HEADER PROTEIN BINDING 08-DEC-20 7DMY TITLE THE CRYSTAL STRUCTURE OF CPD7 IN COMPLEX WITH BPTF BROMODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN; COMPND 5 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING TRANSCRIPTION FACTOR, COMPND 6 FETAL ALZ-50 CLONE 1 PROTEIN,FETAL ALZHEIMER ANTIGEN; COMPND 7 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: BPTF, FAC1, FALZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR;BPTF;BROMODOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.XIONG,Y.GUO,S.YANG REVDAT 2 29-NOV-23 7DMY 1 REMARK REVDAT 1 20-OCT-21 7DMY 0 JRNL AUTH L.XIONG,X.MAO,Y.GUO,Y.ZHOU,M.CHEN,P.CHEN,S.YANG,L.LI JRNL TITL DISCOVERY OF SELECTIVE BPTF BROMODOMAIN INHIBITORS BY JRNL TITL 2 SCREENING AND STRUCTURE-BASED OPTIMIZATION. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 545 125 2021 JRNL REFN ESSN 1090-2104 JRNL PMID 33548625 JRNL DOI 10.1016/J.BBRC.2021.01.067 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 9146 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.390 REMARK 3 FREE R VALUE TEST SET COUNT : 493 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 3.4200 - 3.1739 0.99 2190 134 0.2160 0.2229 REMARK 3 2 3.1739 - 2.5194 0.99 2202 99 0.2675 0.3323 REMARK 3 3 2.5194 - 2.2010 0.98 2114 145 0.2872 0.3354 REMARK 3 4 2.2010 - 2.0000 0.98 2147 115 0.3115 0.4010 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.54 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 : 0.013 1054 REMARK 3 ANGLE : 1.449 1431 REMARK 3 CHIRALITY : 0.057 148 REMARK 3 PLANARITY : 0.009 181 REMARK 3 DIHEDRAL : 15.463 636 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 7DMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019764. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-20 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97875 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9269 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 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: 3UV2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 20% PEG 3350, REMARK 280 PH 7.1, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 37.50550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.46550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.50550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.46550 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 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 MET A 2768 REMARK 465 HIS A 2769 REMARK 465 HIS A 2770 REMARK 465 HIS A 2771 REMARK 465 HIS A 2772 REMARK 465 HIS A 2773 REMARK 465 HIS A 2774 REMARK 465 SER A 2775 REMARK 465 SER A 2776 REMARK 465 GLY A 2777 REMARK 465 VAL A 2778 REMARK 465 ASP A 2779 REMARK 465 LEU A 2780 REMARK 465 GLY A 2781 REMARK 465 THR A 2782 REMARK 465 GLU A 2783 REMARK 465 ASN A 2784 REMARK 465 LEU A 2785 REMARK 465 TYR A 2786 REMARK 465 PHE A 2787 REMARK 465 GLN A 2788 REMARK 465 SER A 2789 REMARK 465 MET A 2790 REMARK 465 SER A 2791 REMARK 465 THR A 2792 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 SER A 2896 CB OG 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 HH TYR A 2807 O TYR A 2860 1.42 REMARK 500 O VAL A 2830 HH TYR A 2839 1.48 REMARK 500 OE1 GLU A 2804 HH21 ARG A 2858 1.49 REMARK 500 OH TYR A 2807 O TYR A 2860 1.