HEADER LIGASE 19-OCT-22 8BDO TITLE VCB IN COMPLEX WITH COMPOUND 21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGIN-B; COMPND 3 CHAIN: A, D; 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, E; 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, F; COMPND 18 SYNONYM: PROTEIN G7,PVHL; COMPND 19 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 KEYWDS PROTAC, DEGRADER, COMPLEX, E3 LIGASE, VHL, VCB, LIGASE, VH032 EXPDTA X-RAY DIFFRACTION AUTHOR F.J.SORRELL,J.E.MUELLER,M.LEHMANN,A.WEGENER REVDAT 5 16-OCT-24 8BDO 1 REMARK REVDAT 4 07-FEB-24 8BDO 1 REMARK REVDAT 3 26-APR-23 8BDO 1 JRNL REVDAT 2 22-MAR-23 8BDO 1 JRNL REVDAT 1 15-FEB-23 8BDO 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. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 174.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17781 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.321 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 890 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1309 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4160 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5312 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.25000 REMARK 3 B22 (A**2) : 2.96000 REMARK 3 B33 (A**2) : -7.21000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.512 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.611 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 35.292 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5516 ; 0.005 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5233 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7497 ; 1.403 ; 1.665 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12044 ; 1.082 ; 1.586 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 659 ; 7.186 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;32.140 ;21.010 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 913 ;17.088 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;16.636 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 727 ; 0.047 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6139 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1249 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 104 D 1 104 2880 0.090 0.050 REMARK 3 2 B 16 112 E 16 112 2561 0.080 0.050 REMARK 3 3 C 62 204 F 62 204 4475 0.080 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 8BDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292126046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-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 : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18741 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 174.