HEADER LIGASE 12-OCT-22 8BB5 TITLE STRUCTURE OF HUMAN WDR5 AND PVHL:ELONGINC:ELONGINB BOUND TO PROTAC TITLE 2 WITH ARYL LINKER 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: WD REPEAT-CONTAINING PROTEIN 5; COMPND 22 CHAIN: D; COMPND 23 SYNONYM: BMP2-INDUCED 3-KB GENE PROTEIN; 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: WDR5, BIG3; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3-LIGASE, WDR5, VHL, ELONGIN, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KRAEMER,A.DOELLE,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 31-JAN-24 8BB5 1 REMARK REVDAT 2 22-NOV-23 8BB5 1 JRNL REVDAT 1 09-NOV-22 8BB5 0 JRNL AUTH M.P.SCHWALM,A.KRAMER,A.DOLLE,J.WECKESSER,X.YU,J.JIN, JRNL AUTH 2 K.SAXENA,S.KNAPP JRNL TITL TRACKING THE PROTAC DEGRADATION PATHWAY IN LIVING CELLS JRNL TITL 2 HIGHLIGHTS THE IMPORTANCE OF TERNARY COMPLEX MEASUREMENT FOR JRNL TITL 3 PROTAC OPTIMIZATION. JRNL REF CELL CHEM BIOL V. 30 753 2023 JRNL REFN ESSN 2451-9456 JRNL PMID 37354907 JRNL DOI 10.1016/J.CHEMBIOL.2023.06.002 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 40492 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2090 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2914 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5065 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 123 REMARK 3 SOLVENT ATOMS : 334 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.59000 REMARK 3 B22 (A**2) : 6.97000 REMARK 3 B33 (A**2) : -3.38000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.246 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.294 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5306 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4818 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7190 ; 1.419 ; 1.642 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11225 ; 0.469 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 644 ; 7.886 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 28 ; 6.992 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 858 ;15.321 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 807 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6109 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1035 ; 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 201 REMARK 3 ORIGIN FOR THE GROUP (A): -23.0927 -10.9452 -68.5397 REMARK 3 T TENSOR REMARK 3 T11: 0.3120 T22: 0.2401 REMARK 3 T33: 0.2339 T12: 0.0250 REMARK 3 T13: -0.0054 T23: 0.0204 REMARK 3 L TENSOR REMARK 3 L11: 1.2557 L22: 1.7460 REMARK 3 L33: 3.6212 L12: 0.2234 REMARK 3 L13: 0.3605 L23: 1.4467 REMARK 3 S TENSOR REMARK 3 S11: 0.0365 S12: 0.1507 S13: -0.1127 REMARK 3 S21: -0.2026 S22: 0.1313 S23: -0.2407 REMARK 3 S31: 0.0995 S32: 0.4699 S33: -0.1678 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 16 B 112 REMARK 3 ORIGIN FOR THE GROUP (A): -27.5971 -10.4431 -51.2253 REMARK 3 T TENSOR REMARK 3 T11: 0.2372 T22: 0.1074 REMARK 3 T33: 0.1779 T12: 0.0196 REMARK 3 T13: 0.0126 