HEADER SIGNALING PROTEIN 15-MAR-19 6R1W TITLE CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX TITLE 2 WITH COMPOUND 16B 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 6R1W 1 REMARK REVDAT 1 07-AUG-19 6R1W 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 62959 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3291 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4543 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 225 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2553 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 309 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : -0.31000 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): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.964 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2816 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2480 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3840 ; 2.224 ; 1.926 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5742 ; 1.117 ; 2.974 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 354 ; 6.646 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;35.372 ;21.641 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 406 ;11.569 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;11.428 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 376 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3204 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 685 ; 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): 1350 ; 1.431 ; 1.438 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1349 ; 1.431 ; 1.437 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1691 ; 2.177 ; 2.155 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1692 ; 2.176 ; 2.156 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1466 ; 2.320 ; 1.744 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1467 ; 2.320 ; 1.744 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2136 ; 3.474 ; 2.529 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3197 ; 5.640 ;18.321 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3198 ; 5.640 ;18.336 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 6558 0.16 0.05 REMARK 3 2 A 18 122 C 18 122 6078 0.16 0.05 REMARK 3 3 B 18 122 C 18 122 5800 0.18 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 160 REMARK 3 ORIGIN FOR THE GROUP (A): 18.8317 17.4919 3.2030 REMARK 3 T TENSOR REMARK 3 T11: 0.0059 T22: 0.0359 REMARK 3 T33: 0.0142 T12: 0.0051 REMARK 3 T13: -0.0070 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.7420 L22: 0.4415 REMARK 3 L33: 1.6032 L12: -0.0647 REMARK 3 L13: 0.5577 L23: 0.0783 REMARK 3 S TENSOR REMARK 3 S11: 0.0544 S12: -0.0249 S13: -0.0464 REMARK 3 S21: -0.0033 S22: 0.0083 S23: 0.0356 REMARK 3 S31: 0.0513 S32: -0.0195 S33: -0.0627 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 161 REMARK 3 ORIGIN FOR THE GROUP (A): 32.5996 6.6312 23.3517 REMARK 3 T TENSOR REMARK 3 T11: 0.0211 T22: 0.0166 REMARK 3 T33: 0.0046 T12: -0.0089 REMARK 3 T13: 0.0004 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 1.0586 L22: 0.8909 REMARK 3 L33: 0.8668 L12: -0.5907 REMARK 3 L13: -0.2723 L23: -0.1229 REMARK 3 S TENSOR REMARK 3 S11: 0.0242 S12: -0.0338 S13: -0.0570 REMARK 3 S21: -0.0531 S22: -0.0365 S23: 0.0409 REMARK 3 S31: -0.0298 S32: 0.0625 S33: 0.0123 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 160 REMARK 3 ORIGIN FOR THE GROUP (A): 27.4135 -6.4888 -6.7943 REMARK 3 T TENSOR REMARK 3 T11: 0.0077 T22: 0.0600 REMARK 3 T33: 0.0122 T12: -0.0132 REMARK 3 T13: 0.0043 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.0627 L22: 1.4137 REMARK 3 L33: 1.3637 L12: 0.6226 REMARK 3 L13: 0.5118 L23: 0.1798 REMARK 3 S TENSOR REMARK 3 S11: 0.0329 S12: -0.1603 S13: -0.0140 REMARK 3 S21: 0.0417 S22: -0.0042 S23: 0.0967 REMARK 3 S31: 0.0444 S32: -0.2110 S33: -0.0287 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 6R1W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101253. 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 : 66250 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 47.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.62 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 12.73 REMARK 200 R MERGE FOR SHELL (I) : 0.99000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.850 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 (%): 31.