HEADER LIGASE 21-OCT-22 8BEB TITLE TERNARY COMPLEX BETWEEN VCB, BRD4-BD1 AND PROTAC 49 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGIN-B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ELOB,ELONGIN 18 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION COMPND 5 FACTOR SIII SUBUNIT B,SIII P18,TRANSCRIPTION ELONGATION FACTOR B COMPND 6 POLYPEPTIDE 2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ELONGIN-C; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: ELOC,ELONGIN 15 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION COMPND 12 FACTOR SIII SUBUNIT C,SIII P15,TRANSCRIPTION ELONGATION FACTOR B COMPND 13 POLYPEPTIDE 1; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR; COMPND 17 CHAIN: C; COMPND 18 SYNONYM: PROTEIN G7,PVHL; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 22 CHAIN: D; COMPND 23 SYNONYM: PROTEIN HUNK1; COMPND 24 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: ELOB, TCEB2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: ELOC, TCEB1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: VHL; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 GENE: BRD4, HUNK1; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTAC, DEGRADER, COMPLEX, E3 LIGASE, VHL, VCB, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR F.J.SORRELL,J.E.MUELLER,M.LEHMANN,A.WEGENER REVDAT 4 07-FEB-24 8BEB 1 REMARK REVDAT 3 26-APR-23 8BEB 1 JRNL REVDAT 2 22-MAR-23 8BEB 1 JRNL REVDAT 1 15-FEB-23 8BEB 0 JRNL AUTH J.KRIEGER,F.J.SORRELL,A.A.WEGENER,B.LEUTHNER, JRNL AUTH 2 F.MACHROUHI-PORCHER,M.HECHT,E.M.LEIBROCK,J.E.MULLER, JRNL AUTH 3 J.EISERT,I.V.HARTUNG,S.SCHLESIGER JRNL TITL SYSTEMATIC POTENCY AND PROPERTY ASSESSMENT OF VHL LIGANDS JRNL TITL 2 AND IMPLICATIONS ON PROTAC DESIGN. JRNL REF CHEMMEDCHEM V. 18 00615 2023 JRNL REFN ESSN 1860-7187 JRNL PMID 36749883 JRNL DOI 10.1002/CMDC.202200615 REMARK 2 REMARK 2 RESOLUTION. 3.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.7 REMARK 3 NUMBER OF REFLECTIONS : 9370 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 462 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 127 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 15.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 4 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3599 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : 0.74000 REMARK 3 B12 (A**2) : -0.11000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.593 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.447 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 61.758 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.907 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3771 ; 0.006 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3385 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5149 ; 1.557 ; 1.660 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7898 ; 0.515 ; 1.557 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 450 ; 4.800 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 28 ;11.734 ; 6.