HEADER LIGASE 17-JAN-24 8RQA TITLE CRYSTAL STRUCTURE OF CRBN-MIDI IN COMPLEX WITH LENALIDOMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CEREBLON; COMPND 3 CHAIN: A; COMPND 4 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 KEYWDS E3 LIGASE, PROTAC, TPD, MOLECULAR GLUE, TARGETED PROTEIN DEGRADATION, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.J.RUTTER,A.KROUPOVA,D.ZOLLMAN,A.CIULLI REVDAT 2 30-OCT-24 8RQA 1 JRNL REVDAT 1 25-SEP-24 8RQA 0 JRNL AUTH A.KROUPOVA,V.A.SPITERI,Z.J.RUTTER,H.FURIHATA,D.DARREN, JRNL AUTH 2 S.RAMACHANDRAN,S.CHAKRABORTI,K.HAUBRICH,J.PETHE,D.GONZALES, JRNL AUTH 3 A.J.WIJAYA,M.RODRIGUEZ-RIOS,M.STURBAUT,D.M.LYNCH,W.FARNABY, JRNL AUTH 4 M.A.NAKASONE,D.ZOLLMAN,A.CIULLI JRNL TITL DESIGN OF A CEREBLON CONSTRUCT FOR CRYSTALLOGRAPHIC AND JRNL TITL 2 BIOPHYSICAL STUDIES OF PROTEIN DEGRADERS. JRNL REF NAT COMMUN V. 15 8885 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39406745 JRNL DOI 10.1038/S41467-024-52871-9 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 13023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.302 REMARK 3 R VALUE (WORKING SET) : 0.300 REMARK 3 FREE R VALUE : 0.342 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 660 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 45.5400 - 4.2800 1.00 2603 144 0.2573 0.2724 REMARK 3 2 4.2700 - 3.3900 1.00 2472 157 0.2923 0.3752 REMARK 3 3 3.3900 - 2.9600 1.00 2502 121 0.3388 0.4198 REMARK 3 4 2.9600 - 2.6900 1.00 2465 120 0.3603 0.4191 REMARK 3 5 2.6900 - 2.5000 0.94 2321 118 0.4078 0.4304 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.446 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.44 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 : 0.015 2337 REMARK 3 ANGLE : 1.688 3199 REMARK 3 CHIRALITY : 0.084 377 REMARK 3 PLANARITY : 0.012 409 REMARK 3 DIHEDRAL : 18.309 795 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 8RQA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6199 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13030 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0460 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.78200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.170 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8, 20 % W/V PEG 4000, REMARK 280 1.2 % MYO-INOSITOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 74.12600 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 74.12600 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 25.99450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.85850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.99450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.85850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 74.12600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.99450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.85850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.12600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.99450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.85850 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 604 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 SER A 40 REMARK 465 ALA A 41 REMARK 465 LYS A 42 REMARK 465 LYS A 43 REMARK 465 PRO A 44 REMARK 465 ASN A 45 REMARK 465 ILE A 46 REMARK 465 ILE A 47 REMARK 465 ASN A 48 REMARK 465 PHE A 49 REMARK 465 GLU A 169 REMARK 465 LEU A 170 REMARK 465 ARG A 171 REMARK 465 THR A 172 REMARK 465 GLN A 173 REMARK 465 SER A 174 REMARK 465 GLY A 188 REMARK 465 SER A 189 REMARK 465 GLY A 190 REMARK 465 ASP A 249 REMARK 