HEADER TRANSCRIPTION 11-DEC-19 6TOJ
TITLE CRYSTAL STRUCTURE OF HUMAN BCL6 BTB DOMAIN IN COMPLEX WITH COMPOUND
TITLE 2 17A
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: B-CELL LYMPHOMA 6 PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: BCL-6,B-CELL LYMPHOMA 5 PROTEIN,BCL-5,PROTEIN LAZ-3,ZINC
COMPND 5 FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27,ZINC FINGER PROTEIN 51;
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: BCL6, BCL5, LAZ3, ZBTB27, ZNF51;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: AI;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET48B
KEYWDS CANCER, LYMPHOMA, INHIBITOR, DEGRADER, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR M.J.RODRIGUES,Y.-V.LE BIHAN,R.L.M.VAN MONTFORT
REVDAT 3 24-JAN-24 6TOJ 1 REMARK
REVDAT 2 06-MAY-20 6TOJ 1 JRNL
REVDAT 1 22-APR-20 6TOJ 0
JRNL AUTH B.R.BELLENIE,K.J.CHEUNG,A.VARELA,O.A.PIERRAT,G.W.COLLIE,
JRNL AUTH 2 G.M.BOX,M.D.BRIGHT,S.GOWAN,A.HAYES,M.J.RODRIGUES,K.N.SHETTY,
JRNL AUTH 3 M.CARTER,O.A.DAVIS,A.T.HENLEY,P.INNOCENTI,L.D.JOHNSON,M.LIU,
JRNL AUTH 4 S.DE KLERK,Y.V.LE BIHAN,M.G.LLOYD,P.C.MCANDREW,E.SHEHU,
JRNL AUTH 5 R.TALBOT,H.L.WOODWARD,R.BURKE,V.KIRKIN,R.L.M.VAN MONTFORT,
JRNL AUTH 6 F.I.RAYNAUD,O.W.ROSSANESE,S.HOELDER
JRNL TITL ACHIEVINGIN VIVOTARGET DEPLETION THROUGH THE DISCOVERY AND
JRNL TITL 2 OPTIMIZATION OF BENZIMIDAZOLONE BCL6 DEGRADERS.
JRNL REF J.MED.CHEM. V. 63 4047 2020
JRNL REFN ISSN 0022-2623
JRNL PMID 32275432
JRNL DOI 10.1021/ACS.JMEDCHEM.9B02076
REMARK 2
REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.10.3
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.62
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 19739
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.186
REMARK 3 R VALUE (WORKING SET) : 0.185
REMARK 3 FREE R VALUE : 0.205
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 987
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 49
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.86
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 403
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2264
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 383
REMARK 3 BIN R VALUE (WORKING SET) : 0.2247
REMARK 3 BIN FREE R VALUE : 0.2552
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.96
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 20
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1029
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 43
REMARK 3 SOLVENT ATOMS : 107
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 37.53
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.08
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.24340
REMARK 3 B22 (A**2) : 2.24340
REMARK 3 B33 (A**2) : -4.48680
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.210
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.110
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.102
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.100
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.096
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 1183 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 1605 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 428 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES : 230 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 1183 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 153 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : 11 ; 1.000 ; HARMONIC
