HEADER SIGNALING PROTEIN 13-MAR-19 6R13 TITLE CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX TITLE 2 WITH COMPOUND 7F 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, KEYWDS 2 HYDROLYSIS PRODUCT, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.HEIM,M.D.HARTMANN REVDAT 2 24-JAN-24 6R13 1 REMARK REVDAT 1 07-AUG-19 6R13 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. 1.65 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34483 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1816 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2502 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.3780 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2198 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -0.55000 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): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.131 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2380 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2065 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3223 ; 1.713 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4745 ; 0.971 ; 2.991 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 295 ; 5.942 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;35.260 ;21.481 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 337 ;12.315 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;11.374 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 315 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2716 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 578 ; 0.002 ; 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): 1160 ; 0.875 ; 1.788 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1159 ; 0.875 ; 1.787 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1443 ; 1.463 ; 2.666 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1444 ; 1.462 ; 2.667 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1220 ; 1.153 ; 1.921 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1221 ; 1.153 ; 1.922 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1774 ; 1.828 ; 2.838 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2572 ; 5.175 ;20.625 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2547 ; 5.054 ;20.213 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 : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 19 122 B 19 122 6302 0.12 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 16 A 160 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0749 17.2762 2.4210 REMARK 3 T TENSOR REMARK 3 T11: 0.0020 T22: 0.0894 REMARK 3 T33: 0.0844 T12: 0.0017 REMARK 3 T13: -0.0059 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 2.1543 L22: 1.0555 REMARK 3 L33: 2.5312 L12: 0.0912 REMARK 3 L13: 1.0874 L23: 0.2568 REMARK 3 S TENSOR REMARK 3 S11: 0.0272 S12: 0.0147 S13: -0.0821 REMARK 3 S21: 0.0307 S22: 0.0171 S23: 0.0844 REMARK 3 S31: 0.0084 S32: -0.0082 S33: -0.0443 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 19 B 161 REMARK 3 ORIGIN FOR THE GROUP (A): 31.9886 7.6034 23.7706 REMARK 3 T TENSOR REMARK 3 T11: 0.0231 T22: 0.0849 REMARK 3 T33: 0.0743 T12: -0.0281 REMARK 3 T13: 0.0145 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 1.3868 L22: 2.4027 REMARK 3 L33: 2.4004 L12: -1.1444 REMARK 3 L13: -0.1305 L23: -0.7414 REMARK 3 S TENSOR REMARK 3 S11: 0.0469 S12: -0.0983 S13: -0.0054 REMARK 3 S21: -0.0581 S22: -0.0939 S23: -0.0706 REMARK 3 S31: -0.0572 S32: 0.1351 S33: 0.0471 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 18 C 150 REMARK 3 ORIGIN FOR THE GROUP (A): 28.8382 -2.9371 -7.9347 REMARK 3 T TENSOR REMARK 3 T11: 0.1995 T22: 0.4867 REMARK 3 T33: 0.3648 T12: -0.0649 REMARK 3 T13: -0.0145 T23: -0.0732 REMARK 3 L TENSOR REMARK 3 L11: 4.1806 L22: 0.7012 REMARK 3 L33: 1.3832 L12: 1.2909 REMARK 3 L13: 2.3388 L23: 0.5728 REMARK 3 S TENSOR REMARK 3 S11: 0.1551 S12: -0.4623 S13: -0.1691 REMARK 3 S21: -0.0724 S22: -0.0063 S23: 0.0720 REMARK 3 S31: 0.1494 S32: -0.3455 S33: -0.1488 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6R13 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_1292101249. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-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 : 36299 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 48.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 0.82000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.350 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 (%): 31.