HEADER TRANSCRIPTION/INHIBITOR 08-FEB-18 6CD5 TITLE CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX TITLE 2 WITH THE INHIBITOR XMD17-26 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 44-168; COMPND 5 SYNONYM: PROTEIN HUNK1; COMPND 6 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: BRD4, HUNK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, INHIBITOR, BRD4, TRANSCRIPTION, TRANSCRIPTION-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.XU,S.C.BLACKLOW REVDAT 5 04-OCT-23 6CD5 1 REMARK REVDAT 4 21-JUL-21 6CD5 1 REMARK REVDAT 3 01-JAN-20 6CD5 1 REMARK REVDAT 2 20-FEB-19 6CD5 1 REMARK REVDAT 1 16-JAN-19 6CD5 0 JRNL AUTH J.WANG,T.ERAZO,F.M.FERGUSON,D.L.BUCKLEY,N.GOMEZ, JRNL AUTH 2 P.MUNOZ-GUARDIOLA,N.DIEGUEZ-MARTINEZ,X.DENG,M.HAO, JRNL AUTH 3 W.MASSEFSKI,O.FEDOROV,N.K.OFFEI-ADDO,P.M.PARK,L.DAI, JRNL AUTH 4 A.DIBONA,K.BECHT,N.D.KIM,M.R.MCKEOWN,J.M.ROBERTS,J.ZHANG, JRNL AUTH 5 T.SIM,D.R.ALESSI,J.E.BRADNER,J.M.LIZCANO,S.C.BLACKLOW,J.QI, JRNL AUTH 6 X.XU,N.S.GRAY JRNL TITL STRUCTURAL AND ATROPISOMERIC FACTORS GOVERNING THE JRNL TITL 2 SELECTIVITY OF PYRIMIDO-BENZODIAZIPINONES AS INHIBITORS OF JRNL TITL 3 KINASES AND BROMODOMAINS. JRNL REF ACS CHEM. BIOL. V. 13 2438 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 30102854 JRNL DOI 10.1021/ACSCHEMBIO.7B00638 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1045 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 36.2817 - 3.0221 1.00 2923 147 0.1630 0.1694 REMARK 3 2 3.0221 - 2.3988 1.00 2815 141 0.1747 0.1967 REMARK 3 3 2.3988 - 2.0956 1.00 2761 141 0.1621 0.1932 REMARK 3 4 2.0956 - 1.9041 1.00 2720 171 0.1546 0.1836 REMARK 3 5 1.9041 - 1.7676 1.00 2724 151 0.1718 0.1948 REMARK 3 6 1.7676 - 1.6634 1.00 2740 133 0.1959 0.2328 REMARK 3 7 1.6634 - 1.5801 1.00 2701 161 0.2363 0.2845 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.320 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 : 0.012 1133 REMARK 3 ANGLE : 1.313 1540 REMARK 3 CHIRALITY : 0.071 160 REMARK 3 PLANARITY : 0.010 197 REMARK 3 DIHEDRAL : 7.162 689 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 42 THROUGH 60 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8003 4.5349 -23.1748 REMARK 3 T TENSOR REMARK 3 T11: 0.1090 T22: 0.0814 REMARK 3 T33: 0.0959 T12: -0.0113 REMARK 3 T13: 0.0151 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.0087 L22: 0.0627 REMARK 3 L33: 0.0884 L12: -0.0681 REMARK 3 L13: 0.0177 L23: 0.0084 REMARK 3 S TENSOR REMARK 3 S11: 0.0015 S12: -0.0288 S13: -0.0005 REMARK 3 S21: -0.0559 S22: 0.0253 S23: -0.0697 REMARK 3 S31: -0.0288 S32: 0.0172 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 61 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9463 -12.1474 -21.4471 REMARK 3 T TENSOR REMARK 3 T11: 0.1312 T22: 0.1070 REMARK 3 T33: 0.0976 T12: -0.0291 REMARK 3 T13: 0.0040 T23: -0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.0436 L22: 0.0038 REMARK 3 L33: 0.0118 L12: 0.0177 REMARK 3 L13: -0.0277 L23: -0.0079 REMARK 3 S TENSOR REMARK 3 S11: -0.0192 S12: 0.0460 S13: -0.0923 REMARK 3 S21: -0.2295 S22: 0.0656 S23: -0.0584 REMARK 3 S31: 0.0974 S32: -0.1434 S33: 0.0003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 69 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5562 -6.8003 -13.8584 REMARK 3 T TENSOR REMARK 3 T11: 0.0969 T22: 0.0897 REMARK 3 T33: 0.1005 T12: -0.0133 REMARK 3 T13: -0.0108 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.0002 L22: 0.0041 REMARK 3 L33: 0.0065 L12: -0.0044 REMARK 3 L13: -0.0043 L23: 0.0075 REMARK 3 S TENSOR REMARK 3 S11: -0.0962 S12: 0.0104 S13: 0.0008 REMARK 3 S21: 0.0041 S22: -0.0787 S23: -0.0234 REMARK 3 S31: -0.0374 S32: -0.0929 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 76 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9577 -0.6703 -5.8388 REMARK 3 T TENSOR REMARK 3 T11: 0.0850 T22: 0.0909 REMARK 3 T33: 0.0929 T12: -0.0071 REMARK 3 T13: -0.0049 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 0.0126 L22: 0.0030 REMARK 3 L33: 0.0007 L12: 0.0096 REMARK 3 L13: 0.0058 L23: 0.0021 REMARK 3 S TENSOR REMARK 3 S11: -0.0005 S12: 0.0716 S13: 0.0382 REMARK 3 S21: 0.0228 S22: 0.0318 S23: 0.1203 REMARK 3 S31: 0.0477 S32: -0.0913 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 84 THROUGH 106 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7266 11.3736 -7.2844 REMARK 3 T TENSOR REMARK 3 T11: 0.0686 T22: 0.0650 REMARK 3 T33: 0.0790 T12: -0.0017 REMARK 3 T13: 0.0003 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 0.0856 L22: 0.1081 REMARK 3 L33: 0.0520 L12: 0.0984 REMARK 3 L13: -0.0485 L23: -0.0870 REMARK 3 S TENSOR REMARK 3 S11: 0.0361 S12: -0.0243 S13: 0.0125 REMARK 3 S21: 0.0187 S22: -0.0003 S23: 0.0397 REMARK 3 S31: -0.0094 S32: -0.0133 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 107 THROUGH 121 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4513 -1.9873 -22.0060 REMARK 3 T TENSOR REMARK 3 T11: 0.1092 T22: 0.0865 REMARK 3 T33: 0.0837 T12: -0.0091 REMARK 3 T13: -0.0010 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.0179 L22: 0.0222 REMARK 3 L33: 0.0729 L12: 0.0161 REMARK 3 L13: -0.0584 L23: -0.0153 REMARK 3 S TENSOR REMARK 3 S11: -0.0484 S12: 0.0713 S13: 0.0199 REMARK 3 S21: -0.2068 S22: 0.0125 S23: 0.0436 REMARK 3 S31: 0.0059 S32: -0.1058 S33: 0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 122 THROUGH 139 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7181 -1.9532 -8.8909 REMARK 3 T TENSOR REMARK 3 T11: 0.0889 T22: 0.0913 REMARK 3 T33: 0.0852 T12: -0.0110 REMARK 3 T13: -0.0058 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 0.1132 L22: 0.0154 REMARK 3 L33: 0.0568 L12: 0.0273 REMARK 3 L13: 0.0500 L23: -0.0137 REMARK 3 S TENSOR REMARK 3 S11: 0.0272 S12: -0.0225 S13: -0.0054 REMARK 3 S21: -0.0230 S22: 0.0439 S23: -0.0418 REMARK 3 S31: 0.0674 S32: -0.0331 S33: 0.0200 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 140 THROUGH 144 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4617 3.4508 6.1773 REMARK 3 T TENSOR REMARK 3 T11: 0.0844 T22: 0.1601 REMARK 3 T33: 0.1061 T12: -0.0046 REMARK 3 T13: 0.0073 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.0048 L22: 0.0058 REMARK 3 L33: 0.0002 L12: 0.0037 REMARK 3 L13: -0.0016 L23: -0.0027 REMARK 3 S TENSOR REMARK 3 S11: 0.0984 S12: -0.0653 S13: -0.1421 REMARK 3 S21: 0.0735 S22: 0.1528 S23: 0.0491 REMARK 3 S31: -0.0215 S32: 0.1284 S33: -0.0004 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 145 THROUGH 166 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1511 -9.9467 -5.7618 REMARK 3 T TENSOR REMARK 3 T11: 0.0784 T22: 0.0593 REMARK 3 T33: 0.0782 T12: 0.0071 REMARK 3 T13: 0.0166 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.0646 L22: 0.0663 REMARK 3 L33: 0.0592 L12: -0.0751 REMARK 3 L13: 0.0892 L23: -0.0300 REMARK 3 S TENSOR REMARK 3 S11: -0.0430 S12: -0.0771 S13: -0.0161 REMARK 3 S21: 0.0306 S22: -0.0303 S23: 0.0887 REMARK 3 S31: 0.0609 S32: 0.0702 S33: -0.0110 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 6CD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232567. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20478 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 84.