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 1494 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 0.99
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.49
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.81
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 6
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: {A|-1 - 27}
REMARK 3 ORIGIN FOR THE GROUP (A): 7.3195 86.2503 176.1610
REMARK 3 T TENSOR
REMARK 3 T11: -0.0704 T22: -0.0278
REMARK 3 T33: -0.0887 T12: -0.0260
REMARK 3 T13: -0.0289 T23: 0.0499
REMARK 3 L TENSOR
REMARK 3 L11: 3.3747 L22: 2.1471
REMARK 3 L33: 6.4051 L12: 0.8114
REMARK 3 L13: -2.7146 L23: -1.1188
REMARK 3 S TENSOR
REMARK 3 S11: 0.0516 S12: 0.0052 S13: 0.3918
REMARK 3 S21: 0.1288 S22: 0.0465 S23: -0.0297
REMARK 3 S31: -0.2198 S32: 0.4769 S33: -0.0981
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: {A|28 - 46}
REMARK 3 ORIGIN FOR THE GROUP (A): -7.3856 73.5115 194.3780
REMARK 3 T TENSOR
REMARK 3 T11: 0.0168 T22: 0.0595
REMARK 3 T33: -0.0463 T12: -0.0403
REMARK 3 T13: 0.0433 T23: 0.0570
REMARK 3 L TENSOR
REMARK 3 L11: 2.9455 L22: 4.2543
REMARK 3 L33: 5.6362 L12: -0.7102
REMARK 3 L13: -1.5692 L23: -1.3097
REMARK 3 S TENSOR
REMARK 3 S11: 0.1014 S12: -0.3441 S13: -0.1508
REMARK 3 S21: 0.4831 S22: 0.1954 S23: 0.4496
REMARK 3 S31: 0.0527 S32: -0.3034 S33: -0.2969
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: {A|47 - 92}
REMARK 3 ORIGIN FOR THE GROUP (A): -0.0959 67.8192 190.7880
REMARK 3 T TENSOR
REMARK 3 T11: 0.0243 T22: -0.0628
REMARK 3 T33: -0.0425 T12: -0.0432
REMARK 3 T13: -0.0255 T23: 0.0297
REMARK 3 L TENSOR
REMARK 3 L11: 1.9980 L22: 4.0691
REMARK 3 L33: 2.5994 L12: 1.5730
REMARK 3 L13: 0.1080 L23: -0.8761
REMARK 3 S TENSOR
REMARK 3 S11: 0.1084 S12: -0.0905 S13: -0.1386
REMARK 3 S21: 0.1898 S22: 0.0111 S23: 0.1176
REMARK 3 S31: 0.2815 S32: -0.1787 S33: -0.1195
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: {A|93 - 101}
REMARK 3 ORIGIN FOR THE GROUP (A): 11.1061 80.2001 198.8410
REMARK 3 T TENSOR
REMARK 3 T11: 0.1136 T22: -0.0011
REMARK 3 T33: -0.0617 T12: -0.0976
REMARK 3 T13: -0.0676 T23: 0.0024
REMARK 3 L TENSOR
REMARK 3 L11: 4.3338 L22: 3.6150
REMARK 3 L33: 0.0000 L12: 0.8010
REMARK 3 L13: -0.1144 L23: 0.8145
REMARK 3 S TENSOR
REMARK 3 S11: 0.1547 S12: -0.2538 S13: 0.1327
REMARK 3 S21: 0.2536 S22: -0.2322 S23: -0.2221
REMARK 3 S31: -0.1009 S32: -0.0580 S33: 0.0775
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: {A|102 - 114}
REMARK 3 ORIGIN FOR THE GROUP (A): 9.8618 67.6909 197.5550
REMARK 3 T TENSOR
REMARK 3 T11: 0.0528 T22: -0.0967
REMARK 3 T33: -0.0432 T12: -0.0441
REMARK 3 T13: -0.0911 T23: 0.0786
REMARK 3 L TENSOR
REMARK 3 L11: 2.5655 L22: 3.1839
REMARK 3 L33: 4.0441 L12: -0.3165
REMARK 3 L13: -0.0657 L23: -2.0641
REMARK 3 S TENSOR
REMARK 3 S11: 0.1204 S12: -0.2422 S13: -0.3555
REMARK 3 S21: 0.4870 S22: -0.2037 S23: -0.4728
REMARK 3 S31: 0.2326 S32: 0.2275 S33: 0.0832
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: {A|115 - 129}
REMARK 3 ORIGIN FOR THE GROUP (A): 19.5455 71.4857 196.6980
REMARK 3 T TENSOR
REMARK 3 T11: 0.0053 T22: -0.0067
REMARK 3 T33: 0.0915 T12: -0.0234
REMARK 3 T13: -0.1191 T23: 0.0981
REMARK 3 L TENSOR
REMARK 3 L11: 5.4261 L22: 4.9333
REMARK 3 L33: 0.0038 L12: -0.6167
REMARK 3 L13: 1.3987 L23: -1.0077
REMARK 3 S TENSOR
REMARK 3 S11: 0.0915 S12: 0.1133 S13: -0.0934
REMARK 3 S21: 0.1352 S22: -0.3186 S23: -0.6665
REMARK 3 S31: -0.0515 S32: 0.2349 S33: 0.2271
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6TOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-19.
