HEADER TRANSCRIPTION 11-DEC-19 6TOK
TITLE CRYSTAL STRUCTURE OF HUMAN BCL6 BTB DOMAIN IN COMPLEX WITH COMPOUND
TITLE 2 23D
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;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: ALA-TRP-VAL-ILE-PRO-ALA;
COMPND 9 CHAIN: B;
COMPND 10 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;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 14 ORGANISM_TAXID: 32630
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 6TOK 1 REMARK
REVDAT 2 06-MAY-20 6TOK 1 JRNL
REVDAT 1 22-APR-20 6TOK 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. 1.43 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) : 1.43
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.85
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 44230
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) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.182
REMARK 3 FREE R VALUE : 0.187
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980
REMARK 3 FREE R VALUE TEST SET COUNT : 2204
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 : 50
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.44
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 885
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2466
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 847
REMARK 3 BIN R VALUE (WORKING SET) : 0.2463
REMARK 3 BIN FREE R VALUE : 0.2545
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.29
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 38
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 : 1021
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 96
REMARK 3 SOLVENT ATOMS : 178
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 26.08
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.52
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.26890
REMARK 3 B22 (A**2) : -1.26890
REMARK 3 B33 (A**2) : 2.53780
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) : 0.180
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.055
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.052
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.050
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.048
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 : 0.966
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 1274 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 1716 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 449 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES : 243 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 1274 ; 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 : 161 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : 18 ; 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 : 1500 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.011
REMARK 3 BOND ANGLES (DEGREES) : 0.97
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.30
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 13.34
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 7
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: {A|5 - 33}
REMARK 3 ORIGIN FOR THE GROUP (A): 31.3795 -27.0999 13.3216
REMARK 3 T TENSOR
REMARK 3 T11: -0.0360 T22: -0.0264
REMARK 3 T33: -0.0317 T12: -0.0151
REMARK 3 T13: -0.0012 T23: -0.0266
REMARK 3 L TENSOR
REMARK 3 L11: 2.4675 L22: 1.4993
REMARK 3 L33: 3.3634 L12: 0.3636
REMARK 3 L13: 0.3312 L23: 0.8936
REMARK 3 S TENSOR
REMARK 3 S11: 0.1201 S12: 0.1416 S13: -0.1945
REMARK 3 S21: 0.1911 S22: 0.0021 S23: -0.0800
REMARK 3 S31: 0.3231 S32: -0.1173 S33: -0.1222
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: {A|34 - 46}
REMARK 3 ORIGIN FOR THE GROUP (A): 39.9859 -13.7326 31.8488
REMARK 3 T TENSOR
REMARK 3 T11: 0.0256 T22: -0.0381
REMARK 3 T33: -0.0951 T12: -0.0641
REMARK 3 T13: -0.0180 T23: -0.0643
REMARK 3 L TENSOR
REMARK 3 L11: 1.8505 L22: 1.6004
REMARK 3 L33: 0.9289 L12: -0.2390
REMARK 3 L13: 0.9053 L23: 0.0484
REMARK 3 S TENSOR
REMARK 3 S11: 0.0844 S12: -0.3649 S13: 0.1412
REMARK 3 S21: 0.5099 S22: 0.1056 S23: -0.1466
REMARK 3 S31: -0.1339 S32: 0.2692 S33: -0.1900
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: {A|47 - 92}
REMARK 3 ORIGIN FOR THE GROUP (A): 33.5613 -11.0081 24.5339
REMARK 3 T TENSOR
REMARK 3 T11: 0.0187 T22: -0.0705
REMARK 3 T33: -0.0193 T12: -0.0496
REMARK 3 T13: 0.0413 T23: -0.0281
REMARK 3 L TENSOR