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.32500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 2.63000 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 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-20% PEG 8000, 0.2 M MAGNESIUM REMARK 280 ACETATE AND 0.1 M SODIUM CACODYLATE PH 6.5, 1MM COMPOUND SOAK, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 174.85200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 174.85200 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.15300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.62800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.15300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.62800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 174.85200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.15300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.62800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 174.85200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.15300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.62800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 ALA A 81 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 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 ALA D 81 REMARK 465 ASP D 82 REMARK 465 PRO E 49 REMARK 465 GLY E 50 REMARK 465 GLN E 51 REMARK 465 PHE E 52 REMARK 465 ALA E 53 REMARK 465 GLU E 54 REMARK 465 ASN E 55 REMARK 465 GLU E 56 REMARK 465 GLY F 52 REMARK 465 SER F 53 REMARK 465 MET F 54 REMARK 465 GLU F 55 REMARK 465 ALA F 56 REMARK 465 GLY F 57 REMARK 465 ARG F 58 REMARK 465 PRO F 59 REMARK 465 ARG F 60 REMARK 465 PRO F 61 REMARK 465 ARG F 205 REMARK 465 ILE F 206 REMARK 465 ALA F 207 REMARK 465 HIS F 208 REMARK 465 GLN F 209 REMARK 465 ARG F 210 REMARK 465 MET F 211 REMARK 465 GLY F 212 REMARK 465 ASP F 213 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 36 CG CD CE NZ REMARK 470 ASP A 83 CG OD1 OD2 REMARK 470 SER B 47 OG REMARK 470 VAL C 62 CG1 CG2 REMARK 470 ASP C 143 CG OD1 OD2 REMARK 470 ARG C 177 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 201 CG CD1 CD2 REMARK 470 GLN C 203 CG CD OE1 NE2 REMARK 470 GLU C 204 CG CD OE1 OE2 REMARK 470 LYS D 46 CD CE NZ REMARK 470 ASP D 52 CG OD1 OD2 REMARK 470 LYS D 55 CG CD CE NZ REMARK 470 ASP D 83 CG OD1 OD2 REMARK 470 SER E 47 OG REMARK 470 THR E 57 OG1 CG2 REMARK 470 ASP E 111 CG OD1 OD2 REMARK 470 VAL F 62 CG1 CG2 REMARK 470 VAL F 142 CG1 CG2 REMARK 470 ARG F 177 CG CD NE CZ NH1 NH2 REMARK 470 LYS F 196 CG CD CE NZ REMARK 470 GLN F 203 CG CD OE1 NE2 REMARK 470 GLU F 204 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 OE1 GLU F 199 O HOH F 401 2.13 REMARK 500 CD2 HIS C 191 O HOH C 404 2.19 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 -115.03 61.32 REMARK 500 ASP A 48 4.50 82.01 REMARK 500 ARG C 79 52.33 -103.05 REMARK 500 SER C 111 -167.17 -127.67 REMARK 500 SER C 111 -167.17 -128.73 REMARK 500 HIS C 125 19.02 51.26 REMARK 500 GLN C 132 -13.18 83.12 REMARK 500 ASP C 179 74.44 -104.96 REMARK 500 ASP C 190 61.94 -66.64 REMARK 500 GLN C 203 155.92 166.66 REMARK 500 HIS D 10 -116.88 59.99 REMARK 500 ASP D 47 -116.73 65.55 REMARK 500 THR D 66 -43.27 -134.86 REMARK 500 ASN E 85 31.34 73.35 REMARK 500 PRO E 97 -39.77 -38.03 REMARK 500 ASP E 111 -94.34 -71.85 REMARK 500 ARG F 79 50.97 -102.65 REMARK 500 SER F 111 -167.33 -128.23 REMARK 500 HIS F 125 19.75 52.07 REMARK 500 GLN F 132 -15.16 84.22 REMARK 500 ASP F 179 72.32 -105.10 REMARK 500 ASP F 190 61.97 -65.