HEADER SIGNALING PROTEIN 14-MAR-19 6R1D TITLE CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX TITLE 2 WITH COMPOUND 7D, CO-CRYSTALLIZED COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEREBLON ISOFORM 4; COMPND 3 CHAIN: A, B; 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 6R1D 1 REMARK REVDAT 1 07-AUG-19 6R1D 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. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 74053 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) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3898 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) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4820 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.3230 REMARK 3 BIN FREE R VALUE SET COUNT : 254 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1663 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 274 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : -0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.70000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.027 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.028 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.019 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.922 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1882 ; 0.031 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1649 ; 0.015 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2575 ; 2.449 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3835 ; 1.973 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 247 ; 6.230 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;31.055 ;22.258 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 291 ;11.320 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;14.431 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 250 ; 0.455 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2184 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 473 ; 0.015 ; 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): 888 ; 1.771 ; 1.267 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 889 ; 1.770 ; 1.267 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1113 ; 1.890 ; 1.913 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1114 ; 1.889 ; 1.912 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 994 ;16.057 ; 1.633 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 995 ;16.049 ; 1.633 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1443 ;18.744 ; 2.325 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2190 ;12.742 ;17.409 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2132 ;11.260 ;16.355 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3531 ; 8.179 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 162 ;46.684 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3569 ;21.719 ; 5.000 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 20 123 B 20 123 6492 0.14 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6R1D 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_1292101257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-17 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 : 77977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 39.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.640 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4V2Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 % PEG 6K, 5 % GLYCEROL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.24100 REMARK 290 SMTRY3 2 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: 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 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 ALA A 16 REMARK 465 PRO A 17 REMARK 465 GLY A 18 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 ALA B 19 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 GLN A 108 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 NH2 ARG B 23 O HOH B 301 1.79 REMARK 500 O HOH B 306 O HOH B 354 2.12 REMARK 500 OE1 GLN B 26 O HOH B 302 2.12 REMARK 500 O HOH B 313 O HOH B 319 2.13 REMARK 500 O HOH A 375 O HOH A 439 2.15 REMARK 500 NH1 ARG B 33 O HOH B 303 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 323 O HOH A 338 1655 2.02 REMARK 500 O HOH A 349 O HOH B 314 1565 2.12 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 SER A 20 CA SER A 20 CB -0.114 REMARK 500 SER A 