REMARK 3 L11: 1.2940 L22: 2.7006
REMARK 3 L33: 2.5439 L12: 0.9262
REMARK 3 L13: -0.2574 L23: 1.1439
REMARK 3 S TENSOR
REMARK 3 S11: 0.2020 S12: -0.0641 S13: 0.1313
REMARK 3 S21: 0.1813 S22: -0.0304 S23: -0.0466
REMARK 3 S31: -0.2948 S32: 0.0505 S33: -0.1716
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: {A|93 - 101}
REMARK 3 ORIGIN FOR THE GROUP (A): 22.6734 -23.8870 32.3572
REMARK 3 T TENSOR
REMARK 3 T11: 0.1252 T22: 0.0150
REMARK 3 T33: -0.0437 T12: -0.1404
REMARK 3 T13: 0.0621 T23: -0.0277
REMARK 3 L TENSOR
REMARK 3 L11: 3.5681 L22: 1.2931
REMARK 3 L33: 1.1146 L12: 1.5832
REMARK 3 L13: -0.7176 L23: -2.8038
REMARK 3 S TENSOR
REMARK 3 S11: 0.2048 S12: -0.3213 S13: -0.0456
REMARK 3 S21: 0.3332 S22: -0.2843 S23: 0.2019
REMARK 3 S31: 0.0939 S32: 0.1285 S33: 0.0795
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: {A|102 - 114}
REMARK 3 ORIGIN FOR THE GROUP (A): 23.5941 -10.8914 31.4441
REMARK 3 T TENSOR
REMARK 3 T11: 0.0131 T22: -0.0687
REMARK 3 T33: -0.0353 T12: -0.0601
REMARK 3 T13: 0.1112 T23: -0.0690
REMARK 3 L TENSOR
REMARK 3 L11: 1.2959 L22: 3.8541
REMARK 3 L33: 3.7187 L12: 1.3738
REMARK 3 L13: 0.9101 L23: 1.1848
REMARK 3 S TENSOR
REMARK 3 S11: 0.2656 S12: -0.2204 S13: 0.2663
REMARK 3 S21: 0.5148 S22: -0.3075 S23: 0.4874
REMARK 3 S31: -0.1089 S32: -0.5791 S33: 0.0419
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: {A|115 - 129}
REMARK 3 ORIGIN FOR THE GROUP (A): 13.5219 -15.0141 31.8140
REMARK 3 T TENSOR
REMARK 3 T11: -0.0059 T22: 0.0865
REMARK 3 T33: 0.0576 T12: -0.0771
REMARK 3 T13: 0.1345 T23: -0.0978
REMARK 3 L TENSOR
REMARK 3 L11: 5.0051 L22: 2.9793
REMARK 3 L33: 0.0000 L12: -1.2303
REMARK 3 L13: -3.5724 L23: 0.9638
REMARK 3 S TENSOR
REMARK 3 S11: 0.0021 S12: 0.0922 S13: 0.0251
REMARK 3 S21: 0.2848 S22: -0.1780 S23: 0.4094
REMARK 3 S31: 0.0956 S32: -0.3069 S33: 0.1759
REMARK 3
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: {B|0 - 5}
REMARK 3 ORIGIN FOR THE GROUP (A): 19.1649 -32.9476 2.1158
REMARK 3 T TENSOR
REMARK 3 T11: -0.0973 T22: 0.1261
REMARK 3 T33: -0.0280 T12: -0.0618
REMARK 3 T13: -0.0289 T23: -0.0873
REMARK 3 L TENSOR
REMARK 3 L11: 1.9057 L22: 0.5761
REMARK 3 L33: 0.5224 L12: 0.8455
REMARK 3 L13: -0.6069 L23: 0.4959
REMARK 3 S TENSOR
REMARK 3 S11: 0.0514 S12: 0.0323 S13: 0.0367
REMARK 3 S21: -0.0292 S22: -0.0033 S23: 0.0125
REMARK 3 S31: 0.1322 S32: 0.0141 S33: -0.0481
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6TOK 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_1292104969.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-MAY-17
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7
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) : 0.9282
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 : DIALS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44308
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430
REMARK 200 RESOLUTION RANGE LOW (A) : 59.400
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 12.40
REMARK 200 R MERGE (I) : 0.06300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 10.70
REMARK 200 R MERGE FOR SHELL (I) : 3.26200
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 (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2 MICROLITER OF THE BCL6-BTB/WVIP
REMARK 280 COMPLEX AT 4 MG/ML PLUS 1 MICROLITER OF A CRYSTALLISATION
REMARK 280 SOLUTION CONSISTING OF 1 M K2HPO4, 0.7 M NAH2PO4, 75 MM SODIUM
REMARK 280 ACETATE BUFFER PH 4.5 AND 2 % DMSO, AGAINST 350 MICROLITER OF
REMARK 280 CRYSTALLISATION SOLUTION., PH 7, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 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 56.24233
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 112.48467
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 84.36350
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 140.60583
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 28.12117
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 56.24233
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 112.48467
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 140.60583
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 84.36350
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 28.12117
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 11070 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14190 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 25.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 34.29700
