HEADER TRANSCRIPTION/INHIBITOR 30-AUG-19 6U6L TITLE BRD4-BD2 IN COMPLEX WITH THE CYCLIC PEPTIDE 3.1_2 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_2; COMPND 8 CHAIN: B; 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 6U6L 1 REMARK REVDAT 3 11-OCT-23 6U6L 1 REMARK REVDAT 2 03-MAR-21 6U6L 1 JRNL REVDAT 1 19-AUG-20 6U6L 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4472 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.250 REMARK 3 FREE R VALUE TEST SET COUNT : 235 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 44.7600 - 3.2800 1.00 2176 116 0.2066 0.2134 REMARK 3 2 3.2800 - 2.6000 1.00 2061 119 0.2388 0.3045 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) : 0.299 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.517 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.86 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 : 0.002 1079 REMARK 3 ANGLE : 0.525 1442 REMARK 3 CHIRALITY : 0.034 145 REMARK 3 PLANARITY : 0.003 182 REMARK 3 DIHEDRAL : 9.462 656 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 6U6L 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_1000243900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-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 : MX1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4501 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 44.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 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: 5UVV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M HEPES PH REMARK 280 7.5, 25% W/V PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K 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 28.25700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.66800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.25700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.66800 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: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 514 LIES ON A SPECIAL POSITION. 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 342 REMARK 465 GLY A 343 REMARK 465 PRO A 344 REMARK 465 LEU A 345 REMARK 465 GLY A 346 REMARK 465 SER A 347 REMARK 465 GLU A 460 REMARK 465 PRO A 461 REMARK 465 GLU A 462 REMARK 465 GLU A 463 REMARK 465 PRO A 464 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 367 CD CE NZ REMARK 480 ARG A 410 CD NE CZ NH1 NH2 REMARK 480 ARG A 413 CD NE CZ NH1 NH2 REMARK 480 ALY B 12 OH CH CH3 NZ CE CD CG 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 LYS A 456 38.16 -88.41 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 NH2 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues ALY B 12 REMARK 800 through GLN B 13 bound to THR B 11 DBREF 6U6L A 347 464 UNP O60885 BRD4_HUMAN 347 464 DBREF 6U6L B 0 14 PDB 6U6L 6U6L 0 14 SEQADV 6U6L GLN A 342 UNP O60885 EXPRESSION TAG SEQADV 6U6L GLY A 343 UNP O60885 EXPRESSION TAG SEQADV 6U6L PRO A 344 UNP O60885 EXPRESSION TAG SEQADV 6U6L LEU A 345 UNP O60885 EXPRESSION TAG SEQADV 6U6L GLY A 346 UNP O60885 EXPRESSION TAG SEQRES 1 A 123 GLN GLY PRO LEU GLY SER SER LYS VAL SER GLU GLN LEU SEQRES 2 A 123 LYS CYS CYS SER GLY ILE LEU LYS GLU MET PHE ALA LYS SEQRES 3 A 123 LYS HIS ALA ALA TYR ALA TRP PRO PHE TYR LYS PRO VAL SEQRES 4 A 123 ASP VAL GLU ALA LEU GLY LEU HIS ASP TYR CYS ASP ILE SEQRES 5 A 123 ILE LYS HIS PRO MET ASP MET SER THR ILE LYS SER LYS SEQRES 6 A 123 LEU GLU ALA ARG GLU TYR ARG ASP ALA GLN GLU PHE GLY SEQRES 7 A 123 ALA ASP VAL ARG LEU MET PHE SER ASN CYS TYR LYS TYR SEQRES 8 A 123 ASN PRO PRO ASP HIS GLU VAL VAL ALA MET ALA ARG LYS SEQRES 9 A 123 LEU GLN ASP VAL PHE GLU MET ARG PHE ALA LYS MET PRO SEQRES 10 A 123 ASP GLU PRO GLU GLU PRO SEQRES 1 B 15 ACE TRP LYS THR ILE ALY GLY ALY THR TRP ARG THR ALY SEQRES 2 B 15 GLN CYS HET ACE B 0 3 HET ALY B 5 12 HET ALY B 7 12 HET ALY B 12 12 HET NH2 B 101 1 HET GOL B 102 6 HETNAM ACE ACETYL GROUP HETNAM ALY N(6)-ACETYLLYSINE HETNAM NH2 AMINO GROUP HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ACE C2 H4 O FORMUL 2 ALY 3(C8 H16 N2 O3) FORMUL 3 NH2 H2 N FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *16(H2 O) HELIX 1 AA1 SER A 348 ALA A 366 1 19 HELIX 2 AA2 HIS A 369 TRP A 374 1 6 HELIX 3 AA3 PRO A 375 TYR A 377 5 3 HELIX 4 AA4 ASP A 389 ILE A 394 1 6 HELIX 5 AA5 ASP A 399 ALA A 409 1 11 HELIX 6 AA6 ASP A 414 ASN A 433 1 20 HELIX 7 AA7 HIS A 437 LYS A 456 1 20 SHEET 1 AA1 2 LYS B 2 ILE B 4 0 SHEET 2 AA1 2 ALY B 7 TRP B 9 -1 O TRP B 9 N LYS B 2 LINK C ACE B 0 N TRP B 1 1555 1555 1.33 LINK CH3 ACE B 0 SG CYS B 14 1555 1555 1.77 LINK C ILE B 4 N ALY B 5 1555 1555 1.33 LINK C ALY B 5 N GLY B 6 1555 1555 1.33 LINK C GLY B 6 N ALY B 7 1555 1555 1.33 LINK C ALY B 7 N THR B 8 1555 1555 1.33 LINK C THR B 11 N ALY B 12 1555 1555 1.33 LINK C ALY B 12 N GLN B 13 1555 1555 1.33 LINK C CYS B 14 N NH2 B 101 1555 1555 1.43 SITE 1 AC1 4 THR B 11 ALY B 12 GLN B 13 CYS B 14 SITE 1 AC2 1 ALY B 7 SITE 1 AC3 5 LYS A 378 SER A 405 THR B 11 CYS B 14 SITE 2 AC3 5 NH2 B 101 CRYST1 32.399 56.514 73.336 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 0.030865 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013636 0.00000