HEADER TRANSCRIPTION/INHIBITOR 30-AUG-19 6U6K TITLE BRD4-BD1 IN COMPLEX WITH THE CYCLIC PEPTIDE 3.1_3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN HUNK1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CYCLIC PEPTIDE 3.1_3; COMPND 8 CHAIN: C; COMPND 9 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS BET, BROMODOMAIN, MACROCYCLIC PEPTIDE, BRD4, INHIBITOR, RAPID, KEYWDS 2 TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.PATEL,J.L.WALSHE,L.J.WALPORT,J.P.MACKAY REVDAT 4 15-NOV-23 6U6K 1 REMARK REVDAT 3 11-OCT-23 6U6K 1 REMARK REVDAT 2 03-MAR-21 6U6K 1 JRNL REVDAT 1 19-AUG-20 6U6K 0 JRNL AUTH K.PATEL,L.J.WALPORT,J.L.WALSHE,P.D.SOLOMON,J.K.K.LOW, JRNL AUTH 2 D.H.TRAN,K.S.MOURADIAN,A.P.G.SILVA,L.WILKINSON-WHITE, JRNL AUTH 3 A.NORMAN,C.FRANCK,J.M.MATTHEWS,J.M.GUSS,R.J.PAYNE, JRNL AUTH 4 T.PASSIOURA,H.SUGA,J.P.MACKAY JRNL TITL CYCLIC PEPTIDES CAN ENGAGE A SINGLE BINDING POCKET THROUGH JRNL TITL 2 HIGHLY DIVERGENT MODES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 26728 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 33046654 JRNL DOI 10.1073/PNAS.2003086117 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 16475 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 842 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 39.6200 - 3.0900 1.00 2677 147 0.1631 0.1996 REMARK 3 2 3.0900 - 2.4500 0.99 2579 145 0.1941 0.2259 REMARK 3 3 2.4500 - 2.1400 1.00 2603 142 0.1833 0.2132 REMARK 3 4 2.1400 - 1.9500 1.00 2608 137 0.1811 0.2458 REMARK 3 5 1.9500 - 1.8100 1.00 2586 133 0.2019 0.2547 REMARK 3 6 1.8100 - 1.7000 0.99 2580 138 0.2364 0.2604 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) : 0.156 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.629 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.77 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 : 0.007 1191 REMARK 3 ANGLE : 0.934 1619 REMARK 3 CHIRALITY : 0.049 171 REMARK 3 PLANARITY : 0.007 207 REMARK 3 DIHEDRAL : 9.670 724 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6U6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000243897. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-18 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16495 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 39.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 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) : NULL 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: PHASER REMARK 200 STARTING MODEL: 4LYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MMT 7.0 25 % W/V PEG 1500, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 60.97850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.95150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.97850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.95150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 GLN A 36 REMARK 465 GLY A 37 REMARK 465 PRO A 38 REMARK 465 LEU A 39 REMARK 465 GLY A 40 REMARK 465 SER A 41 REMARK 465 GLU A 168 REMARK 465 PRO A 169 REMARK 465 GLU A 170 REMARK 465 PHE A 171 REMARK 465 PRO A 172 REMARK 465 GLY A 173 REMARK 465 ARG A 174 REMARK 465 LEU A 175 