HEADER SIGNALING PROTEIN 14-MAR-19 6R1A TITLE CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX TITLE 2 WITH COMPOUND 20B COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEREBLON ISOFORM 4; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MAGNETOSPIRILLUM GRYPHISWALDENSE MSR-1; SOURCE 3 ORGANISM_TAXID: 431944; SOURCE 4 GENE: MGR_0879; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEOLYSIS TARGETING CHIMERA, PROTAC, PROTEIN DEGRADATION, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.HEIM,M.D.HARTMANN REVDAT 2 24-JAN-24 6R1A 1 REMARK REVDAT 1 07-AUG-19 6R1A 0 JRNL AUTH C.HEIM,D.PLIATSIKA,F.MOUSAVIZADEH,K.BAR,B.HERNANDEZ ALVAREZ, JRNL AUTH 2 A.GIANNIS,M.D.HARTMANN JRNL TITL DE-NOVO DESIGN OF CEREBLON (CRBN) EFFECTORS GUIDED BY JRNL TITL 2 NATURAL HYDROLYSIS PRODUCTS OF THALIDOMIDE DERIVATIVES. JRNL REF J.MED.CHEM. V. 62 6615 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31251063 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00454 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 41826 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2201 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) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2816 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 152 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2567 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : 0.53000 REMARK 3 B33 (A**2) : -0.05000 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): 0.088 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.904 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2803 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2444 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3817 ; 1.895 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5640 ; 1.040 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 6.203 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;35.414 ;22.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 398 ;12.438 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;11.105 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 371 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3166 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 673 ; 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): 1343 ; 1.074 ; 1.765 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1342 ; 1.073 ; 1.765 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1679 ; 1.810 ; 2.636 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1680 ; 1.810 ; 2.636 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1460 ; 1.390 ; 1.912 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1457 ; 1.390 ; 1.896 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2122 ; 2.254 ; 2.792 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3152 ; 4.617 ;20.546 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3143 ; 4.329 ;20.392 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 13 122 B 13 122 6500 0.14 0.05 REMARK 3 2 A 16 122 C 16 122 6028 0.17 0.05 REMARK 3 3 B 16 122 C 16 122 5912 0.19 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 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 13 A 391 REMARK 3 ORIGIN FOR THE GROUP (A): 18.8078 17.5015 3.0886 REMARK 3 T TENSOR REMARK 3 T11: 0.0070 T22: 0.0661 REMARK 3 T33: 0.0272 T12: 0.0048 REMARK 