HEADER TRANSCRIPTION 18-MAY-22 8CV6 TITLE PEPTIDE 4.2B IN COMPLEX WITH BRD4.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BRD4 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BD2 (UNP RESIDUES 347-464); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PEPTIDE 4.2E; 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; 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 CYCLIC PEPTIDE INHIBITOR BROMODOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.FRANCK,J.P.MACKAY REVDAT 4 06-DEC-23 8CV6 1 JRNL REVDAT 3 15-NOV-23 8CV6 1 REMARK REVDAT 2 25-OCT-23 8CV6 1 REMARK REVDAT 1 24-MAY-23 8CV6 0 JRNL AUTH C.FRANCK,K.PATEL,L.J.WALPORT,M.CHRISTIE,A.NORMAN, JRNL AUTH 2 T.PASSIOURA,H.SUGA,R.J.PAYNE,J.P.MACKAY JRNL TITL DISCOVERY AND CHARACTERIZATION OF CYCLIC PEPTIDES SELECTIVE JRNL TITL 2 FOR THE C-TERMINAL BROMODOMAINS OF BET FAMILY PROTEINS. JRNL REF STRUCTURE V. 31 912 2023 JRNL REFN ISSN 0969-2126 JRNL PMID 37269828 JRNL DOI 10.1016/J.STR.2023.05.009 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 13402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 625 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 35.6500 - 2.6900 0.99 3252 173 0.1719 0.1995 REMARK 3 2 2.6900 - 2.1400 0.98 3203 159 0.1859 0.2443 REMARK 3 3 2.1400 - 1.8700 0.97 3181 151 0.1855 0.2310 REMARK 3 4 1.8700 - 1.7000 0.96 3141 142 0.2084 0.2866 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) : 0.181 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.23 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 1120 REMARK 3 ANGLE : 1.037 1501 REMARK 3 CHIRALITY : 0.056 151 REMARK 3 PLANARITY : 0.006 190 REMARK 3 DIHEDRAL : 16.474 162 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 8CV6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000264330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-19 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) : 0.953736 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 : 13420 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000 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 (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.56600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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: PDB ENTRY 3UVV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 30% W/V PEG1000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.81800 REMARK 290 SMTRY3 2 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: 1540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 ASP A 459 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 349 N REMARK 480 GLN A 353 NE2 REMARK 480 LYS A 362 CE NZ REMARK 480 LYS A 367 CD CE NZ REMARK 480 LYS A 368 CG CD CE NZ REMARK 480 GLU A 383 CD OE1 OE2 REMARK 480 LYS A 395 CD CE NZ REMARK 480 GLN A 416 OE1 REMARK 480 LYS A 445 NZ REMARK 480 LYS A 456 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 SER A 347 14.53 -149.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALY B 9 -16.54 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CV6 A 347 464 UNP Q5BJ26 Q5BJ26_HUMAN 347 464 DBREF 8CV6 B 1 17 PDB 8CV6 8CV6 1 17 SEQADV 8CV6 GLY A 343 UNP Q5BJ26 EXPRESSION TAG SEQADV 8CV6 PRO A 344 UNP Q5BJ26 EXPRESSION TAG SEQADV 8CV6 LEU A 345 UNP Q5BJ26 EXPRESSION TAG SEQADV 8CV6 GLY A 346 UNP Q5BJ26 EXPRESSION TAG SEQRES 1 A 122 GLY PRO LEU GLY SER SER LYS VAL SER GLU GLN LEU LYS SEQRES 2 A 122 CYS CYS SER GLY ILE LEU LYS GLU MET PHE ALA LYS LYS SEQRES 3 A 122 HIS ALA ALA TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP SEQRES 4 A 122 VAL GLU ALA LEU GLY LEU HIS ASP TYR CYS ASP ILE ILE SEQRES 5 A 122 LYS HIS PRO MET ASP MET SER THR ILE LYS SER LYS LEU SEQRES 6 A 122 GLU ALA ARG GLU TYR ARG ASP ALA GLN GLU PHE GLY ALA SEQRES 7 A 122 ASP VAL ARG LEU MET PHE SER ASN CYS TYR LYS TYR ASN SEQRES 8 A 122 PRO PRO ASP HIS GLU VAL VAL ALA MET ALA ARG LYS LEU SEQRES 9 A 122 GLN ASP VAL PHE GLU MET ARG PHE ALA LYS MET PRO ASP SEQRES 10 A 122 GLU PRO GLU GLU PRO SEQRES 1 B 17 TRP TYR ASP VAL PHE LEU THR ARG ALY TYR GLY ALY ALY SEQRES 2 B 17 LYS VAL ALA CYS HET ALY B 9 12 HET ALY B 12 12 HET ALY B 13 12 HET ACE B 101 3 HET NH2 B 102 1 HETNAM ALY N(6)-ACETYLLYSINE HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 2 ALY 3(C8 H16 N2 O3) FORMUL 3 ACE C2 H4 O FORMUL 4 NH2 H2 N FORMUL 5 HOH *102(H2 O) HELIX 1 AA1 SER A 348 PHE A 365 1 18 HELIX 2 AA2 ALA A 366 LYS A 368 5 3 HELIX 3 AA3 HIS A 369 TRP A 374 1 6 HELIX 4 AA4 PRO A 375 TYR A 377 5 3 HELIX 5 AA5 ASP A 389 ILE A 394 1 6 HELIX 6 AA6 ASP A 399 ALA A 409 1 11 HELIX 7 AA7 ASP A 414 ASN A 433 1 20 HELIX 8 AA8 HIS A 437 ALA A 455 1 19 HELIX 9 AA9 ASP B 3 GLY B 11 1 9 LINK N TRP B 1 C ACE B 101 1555 1555 1.33 LINK C ARG B 8 N ALY B 9 1555 1555 1.33 LINK C ALY B 9 N TYR B 10 1555 1555 1.32 LINK C GLY B 11 N ALY B 12 1555 1555 1.33 LINK C ALY B 12 N ALY B 13 1555 1555 1.33 LINK C ALY B 13 N LYS B 14 1555 1555 1.33 LINK SG CYS B 17 CH3 ACE B 101 1555 1555 1.77 LINK C CYS B 17 N NH2 B 102 1555 1555 1.43 CRYST1 29.442 59.636 36.269 90.00 100.61 90.00 P 1 21 1 2 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 0.033965 0.000000 0.006360 0.00000 SCALE2 0.000000 0.016768 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028051 0.00000