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -59.40415
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 28.12117
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 445 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 463 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 2
REMARK 465 PRO A 3
REMARK 465 GLY A 4
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 ARG A 13 NE CZ NH1 NH2
REMARK 470 GLN A 64 CD OE1 NE2
REMARK 470 GLU A 77 CD OE1 OE2
REMARK 470 GLU A 99 OE2
REMARK 470 LYS A 123 NZ
REMARK 470 LYS A 126 CD CE NZ
REMARK 470 GLU A 129 O
REMARK 470 ALA B 0 N CB
REMARK 470 ALA B 5 CA C O CB
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 SER A 39 -127.87 61.66
REMARK 500 SER A 93 -3.07 79.88
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 NQT 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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 206
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 207
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 212
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 213
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 214
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 215
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 216
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 101
DBREF 6TOK A 5 129 UNP P41182 BCL6_HUMAN 5 129
DBREF 6TOK B 0 5 PDB 6TOK 6TOK 0 5
SEQADV 6TOK GLY A 2 UNP P41182 EXPRESSION TAG
SEQADV 6TOK PRO A 3 UNP P41182 EXPRESSION TAG
SEQADV 6TOK GLY A 4 UNP P41182 EXPRESSION TAG
SEQRES 1 A 128 GLY PRO GLY ALA ASP SER CYS ILE GLN PHE THR ARG HIS
SEQRES 2 A 128 ALA SER ASP VAL LEU LEU ASN LEU ASN ARG LEU ARG SER
SEQRES 3 A 128 ARG ASP ILE LEU THR ASP VAL VAL ILE VAL VAL SER ARG
SEQRES 4 A 128 GLU GLN PHE ARG ALA HIS LYS THR VAL LEU MET ALA CYS
SEQRES 5 A 128 SER GLY LEU PHE TYR SER ILE PHE THR ASP GLN LEU LYS
SEQRES 6 A 128 CYS ASN LEU SER VAL ILE ASN LEU ASP PRO GLU ILE ASN
SEQRES 7 A 128 PRO GLU GLY PHE CYS ILE LEU LEU ASP PHE MET TYR THR
SEQRES 8 A 128 SER ARG LEU ASN LEU ARG GLU GLY ASN ILE MET ALA VAL
SEQRES 9 A 128 MET ALA THR ALA MET TYR LEU GLN MET GLU HIS VAL VAL
SEQRES 10 A 128 ASP THR CYS ARG LYS PHE ILE LYS ALA SER GLU
SEQRES 1 B 6 ALA TRP VAL ILE PRO ALA
HET NQT A 201 32
HET EDO A 202 4
HET EDO A 203 4
HET EDO A 204 8
HET EDO A 205 4
HET EDO A 206 4
HET EDO A 207 4
HET EDO A 208 4
HET EDO A 209 4
HET EDO A 210 4
HET EDO A 211 4
HET EDO A 212 4
HET EDO A 213 4
HET DMS A 214 4
HET DMS A 215 4
HET DMS A 216 4
HET DMS B 101 4
HETNAM NQT 5-[[5-CHLORANYL-2-(3,5-DIMETHYLPYRAZOL-1-YL)PYRIMIDIN-
HETNAM 2 NQT 4-YL]AMINO]-1-METHYL-3-(3-METHYL-3-OXIDANYL-BUTYL)
HETNAM 3 NQT BENZIMIDAZOL-2-ONE
HETNAM EDO 1,2-ETHANEDIOL
HETNAM DMS DIMETHYL SULFOXIDE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 3 NQT C22 H26 CL N7 O2
FORMUL 4 EDO 12(C2 H6 O2)
FORMUL 16 DMS 4(C2 H6 O S)
FORMUL 20 HOH *178(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 GLU A 129 1 16
SHEET 1 AA1 2 GLN A 10 PHE A 11 0
SHEET 2 AA1 2 TRP B 1 VAL B 2 -1 O VAL B 2 N GLN A 10
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 ARG A 28 MET A 51 ALA A 52 CYS A 53
SITE 3 AC1 17 GLY A 55 TYR A 58 GLN A 113 GLU A 115
SITE 4 AC1 17 EDO A 206 EDO A 213 HOH A 348 HOH A 350
SITE 5 AC1 17 HOH A 381
SITE 1 AC2 4 ASP A 63 GLN A 64 ARG A 98 GLU A 99
SITE 1 AC3 4 ARG A 28 ASP A 29 HOH A 331 HOH A 369
SITE 1 AC4 6 ASP A 75 ILE A 78 TYR A 111 EDO A 208
SITE 2 AC4 6 HOH A 385 ALA B 5
SITE 1 AC5 2 ILE A 125 SER A 128
SITE 1 AC6 4 GLU A 115 HIS A 116 NQT A 201 HOH A 318
SITE 1 AC7 4 SER A 16 ASP A 17 HOH A 330 HOH A 371
SITE 1 AC8 2 ARG A 94 EDO A 204
SITE 1 AC9 4 GLU A 41 GLN A 42 PHE A 43 DMS A 214
SITE 1 AD1 3 ARG A 26 ASP A 29 ARG A 44
SITE 1 AD2 3 ARG A 24 EDO A 212 DMS A 215
SITE 1 AD3 5 SER A 27 ARG A 28 EDO A 211 DMS A 215
SITE 2 AD3 5 HOH A 301
SITE 1 AD4 3 TYR A 58 NQT A 201 HOH A 337
SITE 1 AD5 2 GLU A 41 EDO A 209
SITE 1 AD6 4 ASN A 23 SER A 27 EDO A 211 EDO A 212
SITE 1 AD7 5 LEU A 69 SER A 70 VAL A 71 HOH A 342
SITE 2 AD7 5 HOH A 425
SITE 1 AD8 4 VAL A 71 ILE A 72 ASN A 73 TRP B 1
CRYST1 68.594 68.594 168.727 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 0.014579 0.008417 0.000000 0.00000
SCALE2 0.000000 0.016834 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005927 0.00000