3 T13: -0.0054 T23: -0.0238 REMARK 3 L TENSOR REMARK 3 L11: 0.6466 L22: 0.1118 REMARK 3 L33: 1.1433 L12: -0.0543 REMARK 3 L13: 0.4784 L23: 0.1212 REMARK 3 S TENSOR REMARK 3 S11: 0.0460 S12: -0.0229 S13: -0.0303 REMARK 3 S21: -0.0024 S22: 0.0102 S23: 0.0231 REMARK 3 S31: 0.0194 S32: -0.0043 S33: -0.0562 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 13 B 397 REMARK 3 ORIGIN FOR THE GROUP (A): 32.5137 6.6555 23.2348 REMARK 3 T TENSOR REMARK 3 T11: 0.0275 T22: 0.0564 REMARK 3 T33: 0.0248 T12: -0.0015 REMARK 3 T13: -0.0027 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.7925 L22: 0.4550 REMARK 3 L33: 0.7695 L12: -0.4393 REMARK 3 L13: -0.1574 L23: -0.2719 REMARK 3 S TENSOR REMARK 3 S11: 0.0289 S12: -0.0266 S13: -0.0657 REMARK 3 S21: -0.0379 S22: -0.0378 S23: 0.0443 REMARK 3 S31: -0.0155 S32: 0.0646 S33: 0.0090 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 16 C 344 REMARK 3 ORIGIN FOR THE GROUP (A): 27.4162 -6.2120 -6.7143 REMARK 3 T TENSOR REMARK 3 T11: 0.0421 T22: 0.1339 REMARK 3 T33: 0.0864 T12: -0.0217 REMARK 3 T13: 0.0224 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.8534 L22: 1.6109 REMARK 3 L33: 1.7951 L12: 0.2766 REMARK 3 L13: 1.3065 L23: 1.3663 REMARK 3 S TENSOR REMARK 3 S11: 0.1023 S12: -0.2582 S13: -0.2633 REMARK 3 S21: 0.2542 S22: -0.0898 S23: 0.1857 REMARK 3 S31: 0.2475 S32: -0.2245 S33: -0.0125 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 REMARK 4 REMARK 4 6R1A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-18 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44027 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 49.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 0.82000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.710 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4V2Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M AMMONIUM PHOSPHATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 28.27800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.00200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.65450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.00200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.27800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.65450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 3 REMARK 465 ASP A 4 REMARK 465 ALA A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 GLN A 8 REMARK 465 ASN A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 GLN A 12 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 LEU B 3 REMARK 465 ASP B 4 REMARK 465 ALA B 5 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 GLN B 8 REMARK 465 ASN B 9 REMARK 465 SER B 10 REMARK 465 THR B 11 REMARK 465 GLN B 12 REMARK 465 ASP B 124 REMARK 465 ALA C 0 REMARK 465 MET C 1 REMARK 465 PRO C 2 REMARK 465 LEU C 3 REMARK 465 ASP C 4 REMARK 465 ALA C 5 REMARK 465 GLY C 6 REMARK 465 GLY C 7 REMARK 465 GLN C 8 REMARK 465 ASN C 9 REMARK 465 SER C 10 REMARK 465 THR C 11 REMARK 465 GLN C 12 REMARK 465 MET C 13 REMARK 465 VAL C 14 REMARK 465 LEU C 15 REMARK 465 ASP C 124 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 13 CG SD CE REMARK 470 LYS A 81 CE NZ REMARK 470 LYS A 115 CD CE NZ REMARK 470 HIS C 44 CG ND1 CD2 CE1 NE2 REMARK 470 GLN C 106 CG CD OE1 NE2 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 B 23 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 23 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 34 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 CYS A 27 SG 113.6 REMARK 620 3 CYS A 90 SG 108.1 99.8 REMARK 620 4 CYS A 93 SG 110.3 111.7 112.