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 2.5795 L22: 0.7435 REMARK 3 L33: 2.6334 L12: 0.7333 REMARK 3 L13: 1.5846 L23: 0.2131 REMARK 3 S TENSOR REMARK 3 S11: 0.0834 S12: 0.1577 S13: -0.1782 REMARK 3 S21: -0.0062 S22: 0.0126 S23: 0.0081 REMARK 3 S31: 0.2627 S32: -0.0711 S33: -0.0960 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 57 C 301 REMARK 3 ORIGIN FOR THE GROUP (A): -6.8422 -6.9442 -32.2268 REMARK 3 T TENSOR REMARK 3 T11: 0.2061 T22: 0.1061 REMARK 3 T33: 0.1625 T12: -0.0152 REMARK 3 T13: 0.0196 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 2.9241 L22: 0.5176 REMARK 3 L33: 1.4373 L12: -0.6509 REMARK 3 L13: 1.3814 L23: -0.3915 REMARK 3 S TENSOR REMARK 3 S11: -0.0205 S12: -0.0800 S13: -0.1377 REMARK 3 S21: 0.0585 S22: 0.0500 S23: 0.0632 REMARK 3 S31: 0.0833 S32: -0.0960 S33: -0.0295 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 27 D 410 REMARK 3 ORIGIN FOR THE GROUP (A): 22.1979 -1.3151 -0.7778 REMARK 3 T TENSOR REMARK 3 T11: 0.1912 T22: 0.0010 REMARK 3 T33: 0.1555 T12: -0.0006 REMARK 3 T13: -0.0046 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.6061 L22: 1.1417 REMARK 3 L33: 2.2232 L12: -0.0149 REMARK 3 L13: -0.8310 L23: -0.0546 REMARK 3 S TENSOR REMARK 3 S11: 0.0447 S12: -0.0349 S13: 0.0322 REMARK 3 S21: 0.0454 S22: 0.0095 S23: -0.0327 REMARK 3 S31: -0.1138 S32: 0.0324 S33: -0.0543 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 8BB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125958. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-21 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 : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999998 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 : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42660 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 49.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 1.01200 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 2.8.3 REMARK 200 STARTING MODEL: 7Q2J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350, 0.4-1 M KSCN 0.1 M HEPES REMARK 280 PH 6.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 24.06000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.34450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 98.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.06000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.34450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 8730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL 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 LYS B 15 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 SER B 87 REMARK 465 THR B 88 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 MET C 211 REMARK 465 GLY C 212 REMARK 465 ASP C 213 REMARK 465 MET D 14 REMARK 465 GLY D 15 REMARK 465 SER D 16 REMARK 465 SER D 17 REMARK 465 HIS D 18 REMARK 465 HIS D 19 REMARK 465 HIS D 20 REMARK 465 HIS D 21 REMARK 465 HIS D 22 REMARK 465 HIS D 23 REMARK 465 SER D 24 REMARK 465 SER D 25 REMARK 