HEADER TRANSFERASE 02-DEC-15 5F36
TITLE CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN ATAD2 IN COMPLEX WITH
TITLE 2 COMPOUND A12
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 981-1108;
COMPND 5 SYNONYM: AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN,ANCCA;
COMPND 6 EC: 3.6.1.3;
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: ATAD2, L16, PRO2000;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HYDROLASE INHIBITOR COMPLEX, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.DONG,A.CAFLISCH
REVDAT 3 10-JAN-24 5F36 1 REMARK
REVDAT 2 04-NOV-20 5F36 1 JRNL
REVDAT 1 14-DEC-16 5F36 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. 1.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
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) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.69
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 41964
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.170
REMARK 3 R VALUE (WORKING SET) : 0.169
REMARK 3 FREE R VALUE : 0.190
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860
REMARK 3 FREE R VALUE TEST SET COUNT : 2039
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 48.7169 - 3.6980 1.00 2928 151 0.1687 0.1842
REMARK 3 2 3.6980 - 2.9353 1.00 2739 155 0.1820 0.2049
REMARK 3 3 2.9353 - 2.5643 1.00 2703 140 0.1867 0.2064
REMARK 3 4 2.5643 - 2.3299 1.00 2669 164 0.1653 0.1924
REMARK 3 5 2.3299 - 2.1629 1.00 2658 128 0.1565 0.1791
REMARK 3 6 2.1629 - 2.0354 1.00 2676 124 0.1712 0.1860
REMARK 3 7 2.0354 - 1.9334 1.00 2638 149 0.1636 0.1645
REMARK 3 8 1.9334 - 1.8493 1.00 2636 139 0.1522 0.1744
REMARK 3 9 1.8493 - 1.7781 1.00 2651 125 0.1520 0.1627
REMARK 3 10 1.7781 - 1.7167 1.00 2636 127 0.1451 0.1884
REMARK 3 11 1.7167 - 1.6630 1.00 2608 125 0.1435 0.1894
REMARK 3 12 1.6630 - 1.6155 1.00 2655 116 0.1442 0.1439
REMARK 3 13 1.6155 - 1.5729 1.00 2597 138 0.1574 0.1786
REMARK 3 14 1.5729 - 1.5346 1.00 2624 121 0.1571 0.2270
REMARK 3 15 1.5346 - 1.4997 0.96 2507 137 0.1700 0.1867
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) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.890
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 22.95
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.39
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 : 0.009 1124
REMARK 3 ANGLE : 1.105 1523
REMARK 3 CHIRALITY : 0.077 170
REMARK 3 PLANARITY : 0.005 202
REMARK 3 DIHEDRAL : 20.180 438
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 5F36 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-15.
REMARK 100 THE DEPOSITION ID IS D_1000215940.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-MAY-15
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) : 1.00003
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 : SCALA 3.3.22
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42035
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
REMARK 200 RESOLUTION RANGE LOW (A) : 69.112
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 18.90
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.04300
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2
REMARK 200 DATA REDUNDANCY IN SHELL : 17.70
REMARK 200 R MERGE FOR SHELL (I) : 0.81800
REMARK 200 R SYM FOR SHELL (I) : 0.81800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.000
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: 3DAI
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 69.86
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.08
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 91.48000
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 45.74000
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 68.61000
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 22.87000
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 114.35000
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 91.48000
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 45.74000
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 22.87000
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 68.61000
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 114.35000
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: 190 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8070 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 A1327 LIES ON A SPECIAL POSITION.
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 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 ND2 ASN A 995 O HOH A 1301 1.89
REMARK 500 O HOH A 1334 O HOH A 1373 2.16
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 5UE 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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 1203
DBREF 5F36 A 981 1108 UNP Q6PL18 ATAD2_HUMAN 981 1108
SEQADV 5F36 SER A 979 UNP Q6PL18 EXPRESSION TAG
SEQADV 5F36 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 5UE A1201 14
HET SO4 A1202 5
HET CL A1203 1
HETNAM 5UE [(2~{R})-1-[(4-ETHANOYL-1,3-THIAZOL-2-YL)AMINO]-1-
HETNAM 2 5UE OXIDANYLIDENE-PROPAN-2-YL]AZANIUM
HETNAM SO4 SULFATE ION
HETNAM CL CHLORIDE ION
FORMUL 2 5UE C8 H12 N3 O2 S 1+
FORMUL 3 SO4 O4 S 2-
FORMUL 4 CL CL 1-
FORMUL 5 HOH *101(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 ALA A1060 TYR A1063 ASN A1064 ASP A1071
SITE 2 AC1 6 ILE A1074 HOH A1308
SITE 1 AC2 6 ARG A 987 ARG A 990 ARG A 994 ARG A1067
SITE 2 AC2 6 ARG A1072 HOH A1355
SITE 1 AC3 1 ARG A1077
CRYST1 79.804 79.804 137.220 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 0.012531 0.007235 0.000000 0.00000
SCALE2 0.000000 0.014469 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007288 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