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 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 28.26700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.17950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.72050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.17950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.26700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.72050 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 ALA C 16 REMARK 465 PRO C 17 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 MET B 13 CG SD CE REMARK 470 MET C 54 CG SD CE REMARK 470 GLU C 76 CG CD OE1 OE2 REMARK 470 GLN C 106 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 344 O HOH B 401 1.86 REMARK 500 O HOH A 347 O HOH A 400 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 49 CB PHE A 49 CG -0.124 REMARK 500 PHE A 77 CG PHE A 77 CD1 -0.106 REMARK 500 SER B 20 CB SER B 20 OG -0.126 REMARK 500 GLU B 120 CD GLU B 120 OE1 -0.074 REMARK 500 ARG C 23 CD ARG C 23 NE -0.103 REMARK 500 ARG C 23 CZ ARG C 23 NH1 0.095 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 84 CB - CG - OD1 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG B 23 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 23 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 23 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 23 NE - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ASP B 35 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP B 84 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG C 23 NH1 - CZ - NH2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG C 23 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP C 116 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP C 116 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG C 117 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 27 -11.06 -141.97 REMARK 500 ILE A 31 -55.51 -122.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C 369 DISTANCE = 5.88 ANGSTROMS 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 114.2 REMARK 620 3 CYS A 90 SG 108.4 99.4 REMARK 620 4 CYS A 93 SG 109.9 112.5 111.9 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 114.7 REMARK 620 3 CYS B 90 SG 111.5 103.9 REMARK 620 4 CYS B 93 SG 102.7 113.5 110.7 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 113.5 REMARK 620 3 CYS C 90 SG 109.6 100.8 REMARK 620 4 CYS C 93 SG 108.3 111.6 112.9 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 PO4 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 JPW 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 JPW 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 6R1W A 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 6R1W B 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 6R1W C 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 SEQADV 6R1W ALA A 0 UNP A4TVL0 EXPRESSION TAG SEQADV 6R1W ALA B 0 UNP A4TVL0 EXPRESSION TAG SEQADV 6R1W 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 PO4 B 202 5 HET PO4 B 203 5 HET JPW B 204 20 HET ZN C 201 1 HET JPW C 202 20 HET PO4 C 203 5 HETNAM ZN ZINC ION HETNAM EF2 S-THALIDOMIDE HETNAM PO4 PHOSPHATE ION HETNAM JPW (4-AZANYLCYCLOHEXYL)METHYL ~{N}-[(3~{S})-2,6- HETNAM 2 JPW BIS(OXIDANYLIDENE)PIPERIDIN-3-YL]CARBAMATE FORMUL 4 ZN 3(ZN 2+) FORMUL 5 EF2 C13 H10 N2 O4 FORMUL 6 PO4 4(O4 P 3-) FORMUL 10 JPW 2(C13 H21 N3 O4) FORMUL 14 HOH *309(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 PHE A 56 N VAL A 48 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 ILE B 31 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 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 THR B 86 O HIS B 100 SHEET 6 AA4 6 LEU B 67 SER B 74 -1 N ARG B 68 O LEU B 89 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 PHE C 56 N VAL C 48 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 GLU C 102 -1 N TYR C 101 O PHE C 110 SHEET 5 AA6 6 ASP C 84 CYS C 90 -1 N ALA C 88 O GLY C 98 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 2.29 LINK SG CYS A 27 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 90 ZN ZN A 201 1555 1555 2.37 LINK SG CYS A 93 ZN ZN A 201 1555 1555 2.32 LINK SG CYS B 24 ZN ZN B 201 1555 1555 2.35 LINK SG CYS B 27 ZN ZN B 201 1555 1555 2.34 LINK SG CYS B 90 ZN ZN B 201 1555 1555 2.31 LINK SG CYS B 93 ZN ZN B 201 1555 1555 2.35 LINK SG CYS C 24 ZN ZN C 201 1555 1555 2.31 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 6.91 CISPEP 2 GLN B 106 PRO B 107 0 1.85 CISPEP 3 GLN C 106 PRO C 107 0 7.79 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 GLU A 76 PHE A 77 SITE 2 AC2 10 SER A 78 TRP A 79 TRP A 85 TRP A 99 SITE 3 AC2 10 TYR A 101 HOH A 306 SITE 1 AC3 6 MET A 54 HIS A 96 ARG A 117 HOH A 306 SITE 2 AC3 6 HOH A 366 HOH A 377 SITE 1 AC4 4 CYS B 24 CYS B 27 CYS B 90 CYS B 93 SITE 1 AC5 3 HIS B 96 ARG B 117 HOH B 304 SITE 1 AC6 9 ARG A 25 SER A 105 ARG B 57 GLN B 108 SITE 2 AC6 9 ASP B 116 HOH B 301 HOH B 302 HOH B 305 SITE 3 AC6 9 HOH B 310 SITE 1 AC7 10 ASN B 50 PRO B 51 PHE B 77 SER B 78 SITE 2 AC7 10 TRP B 79 TRP B 85 TRP B 99 TYR B 101 SITE 3 AC7 10 HOH B 356 HOH B 379 SITE 1 AC8 4 CYS C 24 CYS C 27 CYS C 90 CYS C 93 SITE 1 AC9 10 ILE B 87 ASN C 50 PRO C 51 PHE C 77 SITE 2 AC9 10 SER C 78 TRP C 79 TRP C 99 TYR C 101 SITE 3 AC9 10 PO4 C 203 HOH C 313 SITE 1 AD1 4 HIS C 96 ARG C 117 JPW C 202 HOH C 313 CRYST1 56.534 59.441 88.359 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 0.017688 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011317 0.00000