HEADER TRANSCRIPTION/INHIBITOR 31-AUG-19 6U71 TITLE BRD2-BD2 IN COMPLEX WITH THE CYCLIC PEPTIDE 3.1_3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CYCLIC PEPTIDE 3.1_3; 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: BRD2, KIAA9001, RING3; 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, BRD2, 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 6U71 1 REMARK REVDAT 3 11-OCT-23 6U71 1 REMARK REVDAT 2 03-MAR-21 6U71 1 JRNL REVDAT 1 19-AUG-20 6U71 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. 1.47 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 20844 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1044 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 42.0100 - 2.8100 1.00 3019 164 0.1721 0.1927 REMARK 3 2 2.8100 - 2.2300 1.00 2863 155 0.1657 0.2112 REMARK 3 3 2.2300 - 1.9500 0.99 2835 145 0.1416 0.1728 REMARK 3 4 1.9500 - 1.7700 1.00 2805 147 0.1402 0.2117 REMARK 3 5 1.7700 - 1.6400 1.00 2786 148 0.1427 0.1900 REMARK 3 6 1.6400 - 1.5400 0.99 2797 142 0.1451 0.2154 REMARK 3 7 1.5400 - 1.4700 0.97 2695 143 0.1685 0.2558 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.577 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.83 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 : 0.003 1068 REMARK 3 ANGLE : 0.615 1443 REMARK 3 CHIRALITY : 0.066 146 REMARK 3 PLANARITY : 0.004 185 REMARK 3 DIHEDRAL : 10.561 406 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 6U71 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_1000243898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-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 : 20855 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 42.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 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: 3ONI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MMT PH 9.0, 25 % W/V PEG 1500, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 25.90450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.89400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.90450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.89400 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: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7310 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 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 595 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 341 REMARK 465 GLY A 342 REMARK 465 PRO A 343 REMARK 465 LEU A 344 REMARK 465 GLY A 345 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 452 31.11 -85.52 REMARK 500 LYS A 452 31.11 -84.17 REMARK 500 ALY B 6 -35.98 77.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 6U71 A 347 455 UNP P25440 BRD2_HUMAN 347 455 DBREF 6U71 B 0 12 PDB 6U71 6U71 0 12 SEQADV 6U71 GLN A 341 UNP P25440 EXPRESSION TAG SEQADV 6U71 GLY A 342 UNP P25440 EXPRESSION TAG SEQADV 6U71 PRO A 343 UNP P25440 EXPRESSION TAG SEQADV 6U71 LEU A 344 UNP P25440 EXPRESSION TAG SEQADV 6U71 GLY A 345 UNP P25440 EXPRESSION TAG SEQADV 6U71 SER A 346 UNP P25440 EXPRESSION TAG SEQRES 1 A 115 GLN GLY PRO LEU GLY SER SER GLU GLN LEU LYS HIS CYS SEQRES 2 A 115 ASN GLY ILE LEU LYS GLU LEU LEU SER LYS LYS HIS ALA SEQRES 3 A 115 ALA TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP ALA SER SEQRES 4 A 115 ALA LEU GLY LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS SEQRES 5 A 115 PRO MET ASP LEU SER THR VAL LYS ARG LYS MET GLU ASN SEQRES 6 A 115 ARG ASP TYR ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL SEQRES 7 A 115 ARG LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO SEQRES 8 A 115 ASP HIS ASP VAL VAL ALA MET ALA ARG LYS LEU GLN ASP SEQRES 9 A 115 VAL PHE GLU PHE ARG TYR ALA LYS MET PRO ASP SEQRES 1 B 13 ACE TRP TRP ILE ILE PRO ALY VAL LYS ALY GLY CYS NH2 HET ACE B 0 3 HET ALY B 6 12 HET ALY B 9 12 HET NH2 B 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 *116(H2 O) HELIX 1 AA1 SER A 346 LEU A 361 1 16 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 SHEET 1 AA1 2 TRP B 2 ILE B 4 0 SHEET 2 AA1 2 LYS B 8 ALY B 9 -1 O LYS B 8 N ILE B 3 LINK C ACE B 0 N TRP B 1 1555 1555 1.33 LINK CH3 ACE B 0 SG CYS B 11 1555 1555 1.77 LINK C PRO B 5 N ALY B 6 1555 1555 1.33 LINK C ALY B 6 N VAL B 7 1555 1555 1.33 LINK C LYS B 8 N ALY B 9 1555 1555 1.33 LINK C ALY B 9 N GLY B 10 1555 1555 1.33 LINK C CYS B 11 N NH2 B 12 1555 1555 1.43 CRYST1 31.818 51.809 71.788 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 0.031429 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013930 0.00000