REMARK 465 GLU A 176 REMARK 465 ARG A 177 REMARK 465 PRO A 178 REMARK 465 HIS A 179 REMARK 465 ARG A 180 REMARK 465 ASP A 181 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 141 CD CE NZ 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 LEU A 94 70.36 -118.32 REMARK 500 ALY C 6 -37.63 74.56 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 302 DISTANCE = 6.00 ANGSTROMS DBREF 6U6K A 42 168 UNP O60885 BRD4_HUMAN 42 168 DBREF 6U6K C 0 12 PDB 6U6K 6U6K 0 12 SEQADV 6U6K GLN A 36 UNP O60885 EXPRESSION TAG SEQADV 6U6K GLY A 37 UNP O60885 EXPRESSION TAG SEQADV 6U6K PRO A 38 UNP O60885 EXPRESSION TAG SEQADV 6U6K LEU A 39 UNP O60885 EXPRESSION TAG SEQADV 6U6K GLY A 40 UNP O60885 EXPRESSION TAG SEQADV 6U6K SER A 41 UNP O60885 EXPRESSION TAG SEQADV 6U6K PRO A 169 UNP O60885 EXPRESSION TAG SEQADV 6U6K GLU A 170 UNP O60885 EXPRESSION TAG SEQADV 6U6K PHE A 171 UNP O60885 EXPRESSION TAG SEQADV 6U6K PRO A 172 UNP O60885 EXPRESSION TAG SEQADV 6U6K GLY A 173 UNP O60885 EXPRESSION TAG SEQADV 6U6K ARG A 174 UNP O60885 EXPRESSION TAG SEQADV 6U6K LEU A 175 UNP O60885 EXPRESSION TAG SEQADV 6U6K GLU A 176 UNP O60885 EXPRESSION TAG SEQADV 6U6K ARG A 177 UNP O60885 EXPRESSION TAG SEQADV 6U6K PRO A 178 UNP O60885 EXPRESSION TAG SEQADV 6U6K HIS A 179 UNP O60885 EXPRESSION TAG SEQADV 6U6K ARG A 180 UNP O60885 EXPRESSION TAG SEQADV 6U6K ASP A 181 UNP O60885 EXPRESSION TAG SEQRES 1 A 146 GLN GLY PRO LEU GLY SER SER THR ASN PRO PRO PRO PRO SEQRES 2 A 146 GLU THR SER ASN PRO ASN LYS PRO LYS ARG GLN THR ASN SEQRES 3 A 146 GLN LEU GLN TYR LEU LEU ARG VAL VAL LEU LYS THR LEU SEQRES 4 A 146 TRP LYS HIS GLN PHE ALA TRP PRO PHE GLN GLN PRO VAL SEQRES 5 A 146 ASP ALA VAL LYS LEU ASN LEU PRO ASP TYR TYR LYS ILE SEQRES 6 A 146 ILE LYS THR PRO MET ASP MET GLY THR ILE LYS LYS ARG SEQRES 7 A 146 LEU GLU ASN ASN TYR TYR TRP ASN ALA GLN GLU CYS ILE SEQRES 8 A 146 GLN ASP PHE ASN THR MET PHE THR ASN CYS TYR ILE TYR SEQRES 9 A 146 ASN LYS PRO GLY ASP ASP ILE VAL LEU MET ALA GLU ALA SEQRES 10 A 146 LEU GLU LYS LEU PHE LEU GLN LYS ILE ASN GLU LEU PRO SEQRES 11 A 146 THR GLU GLU PRO GLU PHE PRO GLY ARG LEU GLU ARG PRO SEQRES 12 A 146 HIS ARG ASP SEQRES 1 C 13 ACE TRP TRP ILE ILE PRO ALY VAL LYS ALY GLY CYS NH2 HET ACE C 0 3 HET ALY C 6 12 HET ALY C 9 12 HET NH2 C 12 1 HETNAM ACE ACETYL GROUP HETNAM ALY N(6)-ACETYLLYSINE HETNAM NH2 AMINO GROUP FORMUL 2 ACE C2 H4 O FORMUL 2 ALY 2(C8 H16 N2 O3) FORMUL 2 NH2 H2 N FORMUL 3 HOH *110(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 ASN A 162 1 19 SHEET 1 AA1 2 TRP C 2 ILE C 4 0 SHEET 2 AA1 2 LYS C 8 ALY C 9 -1 O LYS C 8 N ILE C 3 LINK C ACE C 0 N TRP C 1 1555 1555 1.34 LINK CH3 ACE C 0 SG CYS C 11 1555 1555 1.77 LINK C PRO C 5 N ALY C 6 1555 1555 1.33 LINK C ALY C 6 N VAL C 7 1555 1555 1.33 LINK C LYS C 8 N ALY C 9 1555 1555 1.33 LINK C ALY C 9 N GLY C 10 1555 1555 1.33 LINK C CYS C 11 N NH2 C 12 1555 1555 1.33 CRYST1 121.957 41.903 29.538 90.00 94.20 90.00 C 1 2 1 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 0.008200 0.000000 0.000603 0.00000 SCALE2 0.000000 0.023865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033946 0.00000