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 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 28.43550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.14150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.27350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.14150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.43550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.27350 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 MET A 13 REMARK 465 VAL A 14 REMARK 465 LEU A 15 REMARK 465 ASP A 124 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 MET B 13 REMARK 465 VAL B 14 REMARK 465 LEU B 15 REMARK 465 ALA B 16 REMARK 465 PRO B 17 REMARK 465 GLY B 18 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 ALA C 16 REMARK 465 PRO C 17 REMARK 465 PHE C 49 REMARK 465 ASN C 50 REMARK 465 PRO C 51 REMARK 465 ALA C 52 REMARK 465 GLY C 53 REMARK 465 MET C 54 REMARK 465 ILE C 55 REMARK 465 ILE C 70 REMARK 465 GLY C 71 REMARK 465 ALA C 72 REMARK 465 PRO C 73 REMARK 465 SER C 74 REMARK 465 GLY C 75 REMARK 465 GLU C 76 REMARK 465 PHE C 77 REMARK 465 SER C 78 REMARK 465 TRP C 79 REMARK 465 PHE C 80 REMARK 465 LYS C 81 REMARK 465 GLY C 82 REMARK 465 TYR C 83 REMARK 465 ASP C 84 REMARK 465 GLY C 103 REMARK 465 GLY C 104 REMARK 465 SER C 105 REMARK 465 GLN C 106 REMARK 465 PRO C 107 REMARK 465 GLN C 108 REMARK 465 THR C 109 REMARK 465 PHE C 110 REMARK 465 ALA C 123 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 GLU B 102 CG CD OE1 OE2 REMARK 470 ILE C 21 CG1 CG2 CD1 REMARK 470 PHE C 22 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG C 25 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 37 CG CD1 CD2 REMARK 470 LEU C 38 CG CD1 CD2 REMARK 470 PHE C 56 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TRP C 85 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP C 85 CZ3 CH2 REMARK 470 THR C 86 OG1 CG2 REMARK 470 ILE C 87 CG1 CG2 CD1 REMARK 470 HIS C 96 CG ND1 CD2 CE1 NE2 REMARK 470 TRP C 99 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP C 99 CZ3 CH2 REMARK 470 ASP C 116 CG OD1 OD2 REMARK 470 ARG C 117 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 120 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 ALA A 19 76.21 -119.25 REMARK 500 ILE A 31 -51.13 -120.94 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 113.2 REMARK 620 3 CYS A 90 SG 109.9 99.4 REMARK 620 4 CYS A 93 SG 108.9 113.3 111.9 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 116.8 REMARK 620 3 CYS B 90 SG 113.2 111.1 REMARK 620 4 CYS B 93 SG 99.6 106.7 108.3 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 112.1 REMARK 620 3 CYS C 90 SG 112.5 101.8 REMARK 620 4 CYS C 93 SG 110.7 108.9 110.5 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 JOK 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 CL 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 DBREF 6R13 A 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 6R13 B 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 6R13 C 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 SEQADV 6R13 ALA A 0 UNP A4TVL0 EXPRESSION TAG SEQADV 6R13 ALA B 0 UNP A4TVL0 EXPRESSION TAG SEQADV 6R13 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 JOK B 202 36 HET PO4 B 203 5 HET CL B 204 1 HET ZN C 201 1 HETNAM ZN ZINC ION HETNAM EF2 S-THALIDOMIDE HETNAM PO4 PHOSPHATE ION HETNAM JOK ~{N}-[(3~{S})-2,5-BIS(OXIDANYLIDENE)PYRROLIDIN-3-YL]-3- HETNAM 2 JOK PHENYL-PROPANAMIDE HETNAM CL CHLORIDE ION FORMUL 4 ZN 3(ZN 2+) FORMUL 5 EF2 C13 H10 N2 O4 FORMUL 6 PO4 2(O4 P 3-) FORMUL 8 JOK C13 H14 N2 O3 FORMUL 10 CL CL 1- FORMUL 12 HOH *163(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 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 PHE A 111 N PHE A 61 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 ILE B 21 CYS B 24 -1 N PHE B 22 O SER B 32 SHEET 3 AA3 3 LEU B 118 GLY B 121 -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 PHE B 110 ILE B 114 -1 O PHE B 111 N PHE B 61 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 GLY C 121 N ILE C 21 SHEET 1 AA6 6 GLU C 45 HIS C 46 0 SHEET 2 AA6 6 VAL C 58 CYS C 60 -1 O VAL C 58 N HIS C 46 SHEET 3 AA6 6 GLY C 112 ILE C 114 -1 O LEU C 113 N TRP C 59 SHEET 4 AA6 6 HIS C 96 HIS C 100 -1 N LEU C 97 O ILE C 114 SHEET 5 AA6 6 THR C 86 CYS C 90 -1 N THR C 86 O HIS C 100 SHEET 6 AA6 6 LEU C 67 ARG C 68 -1 N ARG C 68 O LEU C 89 LINK SG CYS A 24 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 27 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 90 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 93 ZN ZN A 201 1555 1555 2.28 LINK SG CYS B 24 ZN ZN B 201 1555 1555 2.35 LINK SG CYS B 27 ZN ZN B 201 1555 1555 2.31 LINK SG CYS B 90 ZN ZN B 201 1555 1555 2.26 LINK SG CYS B 93 ZN ZN B 201 1555 1555 2.36 LINK SG CYS C 24 ZN ZN C 201 1555 1555 2.30 LINK SG CYS C 27 ZN ZN C 201 1555 1555 2.30 LINK SG CYS C 90 ZN ZN C 201 1555 1555 2.33 LINK SG CYS C 93 ZN ZN C 201 1555 1555 2.32 CISPEP 1 GLN A 106 PRO A 107 0 5.88 CISPEP 2 GLN B 106 PRO B 107 0 2.95 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 90 CYS A 93 SITE 1 AC2 9 ASN A 50 PRO A 51 GLU A 76 PHE A 77 SITE 2 AC2 9 SER A 78 TRP A 79 TRP A 85 TRP A 99 SITE 3 AC2 9 TYR A 101 SITE 1 AC3 3 MET A 54 HIS A 96 ARG A 117 SITE 1 AC4 4 CYS B 24 CYS B 27 CYS B 90 CYS B 93 SITE 1 AC5 8 ASN B 50 PRO B 51 PHE B 77 SER B 78 SITE 2 AC5 8 TRP B 79 TRP B 85 TRP B 99 TYR B 101 SITE 1 AC6 8 GLN B 106 ASP B 116 ARG B 117 HOH B 310 SITE 2 AC6 8 HOH B 324 HOH B 341 HOH B 343 HOH B 348 SITE 1 AC7 4 ARG A 25 ARG B 57 ASP B 116 HOH B 352 SITE 1 AC8 4 CYS C 24 CYS C 27 CYS C 90 CYS C 93 CRYST1 56.871 58.547 88.283 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 0.017584 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011327 0.00000