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8BDI RELATED DB: PDB DBREF 8BDO A 1 104 UNP Q15370 ELOB_HUMAN 1 104 DBREF 8BDO B 17 112 UNP Q15369 ELOC_HUMAN 17 112 DBREF 8BDO C 54 213 UNP P40337 VHL_HUMAN 54 213 DBREF 8BDO D 1 104 UNP Q15370 ELOB_HUMAN 1 104 DBREF 8BDO E 17 112 UNP Q15369 ELOC_HUMAN 17 112 DBREF 8BDO F 54 213 UNP P40337 VHL_HUMAN 54 213 SEQADV 8BDO MET B 16 UNP Q15369 INITIATING METHIONINE SEQADV 8BDO GLY C 52 UNP P40337 EXPRESSION TAG SEQADV 8BDO SER C 53 UNP P40337 EXPRESSION TAG SEQADV 8BDO MET E 16 UNP Q15369 INITIATING METHIONINE SEQADV 8BDO GLY F 52 UNP P40337 EXPRESSION TAG SEQADV 8BDO SER F 53 UNP P40337 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 CAS 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 CAS 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 104 MET ASP VAL PHE LEU MET ILE ARG ARG HIS LYS THR THR SEQRES 2 D 104 ILE PHE THR ASP ALA LYS GLU SER SER THR VAL PHE GLU SEQRES 3 D 104 LEU LYS ARG ILE VAL GLU GLY ILE LEU LYS ARG PRO PRO SEQRES 4 D 104 ASP GLU GLN ARG LEU TYR LYS ASP ASP GLN LEU LEU ASP SEQRES 5 D 104 ASP GLY LYS THR LEU GLY GLU CYS GLY PHE THR SER GLN SEQRES 6 D 104 THR ALA ARG PRO GLN ALA PRO ALA THR VAL GLY LEU ALA SEQRES 7 D 104 PHE ARG ALA ASP ASP THR PHE GLU ALA LEU CAS ILE GLU SEQRES 8 D 104 PRO PHE SER SER PRO PRO GLU LEU PRO ASP VAL MET LYS SEQRES 1 E 97 MET MET TYR VAL LYS LEU ILE SER SER ASP GLY HIS GLU SEQRES 2 E 97 PHE ILE VAL LYS ARG GLU HIS ALA LEU THR SER GLY THR SEQRES 3 E 97 ILE LYS ALA MET LEU SER GLY PRO GLY GLN PHE ALA GLU SEQRES 4 E 97 ASN GLU THR ASN GLU VAL ASN PHE ARG GLU ILE PRO SER SEQRES 5 E 97 HIS VAL LEU SER LYS VAL CYS MET TYR PHE THR TYR LYS SEQRES 6 E 97 VAL ARG TYR THR ASN SER SER THR GLU ILE PRO GLU PHE SEQRES 7 E 97 PRO ILE ALA PRO GLU ILE ALA LEU GLU LEU LEU MET ALA SEQRES 8 E 97 ALA ASN PHE LEU ASP CYS SEQRES 1 F 162 GLY SER MET GLU ALA GLY ARG PRO ARG PRO VAL LEU ARG SEQRES 2 F 162 SER VAL ASN SER ARG GLU PRO SER GLN VAL ILE PHE CAS SEQRES 3 F 162 ASN ARG SER PRO ARG VAL VAL LEU PRO VAL TRP LEU ASN SEQRES 4 F 162 PHE ASP GLY GLU PRO GLN PRO TYR PRO THR LEU PRO PRO SEQRES 5 F 162 GLY THR GLY ARG ARG ILE HIS SER TYR ARG GLY HIS LEU SEQRES 6 F 162 TRP LEU PHE ARG ASP ALA GLY THR HIS ASP GLY LEU LEU SEQRES 7 F 162 VAL ASN GLN THR GLU LEU PHE VAL PRO SER LEU ASN VAL SEQRES 8 F 162 ASP GLY GLN PRO ILE PHE ALA ASN ILE THR LEU PRO VAL SEQRES 9 F 162 TYR THR LEU LYS GLU ARG CYS LEU GLN VAL VAL ARG SER SEQRES 10 F 162 LEU VAL LYS PRO GLU ASN TYR ARG ARG LEU ASP ILE VAL SEQRES 11 F 162 ARG SER LEU TYR GLU ASP LEU GLU ASP HIS PRO ASN VAL SEQRES 12 F 162 GLN LYS ASP LEU GLU ARG LEU THR GLN GLU ARG ILE ALA SEQRES 13 F 162 HIS GLN ARG MET GLY ASP MODRES 8BDO CAS A 89 CYS MODIFIED RESIDUE MODRES 8BDO CAS C 77 CYS MODIFIED RESIDUE MODRES 8BDO CAS D 89 CYS MODIFIED RESIDUE MODRES 8BDO CAS F 77 CYS MODIFIED RESIDUE HET CAS A 89 9 HET CAS C 77 9 HET CAS D 89 9 HET CAS F 77 9 HET QFF C 301 34 HET QFF F 301 34 HETNAM CAS S-(DIMETHYLARSENIC)CYSTEINE HETNAM QFF (2~{S},4~{R})-1-[(2~{R})-3-METHYL-2-(3-METHYL-1,2- HETNAM 2 QFF OXAZOL-5-YL)BUTANOYL]-~{N}-[4-(4-METHYL-1,3-THIAZOL-5- HETNAM 