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A2812 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES 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 ASP A2831 108.01 -47.66 REMARK 500 SER A2910 47.46 -77.93 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 HAF A 3001 DBREF 7DMY A 2791 2911 UNP Q12830 BPTF_HUMAN 2917 3037 SEQADV 7DMY MET A 2768 UNP Q12830 INITIATING METHIONINE SEQADV 7DMY HIS A 2769 UNP Q12830 EXPRESSION TAG SEQADV 7DMY HIS A 2770 UNP Q12830 EXPRESSION TAG SEQADV 7DMY HIS A 2771 UNP Q12830 EXPRESSION TAG SEQADV 7DMY HIS A 2772 UNP Q12830 EXPRESSION TAG SEQADV 7DMY HIS A 2773 UNP Q12830 EXPRESSION TAG SEQADV 7DMY HIS A 2774 UNP Q12830 EXPRESSION TAG SEQADV 7DMY SER A 2775 UNP Q12830 EXPRESSION TAG SEQADV 7DMY SER A 2776 UNP Q12830 EXPRESSION TAG SEQADV 7DMY GLY A 2777 UNP Q12830 EXPRESSION TAG SEQADV 7DMY VAL A 2778 UNP Q12830 EXPRESSION TAG SEQADV 7DMY ASP A 2779 UNP Q12830 EXPRESSION TAG SEQADV 7DMY LEU A 2780 UNP Q12830 EXPRESSION TAG SEQADV 7DMY GLY A 2781 UNP Q12830 EXPRESSION TAG SEQADV 7DMY THR A 2782 UNP Q12830 EXPRESSION TAG SEQADV 7DMY GLU A 2783 UNP Q12830 EXPRESSION TAG SEQADV 7DMY ASN A 2784 UNP Q12830 EXPRESSION TAG SEQADV 7DMY LEU A 2785 UNP Q12830 EXPRESSION TAG SEQADV 7DMY TYR A 2786 UNP Q12830 EXPRESSION TAG SEQADV 7DMY PHE A 2787 UNP Q12830 EXPRESSION TAG SEQADV 7DMY GLN A 2788 UNP Q12830 EXPRESSION TAG SEQADV 7DMY SER A 2789 UNP Q12830 EXPRESSION TAG SEQADV 7DMY MET A 2790 UNP Q12830 EXPRESSION TAG SEQRES 1 A 144 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 144 GLY THR GLU ASN LEU TYR PHE GLN SER MET SER THR GLU SEQRES 3 A 144 ASP ALA MET THR VAL LEU THR PRO LEU THR GLU LYS ASP SEQRES 4 A 144 TYR GLU GLY LEU LYS ARG VAL LEU ARG SER LEU GLN ALA SEQRES 5 A 144 HIS LYS MET ALA TRP PRO PHE LEU GLU PRO VAL ASP PRO SEQRES 6 A 144 ASN ASP ALA PRO ASP TYR TYR GLY VAL ILE LYS GLU PRO SEQRES 7 A 144 MET ASP LEU ALA THR MET GLU GLU ARG VAL GLN ARG ARG SEQRES 8 A 144 TYR TYR GLU LYS LEU THR GLU PHE VAL ALA ASP MET THR SEQRES 9 A 144 LYS ILE PHE ASP ASN CYS ARG TYR TYR ASN PRO SER ASP SEQRES 10 A 144 SER PRO PHE TYR GLN CYS ALA GLU VAL LEU GLU SER PHE SEQRES 11 A 144 PHE VAL GLN LYS LEU LYS GLY PHE LYS ALA SER ARG SER SEQRES 12 A 144 HIS HET HAF A3001 65 HETNAM HAF TERT-BUTYL 3-METHYL-2-[[(3R,5R)-1-METHYL-5-PHENYL- HETNAM 2 HAF PIPERIDIN-3-YL]AMINO]-4-OXIDANYLIDENE-5,7- HETNAM 3 HAF DIHYDROPYRROLO[3,4-D]PYRIMIDINE-6-CARBOXYLATE FORMUL 2 HAF C24 H33 N5 O3 FORMUL 3 HOH *15(H2 O) HELIX 1 AA1 GLU A 2793 THR A 2800 1 8 HELIX 2 AA2 THR A 2803 ALA A 2819 1 17 HELIX 3 AA3 HIS A 2820 LEU A 2827 5 8 HELIX 4 AA4 ALA A 2835 VAL A 2841 5 7 HELIX 5 AA5 ASP A 2847 ARG A 2857 1 11 HELIX 6 AA6 LYS A 2862 ASN A 2881 1 20 HELIX 7 AA7 SER A 2885 SER A 2910 1 26 SITE 1 AC1 9 GLU A2793 TRP A2824 PRO A2825 PRO A2829 SITE 2 AC1 9 VAL A2830 TYR A2880 ASN A2881 PRO A2882 SITE 3 AC1 9 SER A2908 CRYST1 75.011 44.931 40.838 90.00 95.35 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 0.013331 0.000000 0.001248 0.00000 SCALE2 0.000000 0.022256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024594 0.00000