REMARK 100 THE DEPOSITION ID IS D_1292104966.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-JUL-19
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9159
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 : AIMLESS 0.7.4
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19812
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850
REMARK 200 RESOLUTION RANGE LOW (A) : 47.620
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 24.80
REMARK 200 R MERGE (I) : 0.14000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 25.50
REMARK 200 R MERGE FOR SHELL (I) : 3.51100
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: 3BIM
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.43
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 MICROLITER OF BCL6-BTB AT 10 MG/ML
REMARK 280 PLUS 1.5 MICROLITER OF A CRYSTALLISATION SOLUTION CONSISTING OF
REMARK 280 0.1 M TRIS PH 7.5 AND 0.80 M NA/K TARTRATE, AGAINST 300
REMARK 280 MICROLITER OF CRYSTALLISATION SOLUTION., VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+5/6
REMARK 290 6555 X-Y,X,Z+1/6
REMARK 290 7555 Y,X,-Z+1/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+2/3
REMARK 290 10555 -Y,-X,-Z+5/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+1/6
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 55.57667
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 111.15333
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 83.36500
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 138.94167
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 27.78833
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 55.57667
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 111.15333
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 138.94167
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 83.36500
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 27.78833
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: 5270 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13460 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 350 BIOMT1 2 0.500000 0.866025 0.000000 -66.99900
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 116.04567
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 361.24833
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 330 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 407 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 GLY A -14
REMARK 465 PRO A -13
REMARK 465 GLY A -12
REMARK 465 LEU A -11
REMARK 465 ASP A -10
REMARK 465 TYR A -9
REMARK 465 LYS A -8
REMARK 465 ASP A -7
REMARK 465 ASP A -6
REMARK 465 ASP A -5
REMARK 465 ASP A -4
REMARK 465 LYS A -3
REMARK 465 GLU A -2
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 LEU A 0 CD2
REMARK 470 ARG A 13 NE CZ NH1 NH2
REMARK 470 GLN A 64 NE2
REMARK 470 ARG A 98 NE CZ NH1 NH2
REMARK 470 LYS A 126 CD CE NZ
REMARK 470 GLU A 129 C O CB CG CD OE1 OE2
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 A 6 -145.77 -87.81
REMARK 500 CYS A 8 159.39 -47.24
REMARK 500 SER A 39 -121.16 57.96
REMARK 500 SER A 39 -120.16 57.96
REMARK 500 SER A 93 -1.52 77.67
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 NQQ A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205
DBREF 6TOJ A 5 129 UNP P41182 BCL6_HUMAN 5 129