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.63400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 4WIV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM NITRATE, 5% ETHYLENE REMARK 280 GLYCOL, 18% (W/V) PEG3350, VAPOR DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.06000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.43950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.13900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.43950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.06000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.13900 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLU A 167 REMARK 465 GLU A 168 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 LYS A 91 CG CD CE NZ 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 434 O HOH A 455 1.78 REMARK 500 O HOH A 417 O HOH A 523 1.91 REMARK 500 NZ LYS A 55 O HOH A 301 1.93 REMARK 500 O HOH A 419 O HOH A 462 1.95 REMARK 500 O HOH A 434 O HOH A 539 2.01 REMARK 500 O HOH A 304 O HOH A 322 2.03 REMARK 500 O HOH A 541 O HOH A 546 2.08 REMARK 500 O HOH A 433 O HOH A 534 2.08 REMARK 500 O HOH A 333 O HOH A 466 2.09 REMARK 500 O HOH A 438 O HOH A 472 2.12 REMARK 500 O HOH A 389 O HOH A 480 2.15 REMARK 500 O THR A 166 O HOH A 302 2.17 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 422 O HOH A 431 3644 2.03 REMARK 500 O HOH A 345 O HOH A 357 3654 2.18 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 ASN A 52 112.18 -160.41 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 R4L A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 205 DBREF 6CD5 A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 6CD5 SER A 42 UNP O60885 EXPRESSION TAG SEQADV 6CD5 MET A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 A 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 A 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 A 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 A 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 A 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 A 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 A 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 A 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET R4L A 201 46 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET NO3 A 205 4 HETNAM R4L 11-CYCLOPENTYL-2-[[2-METHOXY-4-[4-(4-METHYLPIPERAZIN-1- HETNAM 2 R4L YL)PIPERIDIN-1-YL]CARBONYL-PHENYL]AMINO]-5-METHYL- HETNAM 3 R4L PYRIMIDO[4,5-B][1,4]BENZODIAZEPIN-6-ONE HETNAM EDO 1,2-ETHANEDIOL HETNAM NO3 NITRATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 R4L C35 H44 N8 O3 FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 NO3 N O3 1- FORMUL 7 HOH *249(H2 O) HELIX 1 AA1 THR A 60 VAL A 69 1 10 HELIX 2 AA2 VAL A 69 LYS A 76 1 8 HELIX 3 AA3 ALA A 80 GLN A 84 5 5 HELIX 4 AA4 ASP A 96 ILE A 101 1 6 HELIX 5 AA5 ASP A 106 ASN A 116 1 11 HELIX 6 AA6 ASN A 121 ASN A 140 1 20 HELIX 7 AA7 ASP A 144 GLU A 163 1 20 SITE 1 AC1 13 TRP A 81 PRO A 82 PHE A 83 LEU A 92 SITE 2 AC1 13 ASP A 96 ILE A 100 TYR A 139 ASN A 140 SITE 3 AC1 13 ILE A 146 HOH A 314 HOH A 323 HOH A 336 SITE 4 AC1 13 HOH A 358 SITE 1 AC2 7 MET A 43 ASN A 52 GLN A 62 ALA A 122 SITE 2 AC2 7 ILE A 126 HOH A 330 HOH A 338 SITE 1 AC3 7 ILE A 100 ILE A 101 LYS A 102 THR A 103 SITE 2 AC3 7 ASN A 135 HOH A 318 HOH A 339 SITE 1 AC4 5 LYS A 57 ASP A 144 ASP A 145 HOH A 342 SITE 2 AC4 5 HOH A 366 SITE 1 AC5 8 PHE A 79 TRP A 81 PRO A 95 ASP A 96 SITE 2 AC5 8 LYS A 99 MET A 149 HOH A 346 HOH A 352 CRYST1 40.120 42.278 84.879 90.00 90.00 90.00 P 21 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 0.024925 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011781 0.00000