3 QFF YL)PHENOXY]-4-OXIDANYL-PYRROLIDINE-2-CARBOXAMIDE FORMUL 1 CAS 4(C5 H12 AS N O2 S) FORMUL 7 QFF 2(C24 H28 N4 O5 S) FORMUL 9 HOH *189(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 PRO A 100 LYS A 104 5 5 HELIX 4 AA4 ARG B 33 LEU B 37 1 5 HELIX 5 AA5 SER B 39 SER B 47 1 9 HELIX 6 AA6 PRO B 66 THR B 84 1 19 HELIX 7 AA7 ALA B 96 GLU B 98 5 3 HELIX 8 AA8 ILE B 99 ASP B 111 1 13 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 VAL C 181 ASP C 190 1 10 HELIX 12 AB3 ASN C 193 THR C 202 1 10 HELIX 13 AB4 THR D 23 LYS D 36 1 14 HELIX 14 AB5 PRO D 38 ASP D 40 5 3 HELIX 15 AB6 PRO D 100 LYS D 104 5 5 HELIX 16 AB7 ARG E 33 LEU E 37 1 5 HELIX 17 AB8 SER E 39 SER E 47 1 9 HELIX 18 AB9 PRO E 66 THR E 84 1 19 HELIX 19 AC1 ALA E 96 GLU E 98 5 3 HELIX 20 AC2 ILE E 99 LEU E 110 1 12 HELIX 21 AC3 THR F 157 VAL F 170 1 14 HELIX 22 AC4 LYS F 171 LEU F 178 5 8 HELIX 23 AC5 VAL F 181 ASP F 190 1 10 HELIX 24 AC6 ASN F 193 GLU F 204 1 12 SHEET 1 AA1 8 GLN A 49 LEU A 50 0 SHEET 2 AA1 8 GLN A 42 LYS A 46 -1 N LYS A 46 O GLN A 49 SHEET 3 AA1 8 ALA A 73 PHE A 79 -1 O GLY A 76 N TYR A 45 SHEET 4 AA1 8 ASP A 2 ARG A 9 1 N ARG A 8 O VAL A 75 SHEET 5 AA1 8 THR A 12 LYS A 19 -1 O ALA A 18 N VAL A 3 SHEET 6 AA1 8 GLU B 28 LYS B 32 1 O ILE B 30 N PHE A 15 SHEET 7 AA1 8 TYR B 18 ILE B 22 -1 N LEU B 21 O PHE B 29 SHEET 8 AA1 8 GLU B 59 ASN B 61 1 O VAL B 60 N ILE B 22 SHEET 1 AA2 4 GLY C 106 TYR C 112 0 SHEET 2 AA2 4 PRO C 71 ARG C 79 -1 N VAL C 74 O ILE C 109 SHEET 3 AA2 4 ILE C 147 THR C 152 1 O ALA C 149 N ILE C 75 SHEET 4 AA2 4 LEU C 129 VAL C 130 -1 N LEU C 129 O THR C 152 SHEET 1 AA3 3 PRO C 95 PRO C 97 0 SHEET 2 AA3 3 VAL C 84 LEU C 89 -1 N TRP C 88 O GLN C 96 SHEET 3 AA3 3 LEU C 116 ASP C 121 -1 O LEU C 118 N VAL C 87 SHEET 1 AA4 8 GLN D 49 LEU D 50 0 SHEET 2 AA4 8 GLN D 42 LYS D 46 -1 N LYS D 46 O GLN D 49 SHEET 3 AA4 8 ALA D 73 PHE D 79 -1 O GLY D 76 N TYR D 45 SHEET 4 AA4 8 ASP D 2 ARG D 9 1 N ARG D 8 O VAL D 75 SHEET 5 AA4 8 THR D 12 LYS D 19 -1 O ALA D 18 N VAL D 3 SHEET 6 AA4 8 GLU E 28 LYS E 32 1 O ILE E 30 N THR D 13 SHEET 7 AA4 8 TYR E 18 ILE E 22 -1 N LEU E 21 O PHE E 29 SHEET 8 AA4 8 GLU E 59 ASN E 61 1 O VAL E 60 N ILE E 22 SHEET 1 AA5 4 GLY F 106 TYR F 112 0 SHEET 2 AA5 4 PRO F 71 ARG F 79 -1 N VAL F 74 O ILE F 109 SHEET 3 AA5 4 ILE F 147 THR F 152 1 O ALA F 149 N ILE F 75 SHEET 4 AA5 4 LEU F 129 VAL F 130 -1 N LEU F 129 O THR F 152 SHEET 1 AA6 3 PRO F 95 PRO F 97 0 SHEET 2 AA6 3 VAL F 84 LEU F 89 -1 N TRP F 88 O GLN F 96 SHEET 3 AA6 3 LEU F 116 ASP F 121 -1 O LEU F 118 N VAL F 87 LINK C LEU A 88 N CAS A 89 1555 1555 1.34 LINK C CAS A 89 N ILE A 90 1555 1555 1.34 LINK C PHE C 76 N CAS C 77 1555 1555 1.34 LINK C CAS C 77 N ASN C 78 1555 1555 1.34 LINK C LEU D 88 N CAS D 89 1555 1555 1.34 LINK C CAS D 89 N ILE D 90 1555 1555 1.34 LINK C PHE F 76 N CAS F 77 1555 1555 1.34 LINK C CAS F 77 N ASN F 78 1555 1555 1.34 CRYST1 62.306 67.256 349.704 90.00 90.00 90.00 C 2 2 21 16 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 0.016050 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002860 0.00000