HEADER CYTOSOLIC PROTEIN 12-OCT-17 6EPU
TITLE THE ATAD2 BROMODOMAIN IN COMPLEX WITH COMPOUND 2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN,ANCCA;
COMPND 5 EC: 3.6.1.3;
COMPND 6 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: ATAD2, L16, PRO2000;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS BROMODOMAIN, ATAD2, INHIBITOR, COMPLEX, CYTOSOLIC PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR P.SLEDZ,A.CAFLISCH
REVDAT 3 04-NOV-20 6EPU 1 JRNL
REVDAT 2 13-NOV-19 6EPU 1 JRNL
REVDAT 1 31-OCT-18 6EPU 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. 1.80 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) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.56
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 44856
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.193
REMARK 3 R VALUE (WORKING SET) : 0.192
REMARK 3 FREE R VALUE : 0.218
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940
REMARK 3 FREE R VALUE TEST SET COUNT : 2218
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 48.5739 - 4.5356 1.00 2687 140 0.1700 0.2127
REMARK 3 2 4.5356 - 3.6004 1.00 2677 132 0.1523 0.1812
REMARK 3 3 3.6004 - 3.1454 1.00 2674 139 0.1868 0.1945
REMARK 3 4 3.1454 - 2.8578 1.00 2668 140 0.2090 0.1989
REMARK 3 5 2.8578 - 2.6530 1.00 2674 140 0.1963 0.2318
REMARK 3 6 2.6530 - 2.4966 1.00 2681 140 0.1970 0.2355
REMARK 3 7 2.4966 - 2.3716 1.00 2667 141 0.2051 0.2070
REMARK 3 8 2.3716 - 2.2684 1.00 2665 139 0.2040 0.2175
REMARK 3 9 2.2684 - 2.1810 1.00 2700 140 0.2045 0.2626
REMARK 3 10 2.1810 - 2.1058 1.00 2656 137 0.2054 0.2635
REMARK 3 11 2.1058 - 2.0399 1.00 2677 138 0.2196 0.2449
REMARK 3 12 2.0399 - 1.9816 1.00 2671 142 0.2286 0.2509
REMARK 3 13 1.9816 - 1.9294 1.00 2677 138 0.2341 0.2559
REMARK 3 14 1.9294 - 1.8824 1.00 2679 138 0.2485 0.2739
REMARK 3 15 1.8824 - 1.8396 1.00 2674 144 0.2950 0.3440
REMARK 3 16 1.8396 - 1.8004 0.94 2511 130 0.3367 0.3930
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) : 21.750
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 : 0.006 1120
REMARK 3 ANGLE : 0.867 1520
REMARK 3 CHIRALITY : 0.046 171
REMARK 3 PLANARITY : 0.004 201
REMARK 3 DIHEDRAL : 6.442 974
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 6EPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-OCT-17.
REMARK 100 THE DEPOSITION ID IS D_1200006998.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-NOV-16
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 : X06SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000360
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 : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44912
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 48.556
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 200 DATA REDUNDANCY : 5.170
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8300
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9
REMARK 200 DATA REDUNDANCY IN SHELL : 4.84
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.790
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 69.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.06
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 91.02200
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 45.51100
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 68.26650
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 22.75550
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 113.77750
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 91.02200
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 45.51100
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 22.75550
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 68.26650
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 113.77750
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: 8000 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 CD CE NZ
REMARK 470 ARG A1007 NE CZ NH1 NH2
REMARK 470 LYS A1011 CE NZ
REMARK 470 LYS A1026 CG CD CE NZ
REMARK 470 LYS A1047 CE NZ
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A1439 DISTANCE = 6.20 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue BQH A 1202
DBREF 6EPU A 981 1108 UNP Q6PL18 ATAD2_HUMAN 981 1108
SEQADV 6EPU SER A 979 UNP Q6PL18 EXPRESSION TAG
SEQADV 6EPU 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 SO4 A1201 5
HET BQH A1202 17
HETNAM SO4 SULFATE ION
HETNAM BQH (2~{S})-~{N}-(4-ETHANOYL-1,3-THIAZOL-2-YL)PIPERAZINE-2-
HETNAM 2 BQH CARBOXAMIDE
FORMUL 2 SO4 O4 S 2-
FORMUL 3 BQH C10 H14 N4 O2 S
FORMUL 4 HOH *139(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 6 ARG A 987 ARG A 990 ARG A 994 ARG A1067
SITE 2 AC1 6 ARG A1072 HOH A1330
SITE 1 AC2 5 TYR A1063 ASN A1064 ASP A1071 ILE A1074
SITE 2 AC2 5 HOH A1308
CRYST1 79.765 79.765 136.533 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 0.012537 0.007238 0.000000 0.00000
SCALE2 0.000000 0.014476 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007324 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