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 24 SG REMARK 620 2 CYS B 27 SG 114.1 REMARK 620 3 CYS B 90 SG 110.8 105.8 REMARK 620 4 CYS B 93 SG 102.6 112.4 111.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 24 SG REMARK 620 2 CYS C 27 SG 114.2 REMARK 620 3 CYS C 90 SG 109.0 101.4 REMARK 620 4 CYS C 93 SG 108.6 111.1 112.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EF2 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EF2 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JP8 C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 203 DBREF 6R1A A 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 6R1A B 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 6R1A C 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 SEQADV 6R1A ALA A 0 UNP A4TVL0 EXPRESSION TAG SEQADV 6R1A ALA B 0 UNP A4TVL0 EXPRESSION TAG SEQADV 6R1A ALA C 0 UNP A4TVL0 EXPRESSION TAG SEQRES 1 A 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 A 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 A 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 A 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 A 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 A 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 A 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 A 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 A 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 A 125 ARG LEU ALA GLU GLY PRO ALA ASP SEQRES 1 B 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 B 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 B 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 B 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 B 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 B 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 B 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 B 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 B 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 B 125 ARG LEU ALA GLU GLY PRO ALA ASP SEQRES 1 C 125 ALA MET PRO LEU ASP ALA GLY GLY GLN ASN SER THR GLN SEQRES 2 C 125 MET VAL LEU ALA PRO GLY ALA SER ILE PHE ARG CYS ARG SEQRES 3 C 125 GLN CYS GLY GLN THR ILE SER ARG ARG ASP TRP LEU LEU SEQRES 4 C 125 PRO MET GLY GLY ASP HIS GLU HIS VAL VAL PHE ASN PRO SEQRES 5 C 125 ALA GLY MET ILE PHE ARG VAL TRP CYS PHE SER LEU ALA SEQRES 6 C 125 GLN GLY LEU ARG LEU ILE GLY ALA PRO SER GLY GLU PHE SEQRES 7 C 125 SER TRP PHE LYS GLY TYR ASP TRP THR ILE ALA LEU CYS SEQRES 8 C 125 GLY GLN CYS GLY SER HIS LEU GLY TRP HIS TYR GLU GLY SEQRES 9 C 125 GLY SER GLN PRO GLN THR PHE PHE GLY LEU ILE LYS ASP SEQRES 10 C 125 ARG LEU ALA GLU GLY PRO ALA ASP HET ZN A 201 1 HET EF2 A 202 19 HET PO4 A 203 5 HET ZN B 201 1 HET EF2 B 202 19 HET PO4 B 203 5 HET PO4 B 204 5 HET ZN C 201 1 HET JP8 C 202 18 HET PO4 C 203 5 HETNAM ZN ZINC ION HETNAM EF2 S-THALIDOMIDE HETNAM PO4 PHOSPHATE ION HETNAM JP8 [(2~{R})-PYRROLIDIN-2-YL]METHYL ~{N}-[(3~{S})-2,6- HETNAM 2 JP8 BIS(OXIDANYLIDENE)PIPERIDIN-3-YL]CARBAMATE FORMUL 4 ZN 3(ZN 2+) FORMUL 5 EF2 2(C13 H10 N2 O4) FORMUL 6 PO4 4(O4 P 3-) FORMUL 12 JP8 C11 