20 CB SER A 20 OG -0.082 REMARK 500 ARG A 34 CZ ARG A 34 NH2 -0.113 REMARK 500 GLU A 45 CD GLU A 45 OE2 -0.071 REMARK 500 THR A 86 CB THR A 86 CG2 -0.204 REMARK 500 ARG A 117 CG ARG A 117 CD -0.171 REMARK 500 SER B 20 N SER B 20 CA 0.188 REMARK 500 SER B 20 CA SER B 20 CB 0.154 REMARK 500 ARG B 23 CZ ARG B 23 NH1 0.178 REMARK 500 ARG B 34 CZ ARG B 34 NH2 -0.120 REMARK 500 ASP B 43 CB ASP B 43 CG 0.168 REMARK 500 ASP B 43 CG ASP B 43 OD1 0.164 REMARK 500 GLU B 45 CD GLU B 45 OE2 -0.070 REMARK 500 THR B 86 CB THR B 86 CG2 -0.223 REMARK 500 GLU B 102 CD GLU B 102 OE1 -0.090 REMARK 500 THR B 109 CB THR B 109 CG2 -0.274 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 ARG A 25 CG - CD - NE ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 25 NE - CZ - NH2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 MET A 40 CG - SD - CE ANGL. DEV. = 12.4 DEGREES REMARK 500 MET A 40 CG - SD - CE ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 SER B 20 N - CA - CB ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG B 23 NE - CZ - NH1 ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG B 23 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG B 33 NE - CZ - NH2 ANGL. DEV. = 6.0 DEGREES REMARK 500 MET B 40 CG - SD - CE ANGL. DEV. = -15.9 DEGREES REMARK 500 ASP B 43 CB - CG - OD1 ANGL. DEV. = -15.4 DEGREES REMARK 500 ASP B 43 CB - CG - OD2 ANGL. DEV. = 12.9 DEGREES REMARK 500 THR B 109 OG1 - CB - CG2 ANGL. DEV. = -16.4 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 ILE A 31 -54.28 -121.76 REMARK 500 ALA B 123 43.67 -90.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 116 0.07 SIDE CHAIN 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 113.3 REMARK 620 3 CYS A 90 SG 111.8 102.6 REMARK 620 4 CYS A 93 SG 103.6 114.7 111.1 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 112.0 REMARK 620 3 CYS B 90 SG 111.6 100.4 REMARK 620 4 CYS B 93 SG 105.3 115.9 111.8 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 JP5 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JP5 B 202 DBREF 6R1D A 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 DBREF 6R1D B 1 124 UNP A4TVL0 A4TVL0_9PROT 1 124 SEQADV 6R1D ALA A 0 UNP A4TVL0 EXPRESSION TAG SEQADV 6R1D ALA B 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 HET ZN A 201 1 HET JP5 A 202 18 HET ZN B 201 1 HET JP5 B 202 18 HETNAM ZN ZINC ION HETNAM JP5 (PHENYLMETHYL) ~{N}-[(3~{S})-2,5-BIS(OXIDANYLIDENE) HETNAM 2 JP5 PYRROLIDIN-3-YL]CARBAMATE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 JP5 2(C12 H12 N2 O4) FORMUL 7 HOH *274(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 SER A 20 CYS A 24 -1 N PHE A 22 O SER A 32 SHEET 3 AA1 3 LEU A 118 PRO A 122 -1 O GLY A 121 N ILE A 21 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 THR A 109 ILE A 114 -1 O LEU A 113 N TRP A 59 SHEET 4 AA2 6 HIS A 96 GLY A 103 -1 N TYR A 101 O PHE A 110 SHEET 5 AA2 6 TYR A 83 CYS A 90 -1 N ASP A 84 O GLU A 102 SHEET 6 AA2 6 LEU A 67 SER A 74 -1 N ARG A 68 O LEU A 89 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 ILE B 31 SHEET 3 AA3 3 LEU B 118 GLY B 121 -1 O GLY B 121 N ILE B 21 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 GLY B 103 -1 N TYR B 101 O PHE B 110 SHEET 5 AA4 6 TYR B 83 CYS B 90 -1 N ALA B 88 O GLY B 98 SHEET 6 AA4 6 LEU B 67 SER B 74 -1 N ARG B 68 O LEU B 89 LINK SG CYS A 24 ZN ZN A 201 1555 1555 2.36 LINK SG CYS A 27 ZN ZN A 201 1555 1555 2.31 LINK SG CYS A 90 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 93 ZN ZN A 201 1555 1555 2.31 LINK SG CYS B 24 ZN ZN B 201 1555 1555 2.34 LINK SG CYS B 27 ZN ZN B 201 1555 1555 2.31 LINK SG CYS B 90 ZN ZN B 201 1555 1555 2.34 LINK SG CYS B 93 ZN ZN B 201 1555 1555 2.31 CISPEP 1 GLN B 106 PRO B 107 0 -4.67 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 90 CYS A 93 SITE 1 AC2 12 ASN A 50 PRO A 51 PHE A 77 SER A 78 SITE 2 AC2 12 TRP A 79 TRP A 85 ILE A 87 HIS A 96 SITE 3 AC2 12 TRP A 99 TYR A 101 HOH A 379 ARG B 68 SITE 1 AC3 4 CYS B 24 CYS B 27 CYS B 90 CYS B 93 SITE 1 AC4 10 ARG A 68 ASN B 50 PRO B 51 PHE B 77 SITE 2 AC4 10 SER B 78 TRP B 79 TRP B 85 HIS B 96 SITE 3 AC4 10 TRP B 99 TYR B 101 CRYST1 31.643 52.482 59.242 90.00 95.79 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.031603 0.000000 0.003202 0.00000 SCALE2 0.000000 0.019054 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016966 0.00000