HEADER METAL BINDING PROTEIN 25-MAR-20 7BQU TITLE CEREBLON IN COMPLEX WITH SALL4 AND (S)-THALIDOMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CEREBLON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SAL-LIKE PROTEIN 4; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: ZINC FINGER PROTEIN 797,ZINC FINGER PROTEIN SALL4; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CRBN, AD-006; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: SALL4, ZNF797; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZINC FINGER, E3 UBIQUITIN LIGASE, COMPLEX, THALIDOMIDE, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.FURIHATA,Y.MIYAUCHI,A.ASANO,M.TANOKURA,T.MIYAKAWA REVDAT 3 29-NOV-23 7BQU 1 REMARK REVDAT 2 14-OCT-20 7BQU 1 JRNL REVDAT 1 26-AUG-20 7BQU 0 JRNL AUTH H.FURIHATA,S.YAMANAKA,T.HONDA,Y.MIYAUCHI,A.ASANO,N.SHIBATA, JRNL AUTH 2 M.TANOKURA,T.SAWASAKI,T.MIYAKAWA JRNL TITL STRUCTURAL BASES OF IMID SELECTIVITY THAT EMERGES BY JRNL TITL 2 5-HYDROXYTHALIDOMIDE. JRNL REF NAT COMMUN V. 11 4578 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32929090 JRNL DOI 10.1038/S41467-020-18488-4 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX VER 1.15.1_3469 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 561 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.6740 - 3.0157 1.00 2919 144 0.1697 0.2269 REMARK 3 2 3.0157 - 2.3938 1.00 2780 149 0.2134 0.2553 REMARK 3 3 2.3938 - 2.0913 1.00 2748 138 0.2099 0.2385 REMARK 3 4 2.0913 - 1.9001 1.00 2782 130 0.2203 0.2283 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 1102 REMARK 3 ANGLE : 1.375 1497 REMARK 3 CHIRALITY : 0.046 163 REMARK 3 PLANARITY : 0.011 182 REMARK 3 DIHEDRAL : 7.452 635 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7BQU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11808 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 43.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER VER 1.15.1_3469 REMARK 200 STARTING MODEL: 4TZ4, 5YJ0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 4000, 0.1 M SODIUM ACETATE (PH REMARK 280 5.5), 0.1 M MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.99300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.99300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.48100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.35900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.48100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.35900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.99300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.48100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.35900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 21.99300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.48100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.35900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 642 LIES ON A SPECIAL POSITION. 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 GLY A 313 REMARK 465 PRO A 314 REMARK 465 LEU A 315 REMARK 465 GLY A 316 REMARK 465 SER A 317 REMARK 465 GLY B 405 REMARK 465 PRO B 406 REMARK 465 LEU B 407 REMARK 465 GLY B 408 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 NZ LYS A 413 O HOH A 601 1.62 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 OE2 GLU A 336 O HOH A 601 3656 1.73 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 ARG A 373 CZ ARG A 373 NH1 0.098 REMARK 500 ARG A 373 CZ ARG A 373 NH2 0.082 REMARK 500 CYS A 394 CB CYS A 394 SG -0.109 REMARK 500 SER B 409 CB SER B 409 OG 0.083 REMARK 500 ARG B 418 NE ARG B 418 CZ -0.084 REMARK 500 ARG B 418 CZ ARG B 418 NH1 -0.089 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 373 NH1 - CZ - NH2 ANGL. DEV. = 18.9 DEGREES REMARK 500 ARG A 373 NE - CZ - NH1 ANGL. DEV. = -9.2 DEGREES REMARK 500 ARG A 373 NE - CZ - NH2 ANGL. DEV. = -10.1 DEGREES REMARK 500 SER B 409 N - CA - CB ANGL. DEV. = -11.9 DEGREES REMARK 500 ARG B 418 NE - CZ - NH1 ANGL. DEV. = -10.6 DEGREES REMARK 500 ARG B 418 NE - CZ - NH2 ANGL. DEV. = 4.5 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 GLN A 327 -37.75 78.82 REMARK 500 PRO A 352 4.94 -69.54 REMARK 500 ALA A 395 14.90 56.41 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 ARG A 373 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER B 409 -13.73 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 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 323 SG REMARK 620 2 CYS A 326 SG 118.8 REMARK 620 3 CYS A 391 SG 116.8 107.7 REMARK 620 4 CYS A 394 SG 98.7 115.6 97.