H17 N3 O4 FORMUL 14 HOH *232(H2 O) HELIX 1 AA1 ASP A 35 LEU A 37 5 3 HELIX 2 AA2 PRO A 39 ASP A 43 5 5 HELIX 3 AA3 ASP B 35 LEU B 37 5 3 HELIX 4 AA4 PRO B 39 ASP B 43 5 5 HELIX 5 AA5 ASP C 35 LEU C 37 5 3 SHEET 1 AA1 3 THR A 30 ARG A 33 0 SHEET 2 AA1 3 ILE A 21 CYS A 24 -1 N PHE A 22 O SER A 32 SHEET 3 AA1 3 LEU A 118 GLY A 121 -1 O ALA A 119 N ARG A 23 SHEET 1 AA2 6 GLU A 45 PHE A 49 0 SHEET 2 AA2 6 ILE A 55 PHE A 61 -1 O VAL A 58 N HIS A 46 SHEET 3 AA2 6 PHE A 110 ILE A 114 -1 O LEU A 113 N TRP A 59 SHEET 4 AA2 6 HIS A 96 GLU A 102 -1 N TYR A 101 O PHE A 110 SHEET 5 AA2 6 ASP A 84 CYS A 90 -1 N ASP A 84 O GLU A 102 SHEET 6 AA2 6 LEU A 67 SER A 74 -1 N SER A 74 O TRP A 85 SHEET 1 AA3 3 THR B 30 ARG B 33 0 SHEET 2 AA3 3 SER B 20 CYS B 24 -1 N PHE B 22 O SER B 32 SHEET 3 AA3 3 LEU B 118 PRO B 122 -1 O ALA B 119 N ARG B 23 SHEET 1 AA4 6 GLU B 45 PHE B 49 0 SHEET 2 AA4 6 ILE B 55 PHE B 61 -1 O VAL B 58 N HIS B 46 SHEET 3 AA4 6 THR B 109 ILE B 114 -1 O LEU B 113 N TRP B 59 SHEET 4 AA4 6 HIS B 96 GLU B 102 -1 N TYR B 101 O PHE B 110 SHEET 5 AA4 6 ASP B 84 CYS B 90 -1 N ASP B 84 O GLU B 102 SHEET 6 AA4 6 LEU B 67 SER B 74 -1 N SER B 74 O TRP B 85 SHEET 1 AA5 3 THR C 30 ARG C 33 0 SHEET 2 AA5 3 ILE C 21 CYS C 24 -1 N PHE C 22 O SER C 32 SHEET 3 AA5 3 LEU C 118 GLY C 121 -1 O ALA C 119 N ARG C 23 SHEET 1 AA6 6 GLU C 45 PHE C 49 0 SHEET 2 AA6 6 ILE C 55 PHE C 61 -1 O VAL C 58 N HIS C 46 SHEET 3 AA6 6 THR C 109 ILE C 114 -1 O LEU C 113 N TRP C 59 SHEET 4 AA6 6 HIS C 96 GLY C 103 -1 N TYR C 101 O PHE C 110 SHEET 5 AA6 6 TYR C 83 CYS C 90 -1 N ASP C 84 O GLU C 102 SHEET 6 AA6 6 LEU C 67 SER C 74 -1 N SER C 74 O TRP C 85 LINK SG CYS A 24 ZN ZN A 201 1555 1555 2.32 LINK SG CYS A 27 ZN ZN A 201 1555 1555 2.31 LINK SG CYS A 90 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 93 ZN ZN A 201 1555 1555 2.31 LINK SG CYS B 24 ZN ZN B 201 1555 1555 2.36 LINK SG CYS B 27 ZN ZN B 201 1555 1555 2.33 LINK SG CYS B 90 ZN ZN B 201 1555 1555 2.30 LINK SG CYS B 93 ZN ZN B 201 1555 1555 2.32 LINK SG CYS C 24 ZN ZN C 201 1555 1555 2.30 LINK SG CYS C 27 ZN ZN C 201 1555 1555 2.29 LINK SG CYS C 90 ZN ZN C 201 1555 1555 2.34 LINK SG CYS C 93 ZN ZN C 201 1555 1555 2.29 CISPEP 1 GLN A 106 PRO A 107 0 6.95 CISPEP 2 GLN B 106 PRO B 107 0 5.50 CISPEP 3 GLN C 106 PRO C 107 0 7.57 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 90 CYS A 93 SITE 1 AC2 10 ASN A 50 PRO A 51 PHE A 77 SER A 78 SITE 2 AC2 10 TRP A 79 TRP A 85 TRP A 99 TYR A 101 SITE 3 AC2 10 HOH A 303 HOH A 346 SITE 1 AC3 6 MET A 54 HIS A 96 ARG A 117 HOH A 303 SITE 2 AC3 6 HOH A 349 HOH A 365 SITE 1 AC4 4 CYS B 24 CYS B 27 CYS B 90 CYS B 93 SITE 1 AC5 11 ASN B 50 PRO B 51 GLU B 76 PHE B 77 SITE 2 AC5 11 SER B 78 TRP B 79 TRP B 85 TRP B 99 SITE 3 AC5 11 TYR B 101 HOH B 312 HOH B 343 SITE 1 AC6 3 PHE B 56 HIS B 96 ARG B 117 SITE 1 AC7 8 ARG A 25 SER A 105 ARG B 57 GLN B 108 SITE 2 AC7 8 ASP B 116 HOH B 301 HOH B 304 HOH B 322 SITE 1 AC8 4 CYS C 24 CYS C 27 CYS C 90 CYS C 93 SITE 1 AC9 8 ASN C 50 PRO C 51 PHE C 77 SER C 78 SITE 2 AC9 8 TRP C 79 TRP C 99 TYR C 101 HOH C 307 SITE 1 AD1 5 HIS C 96 ARG C 117 HOH C 305 HOH C 307 SITE 2 AD1 5 HOH C 326 CRYST1 56.556 59.309 88.004 90.00 90.00 90.00 P 21 21 21 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 0.017682 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011363 0.00000