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 600 ;17.211 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 577 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4229 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 711 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 104 REMARK 3 ORIGIN FOR THE GROUP (A): 21.6508 32.4237 19.4947 REMARK 3 T TENSOR REMARK 3 T11: 0.2636 T22: 0.2461 REMARK 3 T33: 0.1732 T12: 0.0528 REMARK 3 T13: 0.0541 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.0269 L22: 2.0651 REMARK 3 L33: 0.2217 L12: -0.8078 REMARK 3 L13: 0.2671 L23: 0.2299 REMARK 3 S TENSOR REMARK 3 S11: -0.0329 S12: 0.0394 S13: 0.1485 REMARK 3 S21: -0.0459 S22: -0.0704 S23: -0.0063 REMARK 3 S31: -0.0470 S32: -0.0534 S33: 0.1033 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 17 B 112 REMARK 3 ORIGIN FOR THE GROUP (A): 25.9557 14.8265 21.0623 REMARK 3 T TENSOR REMARK 3 T11: 0.2057 T22: 0.1531 REMARK 3 T33: 0.1565 T12: 0.0740 REMARK 3 T13: -0.0035 T23: -0.0322 REMARK 3 L TENSOR REMARK 3 L11: 1.2826 L22: 0.6847 REMARK 3 L33: 3.4231 L12: 0.4304 REMARK 3 L13: 1.0817 L23: -0.7995 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: -0.0692 S13: -0.1284 REMARK 3 S21: 0.0018 S22: 0.0389 S23: -0.0882 REMARK 3 S31: 0.0047 S32: -0.1741 S33: -0.0460 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 62 C 202 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1407 -1.2477 -0.1521 REMARK 3 T TENSOR REMARK 3 T11: 0.2372 T22: 0.2988 REMARK 3 T33: 0.2258 T12: 0.0975 REMARK 3 T13: -0.0407 T23: -0.0601 REMARK 3 L TENSOR REMARK 3 L11: 1.1417 L22: 0.6719 REMARK 3 L33: 0.5323 L12: 0.1282 REMARK 3 L13: -0.3089 L23: 0.4980 REMARK 3 S TENSOR REMARK 3 S11: -0.0076 S12: 0.2099 S13: -0.3246 REMARK 3 S21: 0.1420 S22: 0.0836 S23: -0.2232 REMARK 3 S31: 0.0650 S32: -0.0536 S33: -0.0760 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 44 D 167 REMARK 3 ORIGIN FOR THE GROUP (A): 27.3429 -9.4689 -24.4110 REMARK 3 T TENSOR REMARK 3 T11: 0.2289 T22: 0.2910 REMARK 3 T33: 0.1603 T12: 0.0378 REMARK 3 T13: -0.0361 T23: -0.0469 REMARK 3 L TENSOR REMARK 3 L11: 0.8740 L22: 1.0097 REMARK 3 L33: 0.5314 L12: -0.4467 REMARK 3 L13: -0.0783 L23: 0.5541 REMARK 3 S TENSOR REMARK 3 S11: -0.1308 S12: -0.0191 S13: 0.0274 REMARK 3 S21: -0.0024 S22: 0.0237 S23: -0.0949 REMARK 3 S31: -0.1055 S32: -0.0869 S33: 0.1071 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 8BEB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97626 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9832 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.180 REMARK 200 RESOLUTION RANGE LOW (A) : 64.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.4 REMARK 200 DATA REDUNDANCY : 18.30 REMARK 200 R MERGE (I) : 0.35300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 41.2 REMARK 200 DATA REDUNDANCY IN SHELL : 20.90 REMARK 200 R MERGE FOR SHELL (I) : 2.20600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 5NW1, 3MXF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 4% (W/V) REMARK 280 GLYCEROL, 0.1M BIS-TRIS PH5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 61.64333 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 123.28667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 123.28667 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 61.64333 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 MET B 16 REMARK 465 GLY B 48 REMARK 465 PRO B 49 REMARK 465 GLY B 50 REMARK 465 GLN B 51 REMARK 465 PHE B 52 REMARK 465 ALA B 53 REMARK 465 GLU B 54 REMARK 465 ASN B 55 REMARK 465 GLU B 56 REMARK 465 THR B 57 REMARK 465 GLY C 52 REMARK 465 SER C 53 REMARK 465 MET C 54 REMARK 465 GLU C 55 REMARK 465 ALA C 56 REMARK 465 GLY C 57 REMARK 465 ARG C 58 REMARK 465 PRO C 59 REMARK 465 ARG C 60 REMARK 465 PRO C 61 REMARK 465 GLN C 203 REMARK 465 GLU C 204 REMARK 465 ARG C 205 REMARK 465 ILE C 206 REMARK 465 ALA C 207 REMARK 465 HIS C 208 REMARK 465 GLN C 209 REMARK 465 ARG C 210 REMARK 465 MET C 211 REMARK 465 GLY C 212 REMARK 