465 GLY D 26 REMARK 465 CYS D 334 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 1 CG SD CE REMARK 470 ARG A 29 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 48 CG OD1 OD2 REMARK 470 ASP A 52 CG OD1 OD2 REMARK 470 LYS A 55 CE NZ REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 LYS B 80 CE NZ REMARK 470 SER B 86 OG REMARK 470 LYS C 171 CE NZ REMARK 470 ASN C 174 ND2 REMARK 470 ARG C 182 CG CD NE CZ NH1 NH2 REMARK 470 HIS C 208 CG ND1 CD2 CE1 NE2 REMARK 470 ARG C 210 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 159 CG CD CE NZ REMARK 470 LYS D 162 CG CD CE NZ REMARK 470 ARG D 181 CG CD NE CZ NH1 NH2 REMARK 470 ILE D 210 CG1 CG2 CD1 REMARK 470 ASP D 211 CG OD1 OD2 REMARK 470 ASP D 212 CG OD1 OD2 REMARK 470 ASP D 213 CG OD1 OD2 REMARK 470 LYS D 227 CG CD CE NZ REMARK 470 GLU D 322 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 HIS A 10 -116.79 55.99 REMARK 500 ASP A 47 -124.05 59.39 REMARK 500 ALA A 71 69.98 -152.52 REMARK 500 ASP A 82 -116.71 53.56 REMARK 500 ASN B 85 7.90 82.34 REMARK 500 ASP B 111 71.64 46.50 REMARK 500 ARG C 79 40.03 -105.19 REMARK 500 SER C 111 -158.64 -135.43 REMARK 500 SER C 139 -169.54 -108.96 REMARK 500 ALA D 42 70.66 -112.11 REMARK 500 LYS D 67 7.31 81.20 REMARK 500 LYS D 109 10.48 81.93 REMARK 500 ASN D 214 59.99 -106.63 REMARK 500 LEU D 234 44.27 -84.08 REMARK 500 ASN D 257 89.70 -156.91 REMARK 500 LYS D 259 -53.61 -138.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 304 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR C 112 OH REMARK 620 2 Q43 C 302 O2 89.3 REMARK 620 3 HOH C 483 O 88.6 89.3 REMARK 620 4 HOH C 494 O 85.5 174.7 89.7 REMARK 620 5 HOH D 504 O 164.2 79.1 101.7 106.2 REMARK 620 6 HOH D 583 O 79.2 82.3 165.2 97.6 88.7 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7Q2J RELATED DB: PDB DBREF 8BB5 A 1 104 UNP Q15370 ELOB_HUMAN 1 104 DBREF 8BB5 B 16 112 UNP Q15369 ELOC_HUMAN 16 112 DBREF 8BB5 C 54 213 UNP P40337 VHL_HUMAN 54 213 DBREF 8BB5 D 33 334 UNP P61964 WDR5_HUMAN 33 334 SEQADV 8BB5 LYS B 15 UNP Q15369 EXPRESSION TAG SEQADV 8BB5 GLY C 52 UNP P40337 EXPRESSION TAG SEQADV 8BB5 SER C 53 UNP P40337 EXPRESSION TAG SEQADV 8BB5 MET D 14 UNP P61964 INITIATING METHIONINE SEQADV 8BB5 GLY D 15 UNP P61964 EXPRESSION TAG SEQADV 8BB5 SER D 16 UNP P61964 EXPRESSION TAG SEQADV 8BB5 SER D 17 UNP P61964 EXPRESSION TAG SEQADV 8BB5 HIS D 18 UNP P61964 EXPRESSION TAG SEQADV 8BB5 HIS D 19 UNP P61964 EXPRESSION TAG SEQADV 8BB5 HIS D 20 UNP P61964 EXPRESSION TAG SEQADV 8BB5 HIS D 21 UNP P61964 EXPRESSION TAG SEQADV 8BB5 HIS D 22 UNP P61964 EXPRESSION TAG SEQADV 8BB5 HIS D 23 UNP P61964 EXPRESSION TAG SEQADV 8BB5 SER D 24 UNP P61964 EXPRESSION TAG SEQADV 8BB5 SER D 25 UNP P61964 EXPRESSION TAG SEQADV 8BB5 GLY D 26 UNP P61964 EXPRESSION TAG SEQADV 8BB5 LEU D 27 UNP P61964 EXPRESSION TAG SEQADV 8BB5 VAL D 28 UNP P61964 EXPRESSION TAG SEQADV 8BB5 PRO D 29 UNP P61964 EXPRESSION TAG SEQADV 8BB5 ARG D 30 UNP P61964 EXPRESSION TAG SEQADV 8BB5 GLY