465 LYS A 269 REMARK 465 ASP A 270 REMARK 465 ILE A 426 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 ASP A 63 CG OD1 OD2 REMARK 470 MET A 64 SD CE REMARK 470 GLU A 65 OE2 REMARK 470 GLU A 66 CG CD OE1 OE2 REMARK 470 PHE A 67 CG CD1 CD2 CE1 CE2 CZ REMARK 470 HIS A 68 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 70 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 73 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 76 CG OD1 OD2 REMARK 470 ILE A 78 CG1 CG2 CD1 REMARK 470 GLN A 86 CG CD OE1 NE2 REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 ARG A 145 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 ASP A 175 CG OD1 OD2 REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 GLN A 183 CD OE1 NE2 REMARK 470 GLU A 187 CG CD OE1 OE2 REMARK 470 GLU A 251 CG CD OE1 OE2 REMARK 470 LYS A 258 CG CD CE NZ REMARK 470 ARG A 262 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 266 CG CD OE1 OE2 REMARK 470 ASN A 267 CG OD1 ND2 REMARK 470 ASP A 271 CG OD1 OD2 REMARK 470 ASP A 291 CG OD1 OD2 REMARK 470 ASP A 302 CG OD1 OD2 REMARK 470 ILE A 305 CG1 CG2 CD1 REMARK 470 CYS A 318 SG REMARK 470 THR A 319 OG1 CG2 REMARK 470 CYS A 322 SG REMARK 470 LYS A 324 CG CD CE NZ REMARK 470 GLU A 328 CG CD OE1 OE2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 LYS A 334 CG CD CE NZ REMARK 470 ARG A 342 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 343 CG CD OE1 OE2 REMARK 470 LYS A 364 CG CD CE NZ REMARK 470 CYS A 366 SG REMARK 470 LEU A 368 CG CD1 CD2 REMARK 470 ARG A 373 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 377 CG CD OE1 OE2 REMARK 470 GLN A 390 CG CD OE1 NE2 REMARK 470 LYS A 392 CG CD CE NZ REMARK 470 ILE A 393 CG1 CG2 CD1 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 THR A 405 OG1 CG2 REMARK 470 LYS A 406 CG CD CE NZ REMARK 470 LYS A 407 CG CD CE NZ REMARK 470 MET A 409 CG SD CE REMARK 470 LYS A 413 CG CD CE NZ REMARK 470 ILE A 423 CG1 CG2 CD1 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 ASP A 63 -127.19 55.25 REMARK 500 GLU A 65 112.74 81.43 REMARK 500 ASN A 116 -106.64 -86.10 REMARK 500 VAL A 128 -53.09 67.29 REMARK 500 ARG A 162 -62.11 -122.15 REMARK 500 GLN A 178 114.32 77.94 REMARK 500 THR A 319 -130.57 -149.06 REMARK 500 THR A 332 -176.79 -170.63 REMARK 500 CYS A 391 126.50 -39.68 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 69.6 REMARK 620 3 CYS A 391 SG 107.7 121.9 REMARK 620 4 CYS A 394 SG 134.4 121.0 101.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8RQ1 RELATED DB: PDB REMARK 900 APO CRBN MIDI REMARK 900 RELATED ID: 8RQ8 RELATED DB: PDB REMARK 900 CRBN MIDI MEZIGDOMIDE DBREF 8RQA A 41 187 UNP Q96SW2 CRBN_HUMAN 41 187 DBREF 8RQA A 249 426 UNP Q96SW2 CRBN_HUMAN 249 426 SEQADV 8RQA SER A 40 UNP Q96SW2 EXPRESSION TAG SEQADV 8RQA ILE A 78 UNP Q96SW2 CYS 78 ENGINEERED MUTATION SEQADV 8RQA VAL A 92 UNP Q96SW2 ILE 92 ENGINEERED MUTATION SEQADV 8RQA ASN A 116 UNP Q96SW2 LYS 116 ENGINEERED MUTATION SEQADV 8RQA GLU A 134 UNP Q96SW2 GLN 134 ENGINEERED MUTATION SEQADV 8RQA GLY A 188 UNP Q96SW2 LINKER SEQADV 8RQA SER A 189 UNP Q96SW2 LINKER SEQADV 8RQA GLY A 190 UNP Q96SW2 LINKER SEQADV 8RQA TRP A 283 UNP Q96SW2 ARG 283 ENGINEERED MUTATION SEQADV 8RQA ASN A 287 UNP Q96SW2 CYS 287 ENGINEERED MUTATION SEQADV 8RQA SER A 293 UNP Q96SW2 VAL 293 ENGINEERED MUTATION SEQADV 8RQA ASP A 302 UNP Q96SW2 GLY 302 ENGINEERED MUTATION SEQADV 8RQA ARG A 342 UNP Q96SW2 LEU 342 ENGINEERED MUTATION SEQADV 8RQA GLU A 343 UNP Q96SW2 CYS 343 ENGINEERED MUTATION SEQADV 8RQA ILE A 359 UNP Q96SW2 THR 359 ENGINEERED