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 412 SG REMARK 620 2 CYS B 415 SG 105.5 REMARK 620 3 HIS B 428 NE2 106.8 98.1 REMARK 620 4 HIS B 432 NE2 107.1 130.5 106.8 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 EF2 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 501 DBREF 7BQU A 318 426 UNP Q96SW2 CRBN_HUMAN 318 426 DBREF 7BQU B 410 432 UNP Q9UJQ4 SALL4_HUMAN 410 432 SEQADV 7BQU GLY A 313 UNP Q96SW2 EXPRESSION TAG SEQADV 7BQU PRO A 314 UNP Q96SW2 EXPRESSION TAG SEQADV 7BQU LEU A 315 UNP Q96SW2 EXPRESSION TAG SEQADV 7BQU GLY A 316 UNP Q96SW2 EXPRESSION TAG SEQADV 7BQU SER A 317 UNP Q96SW2 EXPRESSION TAG SEQADV 7BQU SER A 366 UNP Q96SW2 CYS 366 ENGINEERED MUTATION SEQADV 7BQU GLY B 405 UNP Q9UJQ4 EXPRESSION TAG SEQADV 7BQU PRO B 406 UNP Q9UJQ4 EXPRESSION TAG SEQADV 7BQU LEU B 407 UNP Q9UJQ4 EXPRESSION TAG SEQADV 7BQU GLY B 408 UNP Q9UJQ4 EXPRESSION TAG SEQADV 7BQU SER B 409 UNP Q9UJQ4 EXPRESSION TAG SEQRES 1 A 114 GLY PRO LEU GLY SER CYS THR SER LEU CYS CYS LYS GLN SEQRES 2 A 114 CYS GLN GLU THR GLU ILE THR THR LYS ASN GLU ILE PHE SEQRES 3 A 114 SER LEU SER LEU CYS GLY PRO MET ALA ALA TYR VAL ASN SEQRES 4 A 114 PRO HIS GLY TYR VAL HIS GLU THR LEU THR VAL TYR LYS SEQRES 5 A 114 ALA SER ASN LEU ASN LEU ILE GLY ARG PRO SER THR GLU SEQRES 6 A 114 HIS SER TRP PHE PRO GLY TYR ALA TRP THR VAL ALA GLN SEQRES 7 A 114 CYS LYS ILE CYS ALA SER HIS ILE GLY TRP LYS PHE THR SEQRES 8 A 114 ALA THR LYS LYS ASP MET SER PRO GLN LYS PHE TRP GLY SEQRES 9 A 114 LEU THR ARG SER ALA LEU LEU PRO THR ILE SEQRES 1 B 28 GLY PRO LEU GLY SER PHE VAL CYS SER VAL CYS GLY HIS SEQRES 2 B 28 ARG PHE THR THR LYS GLY ASN LEU LYS VAL HIS PHE HIS SEQRES 3 B 28 ARG HIS HET EF2 A 501 19 HET ZN A 502 1 HET ZN B 501 1 HETNAM EF2 S-THALIDOMIDE HETNAM ZN ZINC ION FORMUL 3 EF2 C13 H10 N2 O4 FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *48(H2 O) HELIX 1 AA1 ASN A 335 ILE A 337 5 3 HELIX 2 AA2 THR B 421 HIS B 432 1 12 SHEET 1 AA1 3 GLU A 330 THR A 333 0 SHEET 2 AA1 3 SER A 320 CYS A 323 -1 N LEU A 321 O ILE A 331 SHEET 3 AA1 3 LEU A 422 LEU A 423 -1 O LEU A 423 N CYS A 322 SHEET 1 AA2 6 MET A 346 VAL A 350 0 SHEET 2 AA2 6 VAL A 356 VAL A 362 -1 O HIS A 357 N TYR A 349 SHEET 3 AA2 6 LYS A 413 THR A 418 -1 O LEU A 417 N LEU A 360 SHEET 4 AA2 6 HIS A 397 ALA A 404 -1 N PHE A 402 O PHE A 414 SHEET 5 AA2 6 TYR A 384 CYS A 391 -1 N THR A 387 O LYS A 401 SHEET 6 AA2 6 LEU A 368 SER A 375 -1 N ASN A 369 O GLN A 390 SHEET 1 AA3 2 PHE B 410 VAL B 411 0 SHEET 2 AA3 2 ARG B 418 PHE B 419 -1 O PHE B 419 N PHE B 410 LINK SG CYS A 323 ZN ZN A 502 1555 1555 2.31 LINK SG CYS A 326 ZN ZN A 502 1555 1555 2.36 LINK SG CYS A 391 ZN ZN A 502 1555 1555 2.21 LINK SG CYS A 394 ZN ZN A 502 1555 1555 2.24 LINK SG CYS B 412 ZN ZN B 501 1555 1555 2.21 LINK SG CYS B 415 ZN ZN B 501 1555 1555 2.16 LINK NE2 HIS B 428 ZN ZN B 501 1555 1555 2.07 LINK NE2 HIS B 432 ZN ZN B 501 1555 1555 1.88 CISPEP 1 SER A 410 PRO A 411 0 -0.79 CISPEP 2 LEU A 423 PRO A 424 0 2.34 SITE 1 AC1 14 ASN A 351 PRO A 352 HIS A 353 GLU A 377 SITE 2 AC1 14 HIS A 378 SER A 379 TRP A 380 TRP A 386 SITE 3 AC1 14 PHE A 402 CYS B 412 SER B 413 VAL B 414 SITE 4 AC1 14 CYS B 415 GLY B 416 SITE 1 AC2 4 CYS A 323 CYS A 326 CYS A 391 CYS A 394 SITE 1 AC3 4 CYS B 412 CYS B 415 HIS B 428 HIS B 432 CRYST1 70.962 92.718 43.986 90.00 90.00 90.00 C 2 2 21 8 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 0.014092 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022735 0.00000