SEQADV 6TOJ GLY A -14 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ PRO A -13 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ GLY A -12 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ LEU A -11 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ ASP A -10 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ TYR A -9 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ LYS A -8 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ ASP A -7 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ ASP A -6 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ ASP A -5 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ ASP A -4 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ LYS A -3 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ GLU A -2 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ ASN A -1 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ LEU A 0 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ TYR A 1 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ PHE A 2 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ GLN A 3 UNP P41182 EXPRESSION TAG
SEQADV 6TOJ GLY A 4 UNP P41182 EXPRESSION TAG
SEQRES 1 A 144 GLY PRO GLY LEU ASP TYR LYS ASP ASP ASP ASP LYS GLU
SEQRES 2 A 144 ASN LEU TYR PHE GLN GLY ALA ASP SER CYS ILE GLN PHE
SEQRES 3 A 144 THR ARG HIS ALA SER ASP VAL LEU LEU ASN LEU ASN ARG
SEQRES 4 A 144 LEU ARG SER ARG ASP ILE LEU THR ASP VAL VAL ILE VAL
SEQRES 5 A 144 VAL SER ARG GLU GLN PHE ARG ALA HIS LYS THR VAL LEU
SEQRES 6 A 144 MET ALA CYS SER GLY LEU PHE TYR SER ILE PHE THR ASP
SEQRES 7 A 144 GLN LEU LYS CYS ASN LEU SER VAL ILE ASN LEU ASP PRO
SEQRES 8 A 144 GLU ILE ASN PRO GLU GLY PHE CYS ILE LEU LEU ASP PHE
SEQRES 9 A 144 MET TYR THR SER ARG LEU ASN LEU ARG GLU GLY ASN ILE
SEQRES 10 A 144 MET ALA VAL MET ALA THR ALA MET TYR LEU GLN MET GLU
SEQRES 11 A 144 HIS VAL VAL ASP THR CYS ARG LYS PHE ILE LYS ALA SER
SEQRES 12 A 144 GLU
HET NQQ A 201 27
HET EDO A 202 4
HET EDO A 203 4
HET EDO A 204 4
HET EDO A 205 4
HETNAM NQQ 2-CHLORANYL-4-[[1-METHYL-3-(3-METHYL-3-OXIDANYL-BUTYL)-
HETNAM 2 NQQ 2-OXIDANYLIDENE-BENZIMIDAZOL-5-YL]AMINO]PYRIDINE-3-
HETNAM 3 NQQ CARBONITRILE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 NQQ C19 H20 CL N5 O2
FORMUL 3 EDO 4(C2 H6 O2)
FORMUL 7 HOH *107(H2 O)
HELIX 1 AA1 ARG A 13 ARG A 28 1 16
HELIX 2 AA2 HIS A 46 SER A 54 1 9
HELIX 3 AA3 SER A 54 THR A 62 1 9
HELIX 4 AA4 LEU A 65 LEU A 69 5 5
HELIX 5 AA5 ASN A 79 SER A 93 1 15
HELIX 6 AA6 ASN A 101 GLN A 113 1 13
HELIX 7 AA7 MET A 114 ALA A 127 1 14
SHEET 1 AA1 2 TYR A 1 GLN A 3 0
SHEET 2 AA1 2 ILE A 9 PHE A 11 -1 O GLN A 10 N PHE A 2
SHEET 1 AA2 3 GLU A 41 ALA A 45 0
SHEET 2 AA2 3 VAL A 34 VAL A 38 -1 N ILE A 36 O PHE A 43
SHEET 3 AA2 3 VAL A 71 ASN A 73 1 O ILE A 72 N VAL A 37
SITE 1 AC1 17 ASP A 17 ASN A 21 ARG A 24 LEU A 25
SITE 2 AC1 17 MET A 51 ALA A 52 CYS A 53 GLY A 55
SITE 3 AC1 17 TYR A 58 GLN A 113 MET A 114 GLU A 115
SITE 4 AC1 17 EDO A 203 HOH A 303 HOH A 305 HOH A 339
SITE 5 AC1 17 HOH A 353
SITE 1 AC2 3 GLN A 3 ILE A 72 ASN A 73
SITE 1 AC3 4 ASN A 21 ARG A 24 NQQ A 201 HOH A 364
SITE 1 AC4 2 GLU A 41 HOH A 324
SITE 1 AC5 4 ALA A 5 ILE A 78 HOH A 313 HOH A 332
CRYST1 66.999 66.999 166.730 90.00 90.00 120.00 P 61 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 0.014926 0.008617 0.000000 0.00000
SCALE2 0.000000 0.017235 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005998 0.00000