MUTATION SEQADV 8RQA ILE A 423 UNP Q96SW2 LEU 423 ENGINEERED MUTATION SEQRES 1 A 329 SER ALA LYS LYS PRO ASN ILE ILE ASN PHE ASP THR SER SEQRES 2 A 329 LEU PRO THR SER HIS THR TYR LEU GLY ALA ASP MET GLU SEQRES 3 A 329 GLU PHE HIS GLY ARG THR LEU HIS ASP ASP ASP SER ILE SEQRES 4 A 329 GLN VAL ILE PRO VAL LEU PRO GLN VAL MET MET ILE LEU SEQRES 5 A 329 VAL PRO GLY GLN THR LEU PRO LEU GLN LEU PHE HIS PRO SEQRES 6 A 329 GLN GLU VAL SER MET VAL ARG ASN LEU ILE GLN ASN ASP SEQRES 7 A 329 ARG THR PHE ALA VAL LEU ALA TYR SER ASN VAL GLN GLU SEQRES 8 A 329 ARG GLU ALA GLU PHE GLY THR THR ALA GLU ILE TYR ALA SEQRES 9 A 329 TYR ARG GLU GLU GLN ASP PHE GLY ILE GLU ILE VAL LYS SEQRES 10 A 329 VAL LYS ALA ILE GLY ARG GLN ARG PHE LYS VAL LEU GLU SEQRES 11 A 329 LEU ARG THR GLN SER ASP GLY ILE GLN GLN ALA LYS VAL SEQRES 12 A 329 GLN ILE LEU PRO GLU GLY SER GLY ASP ALA GLU THR LEU SEQRES 13 A 329 MET ASP ARG ILE LYS LYS GLN LEU ARG GLU TRP ASP GLU SEQRES 14 A 329 ASN LEU LYS ASP ASP SER LEU PRO SER ASN PRO ILE ASP SEQRES 15 A 329 PHE SER TYR TRP VAL ALA ALA ASN LEU PRO ILE ASP ASP SEQRES 16 A 329 SER LEU ARG ILE GLN LEU LEU LYS ILE ASP SER ALA ILE SEQRES 17 A 329 GLN ARG LEU ARG CYS GLU LEU ASP ILE MET ASN LYS CYS SEQRES 18 A 329 THR SER LEU CYS CYS LYS GLN CYS GLN GLU THR GLU ILE SEQRES 19 A 329 THR THR LYS ASN GLU ILE PHE SER LEU SER ARG GLU GLY SEQRES 20 A 329 PRO MET ALA ALA TYR VAL ASN PRO HIS GLY TYR VAL HIS SEQRES 21 A 329 GLU ILE LEU THR VAL TYR LYS ALA CYS ASN LEU ASN LEU SEQRES 22 A 329 ILE GLY ARG PRO SER THR GLU HIS SER TRP PHE PRO GLY SEQRES 23 A 329 TYR ALA TRP THR VAL ALA GLN CYS LYS ILE CYS ALA SER SEQRES 24 A 329 HIS ILE GLY TRP LYS PHE THR ALA THR LYS LYS ASP MET SEQRES 25 A 329 SER PRO GLN LYS PHE TRP GLY LEU THR ARG SER ALA LEU SEQRES 26 A 329 ILE PRO THR ILE HET LVY A 501 19 HET ZN A 502 1 HETNAM LVY S-LENALIDOMIDE HETNAM ZN ZINC ION FORMUL 2 LVY C13 H13 N3 O3 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *5(H2 O) HELIX 1 AA1 THR A 51 SER A 56 1 6 HELIX 2 AA2 HIS A 103 ASN A 116 1 14 HELIX 3 AA3 GLU A 251 GLU A 263 1 13 HELIX 4 AA4 ASN A 276 LEU A 288 1 13 HELIX 5 AA5 ASP A 291 ILE A 301 1 11 HELIX 6 AA6 SER A 303 LYS A 317 1 15 HELIX 7 AA7 ASN A 335 ILE A 337 5 3 SHEET 1 AA1 5 ILE A 78 PRO A 82 0 SHEET 2 AA1 5 GLN A 179 ILE A 184 -1 O VAL A 182 N GLN A 79 SHEET 3 AA1 5 ILE A 152 LEU A 168 -1 N LYS A 166 O GLN A 183 SHEET 4 AA1 5 ALA A 133 ILE A 141 -1 N THR A 138 O GLN A 163 SHEET 5 AA1 5 THR A 119 TYR A 125 -1 N PHE A 120 O ALA A 139 SHEET 1 AA2 3 THR A 96 LEU A 101 0 SHEET 2 AA2 3 ILE A 152 LEU A 168 -1 O ALA A 159 N LEU A 97 SHEET 3 AA2 3 GLU A 147 ASP A 149 -1 N ASP A 149 O ILE A 152 SHEET 1 AA3 3 GLU A 330 THR A 333 0 SHEET 2 AA3 3 SER A 320 CYS A 323 -1 N LEU A 321 O THR A 332 SHEET 3 AA3 3 LEU A 422 PRO A 424 -1 O ILE A 423 N CYS A 322 SHEET 1 AA4 6 MET A 346 VAL A 350 0 SHEET 2 AA4 6 VAL A 356 VAL A 362 -1 O HIS A 357 N TYR A 349 SHEET 3 AA4 6 TRP A 415 THR A 418 -1 O TRP A 415 N VAL A 362 SHEET 4 AA4 6 HIS A 397 ALA A 404 -1 N TRP A 400 O GLY A 416 SHEET 5 AA4 6 TYR A 384 CYS A 391 -1 N ALA A 389 O GLY A 399 SHEET 6 AA4 6 LEU A 368 SER A 375 -1 N SER A 375 O TRP A 386 LINK SG CYS A 323 ZN ZN A 502 1555 1555 2.37 LINK SG CYS A 326 ZN ZN A 502 1555 1555 2.40 LINK SG CYS A 391 ZN ZN A 502 1555 1555 2.44 LINK SG CYS A 394 ZN ZN A 502 1555 1555 2.96 CISPEP 1 SER A 410 PRO A 411 0 -19.76 CRYST1 51.989 95.717 148.252 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 0.019235 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006745 0.00000