465 ASP C 213 REMARK 465 SER D 42 REMARK 465 MET D 43 REMARK 465 GLU D 168 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 LYS A 104 CG CD CE NZ REMARK 470 SER B 47 OG REMARK 470 LEU B 101 CG CD1 CD2 REMARK 470 VAL C 62 CG1 CG2 REMARK 470 ARG C 69 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 113 CG CD NE CZ NH1 NH2 REMARK 470 VAL C 142 CG1 CG2 REMARK 470 ASP C 143 CG OD1 OD2 REMARK 470 ARG C 176 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 177 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 182 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 186 CG CD OE1 OE2 REMARK 470 GLN C 195 CG CD OE1 NE2 REMARK 470 ARG C 200 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 201 CG CD1 CD2 REMARK 470 GLN D 59 CG CD OE1 NE2 REMARK 470 ARG D 68 CG CD NE CZ NH1 NH2 REMARK 470 GLN D 78 CG CD OE1 NE2 REMARK 470 LYS D 91 CG CD CE NZ REMARK 470 LYS D 102 CG CD CE NZ REMARK 470 LYS D 141 CD CE NZ REMARK 470 LYS D 155 CG CD CE NZ REMARK 470 LYS D 160 CG CD CE NZ REMARK 470 ASN D 162 CG OD1 ND2 REMARK 470 GLU D 167 CG CD OE1 OE2 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 O ARG B 82 OG SER B 86 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG C 107 CB - CA - C ANGL. DEV. = -12.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 10 -120.55 55.14 REMARK 500 ASP A 47 -129.22 64.80 REMARK 500 ASP A 82 -129.46 61.15 REMARK 500 ASN B 85 14.05 37.55 REMARK 500 SER B 87 176.63 177.58 REMARK 500 GLU B 89 83.18 60.97 REMARK 500 ARG C 79 43.70 -103.79 REMARK 500 SER C 111 -163.52 -118.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BEB A 1 104 UNP Q15370 ELOB_HUMAN 1 104 DBREF 8BEB B 17 112 UNP Q15369 ELOC_HUMAN 17 112 DBREF 8BEB C 54 213 UNP P40337 VHL_HUMAN 54 213 DBREF 8BEB D 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 8BEB MET B 16 UNP Q15369 INITIATING METHIONINE SEQADV 8BEB GLY C 52 UNP P40337 EXPRESSION TAG SEQADV 8BEB SER C 53 UNP P40337 EXPRESSION TAG SEQADV 8BEB SER D 42 UNP O60885 EXPRESSION TAG SEQADV 8BEB MET D 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 104 MET ASP VAL PHE LEU MET ILE ARG ARG HIS LYS THR THR SEQRES 2 A 104 ILE PHE THR ASP ALA LYS GLU SER SER THR VAL PHE GLU SEQRES 3 A 104 LEU LYS ARG ILE VAL GLU GLY ILE LEU LYS ARG PRO PRO SEQRES 4 A 104 ASP GLU GLN ARG LEU TYR LYS ASP ASP GLN LEU LEU ASP SEQRES 5 A 104 ASP GLY LYS THR LEU GLY GLU CYS GLY PHE THR SER GLN SEQRES 6 A 104 THR ALA ARG PRO GLN ALA PRO ALA THR VAL GLY LEU ALA SEQRES 7 A 104 PHE ARG ALA ASP ASP THR PHE GLU ALA LEU CYS ILE GLU SEQRES 8 A 104 PRO PHE SER SER PRO PRO GLU LEU PRO ASP VAL MET LYS SEQRES 1 B 97 MET MET TYR VAL LYS LEU ILE SER SER ASP GLY HIS GLU SEQRES 2 B 97 PHE ILE VAL LYS ARG GLU HIS ALA LEU THR SER GLY THR SEQRES 3 B 97 ILE LYS ALA MET LEU SER GLY PRO GLY GLN PHE ALA GLU SEQRES 4 B 97 ASN GLU THR ASN GLU VAL ASN PHE ARG GLU ILE PRO SER SEQRES 5 B 97 HIS VAL LEU SER LYS VAL CYS MET TYR PHE THR TYR LYS SEQRES 6 B 97 VAL ARG TYR THR ASN SER SER THR GLU ILE PRO GLU PHE SEQRES 7 B 97 PRO ILE ALA PRO GLU ILE ALA LEU GLU LEU LEU MET ALA SEQRES 8 B 97 ALA ASN PHE LEU ASP CYS SEQRES 1 C 162 GLY SER MET GLU ALA GLY ARG PRO ARG PRO VAL LEU ARG SEQRES 2 C 162 SER VAL ASN SER ARG GLU PRO SER GLN VAL ILE PHE CYS SEQRES 3 C 162 ASN ARG SER PRO ARG VAL VAL LEU PRO VAL TRP LEU ASN SEQRES 4 C 162 PHE ASP GLY GLU PRO GLN PRO TYR PRO THR LEU PRO PRO SEQRES 5 C 162 GLY THR GLY ARG ARG ILE HIS SER TYR ARG GLY HIS LEU SEQRES 6 C 162 TRP LEU PHE ARG ASP ALA GLY THR HIS ASP GLY LEU LEU SEQRES 7 C 162 