A 377 GLY A 382 1 6 HELIX 6 AA6 ASP A 385 ILE A 390 1 6 HELIX 7 AA7 ASP A 395 ASN A 405 1 11 HELIX 8 AA8 ASP A 410 ASN A 429 1 20 HELIX 9 AA9 HIS A 433 ALA A 451 1 19 CRYST1 31.999 52.461 71.288 90.00 90.00 90.00 P 2 21 21 4 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 0.031251 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014028 0.00000 CONECT 925 926 CONECT 926 925 927 CONECT 927 926 928 CONECT 928 927 929 CONECT 929 928 930 CONECT 930 929 931 CONECT 931 930 932 CONECT 932 931 933 CONECT 933 932 934 CONECT 934 933 935 CONECT 935 934 936 CONECT 936 935 937 CONECT 937 936 938 CONECT 938 937 939 CONECT 939 938 940 CONECT 940 939 941 CONECT 941 940 942 CONECT 942 941 943 CONECT 943 942 944 CONECT 944 943 945 CONECT 945 944 946 CONECT 946 945 947 CONECT 947 946 948 CONECT 948 947 949 CONECT 949 948 950 CONECT 950 949 951 CONECT 951 950 952 CONECT 952 951 CONECT 953 954 CONECT 954 953 955 CONECT 955 954 956 CONECT 956 955 957 CONECT 957 956 958 CONECT 958 957 959 CONECT 959 958 960 CONECT 960 959 961 CONECT 961 960 962 CONECT 962 961 963 CONECT 963 962 964 CONECT 964 963 965 CONECT 965 964 966 CONECT 966 965 967 CONECT 967 966 968 CONECT 968 967 969 CONECT 969 968 970 CONECT 970 969 971 CONECT 971 970 MASTER 236 0 2 9 0 0 0 6 1086 1 47 9 END