HEADER CYTOSOLIC PROTEIN 29-AUG-18 6HIB
TITLE THE ATAD2 BROMODOMAIN IN COMPLEX WITH COMPOUND 14
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: BROMODOMAIN OF ATAD2;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS BROMODOMAIN, ATAD2, INHIBITOR, COMPLEX, CYTOSOLIC PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR P.SLEDZ,A.CAFLISCH
REVDAT 3 17-JAN-24 6HIB 1 REMARK
REVDAT 2 04-NOV-20 6HIB 1 JRNL
REVDAT 1 20-FEB-19 6HIB 0
JRNL AUTH A.DOLBOIS,L.BATISTE,L.WIEDMER,J.DONG,M.BRUTSCH,D.HUANG,
JRNL AUTH 2 N.M.DEERAIN,D.SPILIOTOPOULOS,I.CHENG-SANCHEZ,E.LAUL,
JRNL AUTH 3 C.NEVADO,P.SLEDZ,A.CAFLISCH
JRNL TITL HITTING A MOVING TARGET: SIMULATION AND CRYSTALLOGRAPHY
JRNL TITL 2 STUDY OF ATAD2 BROMODOMAIN BLOCKERS.
JRNL REF ACS MED.CHEM.LETT. V. 11 1573 2020
JRNL REFN ISSN 1948-5875
JRNL PMID 32832026
JRNL DOI 10.1021/ACSMEDCHEMLETT.0C00080
REMARK 2
REMARK 2 RESOLUTION. 2.03 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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.96
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 17621
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.211
REMARK 3 R VALUE (WORKING SET) : 0.208
REMARK 3 FREE R VALUE : 0.231
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010
REMARK 3 FREE R VALUE TEST SET COUNT : 1763
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 48.9699 - 4.7699 1.00 1359 152 0.2023 0.1912
REMARK 3 2 4.7699 - 3.7865 1.00 1267 141 0.1669 0.1955
REMARK 3 3 3.7865 - 3.3079 1.00 1235 137 0.1867 0.2148
REMARK 3 4 3.3079 - 3.0055 1.00 1223 136 0.2113 0.2430
REMARK 3 5 3.0055 - 2.7901 1.00 1221 136 0.2300 0.2521
REMARK 3 6 2.7901 - 2.6257 1.00 1212 133 0.2215 0.2746
REMARK 3 7 2.6257 - 2.4942 1.00 1194 133 0.2127 0.2590
REMARK 3 8 2.4942 - 2.3856 1.00 1194 134 0.2138 0.2294
REMARK 3 9 2.3856 - 2.2938 1.00 1202 133 0.2257 0.2559
REMARK 3 10 2.2938 - 2.2146 1.00 1192 133 0.2918 0.3360
REMARK 3 11 2.2146 - 2.1454 1.00 1198 132 0.2593 0.2887
REMARK 3 12 2.1454 - 2.0840 1.00 1189 133 0.2701 0.2974
REMARK 3 13 2.0840 - 2.0292 0.99 1172 130 0.2921 0.3222
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) : 0.240
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.240
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 : 0.008 1134
REMARK 3 ANGLE : 1.139 1542
REMARK 3 CHIRALITY : 0.045 172
REMARK 3 PLANARITY : 0.007 202
REMARK 3 DIHEDRAL : 9.494 993
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 6HIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-18.
REMARK 100 THE DEPOSITION ID IS D_1200011657.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-OCT-17
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06DA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000031
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32104
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.029
REMARK 200 RESOLUTION RANGE LOW (A) : 48.956
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 5.670
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4200
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2
REMARK 200 DATA REDUNDANCY IN SHELL : 5.04
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: 5F36
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 70.27
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.14
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2M (NH4)2SO4, 0.1M BIS-TRIS PH 5.5,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 92.22467
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.11233
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.16850
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.05617
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 115.28083
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 92.22467
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 46.11233
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 23.05617
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 69.16850
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 115.28083
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8030 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL
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 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 MET A 980 CG SD CE
REMARK 470 LYS A1004 CG CD CE NZ
REMARK 470 ASP A1016 CG OD1 OD2
REMARK 470 GLU A1017 CG CD OE1 OE2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue G6Z A 1201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1202
DBREF 6HIB A 981 1108 UNP Q6PL18 ATAD2_HUMAN 981 1108
SEQADV 6HDN SER A 979 UNP Q6PL18 EXPRESSION TAG
SEQADV 6HDN MET A 980 UNP Q6PL18 EXPRESSION TAG
SEQRES 1 A 130 SER MET GLN GLU GLU ASP THR PHE ARG GLU LEU ARG ILE
SEQRES 2 A 130 PHE LEU ARG ASN VAL THR HIS ARG LEU ALA ILE ASP LYS
SEQRES 3 A 130 ARG PHE ARG VAL PHE THR LYS PRO VAL ASP PRO ASP GLU
SEQRES 4 A 130 VAL PRO ASP TYR VAL THR VAL ILE LYS GLN PRO MET ASP
SEQRES 5 A 130 LEU SER SER VAL ILE SER LYS ILE ASP LEU HIS LYS TYR
SEQRES 6 A 130 LEU THR VAL LYS ASP TYR LEU ARG ASP ILE ASP LEU ILE
SEQRES 7 A 130 CYS SER ASN ALA LEU GLU TYR ASN PRO ASP ARG ASP PRO
SEQRES 8 A 130 GLY ASP ARG LEU ILE ARG HIS ARG ALA CYS ALA LEU ARG
SEQRES 9 A 130 ASP THR ALA TYR ALA ILE ILE LYS GLU GLU LEU ASP GLU
SEQRES 10 A 130 ASP PHE GLU GLN LEU CYS GLU GLU ILE GLN GLU SER ARG
HET G6Z A1201 23
HET SO4 A1202 5
HETNAM G6Z 1-AZANYL-~{N}-[5-(5-AZANYLPYRIDIN-3-YL)-4-ETHANOYL-1,3-
HETNAM 2 G6Z THIAZOL-2-YL]CYCLOBUTANE-1-CARBOXAMIDE
HETNAM SO4 SULFATE ION
FORMUL 2 G6Z C15 H17 N5 O2 S
FORMUL 3 SO4 O4 S 2-
FORMUL 4 HOH *71(H2 O)
HELIX 1 AA1 SER A 979 ILE A 1002 1 24
HELIX 2 AA2 ASP A 1003 THR A 1010 5 8
HELIX 3 AA3 ASP A 1020 ILE A 1025 1 6
HELIX 4 AA4 ASP A 1030 LEU A 1040 1 11
HELIX 5 AA5 THR A 1045 ASN A 1064 1 20
HELIX 6 AA6 ASP A 1068 LEU A 1093 1 26
HELIX 7 AA7 ASP A 1094 SER A 1107 1 14
SITE 1 AC1 7 VAL A1008 VAL A1013 ASN A1064 GLY A1070
SITE 2 AC1 7 ASP A1071 HOH A1305 HOH A1352
SITE 1 AC2 4 ARG A 987 ARG A 990 ARG A 994 ARG A1067
CRYST1 80.020 80.020 138.337 90.00 90.00 120.00 P 65 2 2 12
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 0.012497 0.007215 0.000000 0.00000
SCALE2 0.000000 0.014430 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007229 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