VAL ASN GLN THR GLU LEU PHE VAL PRO SER LEU ASN VAL SEQRES 8 C 162 ASP GLY GLN PRO ILE PHE ALA ASN ILE THR LEU PRO VAL SEQRES 9 C 162 TYR THR LEU LYS GLU ARG CYS LEU GLN VAL VAL ARG SER SEQRES 10 C 162 LEU VAL LYS PRO GLU ASN TYR ARG ARG LEU ASP ILE VAL SEQRES 11 C 162 ARG SER LEU TYR GLU ASP LEU GLU ASP HIS PRO ASN VAL SEQRES 12 C 162 GLN LYS ASP LEU GLU ARG LEU THR GLN GLU ARG ILE ALA SEQRES 13 C 162 HIS GLN ARG MET GLY ASP SEQRES 1 D 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 D 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 D 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 D 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 D 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 D 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 D 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 D 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 D 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 D 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET SO4 A 201 5 HET QIK C 301 69 HETNAM SO4 SULFATE ION HETNAM QIK (2~{S},4~{R})-~{N}-[(1~{S})-3-[4-[2-[(9~{S})-7-(4- HETNAM 2 QIK CHLOROPHENYL)-4,5,13-TRIMETHYL-3-THIA-1,8,11,12- HETNAM 3 QIK TETRAZATRICYCLO[8.3.0.0^{2,6}]TRIDECA-2(6),4,7,10,12- HETNAM 4 QIK PENTAEN-9-YL]ETHANOYLAMINO]BUTYLAMINO]-1-[4-(4-METHYL- HETNAM 5 QIK 1,3-THIAZOL-5-YL)PHENYL]-3-OXIDANYLIDENE-PROPYL]-1- HETNAM 6 QIK [(2~{R})-3-METHYL-2-(3-METHYL-1,2-OXAZOL-5-YL) HETNAM 7 QIK BUTANOYL]-4-OXIDANYL-PYRROLIDINE-2-CARBOXAMIDE FORMUL 5 SO4 O4 S 2- FORMUL 6 QIK C50 H57 CL N10 O6 S2 FORMUL 7 HOH *3(H2 O) HELIX 1 AA1 THR A 23 LYS A 36 1 14 HELIX 2 AA2 PRO A 38 ASP A 40 5 3 HELIX 3 AA3 ARG B 33 LEU B 37 1 5 HELIX 4 AA4 SER B 39 SER B 47 1 9 HELIX 5 AA5 PRO B 66 THR B 84 1 19 HELIX 6 AA6 ALA B 96 ASP B 111 1 16 HELIX 7 AA7 ASN C 141 GLN C 145 5 5 HELIX 8 AA8 THR C 157 VAL C 170 1 14 HELIX 9 AA9 LYS C 171 LEU C 178 5 8 HELIX 10 AB1 VAL C 181 GLU C 189 1 9 HELIX 11 AB2 ASN C 193 THR C 202 1 10 HELIX 12 AB3 THR D 60 VAL D 69 1 10 HELIX 13 AB4 VAL D 69 LYS D 76 1 8 HELIX 14 AB5 ALA D 80 GLN D 84 5 5 HELIX 15 AB6 ASP D 88 ASN D 93 1 6 HELIX 16 AB7 PRO D 95 ILE D 101 1 7 HELIX 17 AB8 ASP D 106 ASN D 117 1 12 HELIX 18 AB9 ASN D 121 ASN D 140 1 20 HELIX 19 AC1 ASP D 144 ASN D 162 1 19 SHEET 1 AA1 4 GLN A 49 LEU A 50 0 SHEET 2 AA1 4 GLN A 42 LYS A 46 -1 N LYS A 46 O GLN A 49 SHEET 3 AA1 4 ALA A 73 ALA A 81 -1 O GLY A 76 N TYR A 45 SHEET 4 AA1 4 THR A 84 PHE A 85 -1 O THR A 84 N ALA A 81 SHEET 1 AA2 8 GLN A 49 LEU A 50 0 SHEET 2 AA2 8 GLN A 42 LYS A 46 -1 N LYS A 46 O GLN A 49 SHEET 3 AA2 8 ALA A 73 ALA A 81 -1 O GLY A 76 N TYR A 45 SHEET 4 AA2 8 ASP A 2 ARG A 9 1 N MET A 6 O VAL A 75 SHEET 5 AA2 8 THR A 12 LYS A 19 -1 O ALA A 18 N VAL A 3 SHEET 6 AA2 8 GLU B 28 LYS B 32 1 O ILE B 30 N THR A 13 SHEET 7 AA2 8 TYR B 18 ILE B 22 -1 N LEU B 21 O PHE B 29 SHEET 8 AA2 8 GLU B 59 ASN B 61 1 O VAL B 60 N LYS B 20 SHEET 1 AA3 4 GLY C 106 TYR C 112 0 SHEET 2 AA3 4 PRO C 71 ASN C 78 -1 N SER C 72 O SER C 111 SHEET 3 AA3 4 ILE C 147 THR C 152 1 O ALA C 149 N ILE C 75 SHEET 4 AA3 4 LEU C 129 VAL C 130 -1 N LEU C 129 O THR C 152 SHEET 1 AA4 3 PRO C 95 PRO C 97 0 SHEET 2 AA4 3 VAL C 84 LEU C 89 -1 N TRP C 88 O GLN C 96 SHEET 3 AA4 3 LEU C 116 ASP C 121 -1 O ARG C 120 N LEU C 85 CRYST1 79.754 79.754 184.930 90.00 90.00 120.00 P 31 2 1 6 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 0.012539 0.007239 0.000000 0.00000 SCALE2 0.000000 0.014478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005407 0.00000