D 31 UNP P61964 EXPRESSION TAG SEQADV 8BB5 SER D 32 UNP P61964 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 98 LYS ALA MET TYR VAL LYS LEU ILE SER SER ASP GLY HIS SEQRES 2 B 98 GLU PHE ILE VAL LYS ARG GLU HIS ALA LEU THR SER GLY SEQRES 3 B 98 THR ILE LYS ALA MET LEU SER GLY PRO GLY GLN PHE ALA SEQRES 4 B 98 GLU ASN GLU THR ASN GLU VAL ASN PHE ARG GLU ILE PRO SEQRES 5 B 98 SER HIS VAL LEU SER LYS VAL CYS MET TYR PHE THR TYR SEQRES 6 B 98 LYS VAL ARG TYR THR ASN SER SER THR GLU ILE PRO GLU SEQRES 7 B 98 PHE PRO ILE ALA PRO GLU ILE ALA LEU GLU LEU LEU MET SEQRES 8 B 98 ALA 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 321 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 D 321 LEU VAL PRO ARG GLY SER PRO ASN TYR ALA LEU LYS PHE SEQRES 3 D 321 THR LEU ALA GLY HIS THR LYS ALA VAL SER SER VAL LYS SEQRES 4 D 321 PHE SER PRO ASN GLY GLU TRP LEU ALA SER SER SER ALA SEQRES 5 D 321 ASP LYS LEU ILE LYS ILE TRP GLY ALA TYR ASP GLY LYS SEQRES 6 D 321 PHE GLU LYS THR ILE SER GLY HIS LYS LEU GLY ILE SER SEQRES 7 D 321 ASP VAL ALA TRP SER SER ASP SER ASN LEU LEU VAL SER SEQRES 8 D 321 ALA SER ASP ASP LYS THR LEU LYS ILE TRP ASP VAL SER SEQRES 9 D 321 SER GLY LYS CYS LEU LYS THR LEU LYS GLY HIS SER ASN SEQRES 10 D 321 TYR VAL PHE CYS CYS ASN PHE ASN PRO GLN SER ASN LEU SEQRES 11 D 321 ILE VAL SER GLY SER PHE ASP GLU SER VAL ARG ILE TRP SEQRES 12 D 321 ASP VAL LYS THR GLY LYS CYS LEU LYS THR LEU PRO ALA SEQRES 13 D 321 HIS SER ASP PRO VAL SER ALA VAL HIS PHE ASN ARG ASP SEQRES 14 D 321 GLY SER LEU ILE VAL SER SER SER TYR ASP GLY LEU CYS SEQRES 15 D 321 ARG ILE TRP ASP THR ALA SER GLY GLN CYS LEU LYS THR SEQRES 16 D 321 LEU ILE ASP ASP ASP ASN PRO PRO VAL SER PHE VAL LYS SEQRES 17 D 321 PHE SER PRO ASN GLY LYS TYR ILE LEU ALA ALA THR LEU SEQRES 18 D 321 ASP ASN THR LEU LYS LEU TRP ASP TYR SER LYS GLY LYS SEQRES 19 D 321 CYS LEU LYS THR TYR THR GLY HIS LYS ASN GLU LYS TYR SEQRES 20 D 321 CYS ILE PHE ALA ASN PHE SER VAL THR GLY GLY LYS TRP SEQRES 21 D 321 ILE VAL SER GLY SER GLU ASP ASN LEU VAL TYR ILE TRP SEQRES 22 D 321 ASN LEU GLN THR LYS GLU ILE VAL GLN LYS LEU GLN GLY SEQRES 23 D 321 HIS THR ASP VAL VAL ILE SER THR ALA CYS HIS PRO THR SEQRES 24 D 321 GLU ASN ILE ILE ALA SER ALA ALA LEU GLU ASN ASP LYS SEQRES 25 D 321 THR ILE LYS LEU TRP LYS SER ASP CYS HET SCN A 201 3 HET SCN A 202 3 HET SCN C 301 3 HET Q43 C 302 76 HET EDO C 303 4 HET K C 304 1 HET SCN D 401 3 HET SCN D 402 3 HET SCN D 403 3 HET SCN D 404 3 HET SCN D 405 3 HET SCN D 406 3 HET EDO D 407 4 HET EDO D 408 4 HET SCN D 409 3 HET EDO D 410 4 HETNAM SCN THIOCYANATE ION HETNAM Q43 ~{N}-[5-[4-[[4-[2-[[(2~{S})-3,3-DIMETHYL-1-[(2~{S}, HETNAM 2 Q43 4~{R})-2-[[4-(4-METHYL-1,3-THIAZOL-5-YL) HETNAM 3 Q43 PHENYL]METHYLCARBAMOYL]-4-OXIDANYL-PYRROLIDIN-1-YL]-1- HETNAM 4 Q43 OXIDANYLIDENE-BUTAN-2-YL]AMINO]-2-OXIDANYLIDENE- HETNAM 5 Q43 ETHYL]PHENYL]METHYLCARBAMOYL]PHENYL]-2-(4- HETNAM 6 Q43 METHYLPIPERAZIN-1-YL)PHENYL]-6-OXIDANYL-4- HETNAM 7 Q43 (TRIFLUOROMETHYL)PYRIDINE-3-CARBOXAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM K POTASSIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 5 SCN 10(C N S 1-) FORMUL 8 Q43 C56 H60 F3 N9 O7 S FORMUL 9 EDO 4(C2 H6 O2) FORMUL 10 K K 1+ FORMUL 21 HOH *334(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 THR A 56 GLY A 61 1 6 HELIX 4 AA4 PRO A 100 LYS A 104 5 5 HELIX 5 AA5 ARG B 33 LEU B 37 1 5 HELIX 6 AA6 SER B 39 SER B 47 1 9 HELIX 7 AA7 PRO B 66 THR B 84 1 19 HELIX 8 AA8 ALA B 96 ASP B 111 1 16 HELIX 9 AA9 THR C 157 VAL C 170 1 14 HELIX 10 AB1 LYS C 171 LEU C 178 5 8 HELIX 11 AB2 ARG C 182 ASP C 190 1 9 HELIX 12 AB3 ASN C 193 ARG C 210 1 18 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 THR A 16 N LEU A 5 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 VAL B 19 O VAL B 31 SHEET 8 AA2 8 GLU B 59 ASN B 61 1 O VAL B 60 N ILE B 22 SHEET 1 AA3 4 GLY C 106 TYR C 112 0 SHEET 2 AA3 4 PRO C 71 ASN C 78 -1 N VAL C 74 O ILE C 109 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 SHEET 1 AA5 4 ALA D 36 LEU D 41 0 SHEET 2 AA5 4 ILE D 327 LYS D 331 -1 O ILE D 327 N LEU D 41 SHEET 3 AA5 4 ILE D 315 ALA D 320 -1 N ILE D 316 O TRP D 330 SHEET 4 AA5 4 VAL D 304 CYS D 309 -1 N ALA D 308 O ALA D 317 SHEET 1 AA6 4 VAL D 48 PHE D 53 0 SHEET 2 AA6 4 TRP D 59 SER D 64 -1 O ALA D 61 N LYS D 52 SHEET 3 AA6 4 ILE D 69 GLY D 73 -1 O TRP D 72 N LEU D 60 SHEET 4 AA6 4 PHE D 79 ILE D 83 -1 O ILE D 83 N ILE D 69 SHEET 1 AA7 4 ILE D 90 TRP D 95 0 SHEET 2 AA7 4 LEU D 101 SER D 106 -1 O ALA D 105 N SER D 91 SHEET 3 AA7 4 THR D 110 ASP D 115 -1 O TRP D 114 N LEU D 102 SHEET 4 AA7 4 CYS D 121 LYS D 126 -1 O LEU D 125 N LEU D 111 SHEET 1 AA8 4 VAL D 132 PHE D 137 0 SHEET 2 AA8 4 LEU D 143 SER D 148 -1 O VAL D 145 N ASN D 136 SHEET 3 AA8 4 VAL D 153 ASP D 157 -1 O TRP D 156 N ILE D 144 SHEET 4 AA8 4 CYS D 163 LEU D 167 -1 O LEU D 167 N VAL D 153 SHEET 1 AA9 4 VAL D 174 PHE D 179 0 SHEET 2 AA9 4 LEU D 185 SER D 190 -1 O VAL D 187 N HIS D 178 SHEET 3 AA9 4 LEU D 194 ASP D 199 -1 O TRP D 198 N ILE D 186 SHEET 4 AA9 4 CYS D 205 ILE D 210 -1 O LYS D 207 N ILE D 197 SHEET 1 AB1 4 VAL D 217 PHE D 222 0 SHEET 2 AB1 4 ILE D 229 THR D 233 -1 O LEU D 230 N LYS D 221 SHEET 3 AB1 4 THR D 237 ASP D 242 -1 O LYS D 239 N ALA D 231 SHEET 4 AB1 4 LYS D 247 TYR D 252 -1 O LEU D 249 N LEU D 240 SHEET 1 AB2 4 ALA D 264 SER D 267 0 SHEET 2 AB2 4 TRP D 273 SER D 276 -1 O VAL D 275 N ASN D 265 SHEET 3 AB2 4 VAL D 283 ASN D 287 -1 O TYR D 284 N SER D 276 SHEET 4 AB2 4 ILE D 293 LEU D 297 -1 O LEU D 297 N VAL D 283 LINK OH TYR C 112 K K C 304 1555 1555 2.84 LINK O2 Q43 C 302 K K C 304 1555 1555 2.75 LINK K K C 304 O HOH C 483 1555 1555 2.64 LINK K K C 304 O HOH C 494 1555 1555 3.03 LINK K K C 304 O HOH D 504 1555 1555 2.72 LINK K K C 304 O HOH D 583 1555 1555 2.81 CRYST1 48.120 86.689 196.600 90.00 90.00 90.00 P 21 21 21 4 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 0.020781 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005086 0.00000