HEADER PEPTIDE BINDING PROTEIN/INHIBITOR 27-FEB-22 7U3G TITLE GID4 IN COMPLEX WITH COMPOUND 67 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSE-INDUCED DEGRADATION PROTEIN 4 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VACUOLAR IMPORT AND DEGRADATION PROTEIN 24 HOMOLOG; COMPND 5 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: GID4, C17ORF39, VID24; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS COMPLEX, INHIBITOR, PROTEIN DEGRADATION, PEPTIDE BINDING PROTEIN, KEYWDS 2 PEPTIDE BINDING PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.K.CHANA,F.SICHERI REVDAT 3 18-OCT-23 7U3G 1 REMARK REVDAT 2 26-OCT-22 7U3G 1 JRNL REVDAT 1 05-OCT-22 7U3G 0 JRNL AUTH C.K.CHANA,P.MAISONNEUVE,G.POSTERNAK,N.G.A.GRINBERG, JRNL AUTH 2 J.POIRSON,S.M.ONA,D.F.CECCARELLI,P.MADER,D.J.ST-CYR,V.PAU, JRNL AUTH 3 I.KURINOV,X.TANG,D.DENG,W.CUI,W.SU,L.KUAI,R.SOLL,M.TYERS, JRNL AUTH 4 H.L.ROST,R.A.BATEY,M.TAIPALE,A.C.GINGRAS,F.SICHERI JRNL TITL DISCOVERY AND STRUCTURAL CHARACTERIZATION OF SMALL MOLECULE JRNL TITL 2 BINDERS OF THE HUMAN CTLH E3 LIGASE SUBUNIT GID4. JRNL REF J.MED.CHEM. V. 65 12725 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36117290 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00509 REMARK 2 REMARK 2 RESOLUTION. 2.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 7213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.420 REMARK 3 FREE R VALUE TEST SET COUNT : 319 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 49.2780 - 2.8274 0.99 3506 170 0.2001 0.2286 REMARK 3 2 2.8274 - 2.2442 0.98 3388 149 0.2455 0.2871 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.20 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3938 -5.8728 -15.3485 REMARK 3 T TENSOR REMARK 3 T11: 0.3711 T22: 0.3908 REMARK 3 T33: 0.2978 T12: -0.0462 REMARK 3 T13: -0.0378 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 4.3233 L22: 6.0521 REMARK 3 L33: 4.6554 L12: -1.4182 REMARK 3 L13: 1.5926 L23: -0.9544 REMARK 3 S TENSOR REMARK 3 S11: -0.0218 S12: 0.2089 S13: -0.0998 REMARK 3 S21: -0.6900 S22: 0.1577 S23: 0.4520 REMARK 3 S31: 0.0932 S32: -0.3121 S33: -0.0973 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 221 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7913 1.7407 -4.7414 REMARK 3 T TENSOR REMARK 3 T11: 0.3295 T22: 0.3240 REMARK 3 T33: 0.4232 T12: 0.0001 REMARK 3 T13: 0.0081 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 7.0506 L22: 8.3220 REMARK 3 L33: 3.0507 L12: -2.1422 REMARK 3 L13: -0.6108 L23: 1.7723 REMARK 3 S TENSOR REMARK 3 S11: -0.1345 S12: -0.0141 S13: 0.0377 REMARK 3 S21: 0.0756 S22: 0.1790 S23: -1.0536 REMARK 3 S31: -0.3715 S32: 0.3912 S33: -0.1580 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 222 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0871 -1.1257 -10.5826 REMARK 3 T TENSOR REMARK 3 T11: 0.3236 T22: 0.2326 REMARK 3 T33: 0.2079 T12: -0.0088 REMARK 3 T13: -0.0084 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 4.8599 L22: 4.7946 REMARK 3 L33: 5.2618 L12: -0.2811 REMARK 3 L13: 0.0143 L23: 1.3403 REMARK 3 S TENSOR REMARK 3 S11: 0.0569 S12: 0.2852 S13: -0.0133 REMARK 3 S21: -0.2602 S22: 0.0912 S23: 0.0783 REMARK 3 S31: -0.1734 S32: -0.1196 S33: -0.0831 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 7U3G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1000263390. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20210205 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20210205 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7218 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 49.278 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.379 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.35 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.420 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 6CCR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1 M BIS-TRIS, 0.2 M REMARK 280 AMMONIUM ACETATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 20.13000 REMARK 290 SMTRY3 2 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 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 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 123 REMARK 465 GLY A 163 REMARK 465 LEU A 164 REMARK 465 SER A 214 REMARK 465 PHE A 215 REMARK 465 ASN A 216 REMARK 465 SER A 217 REMARK 465 ASP A 218 REMARK 465 ASP A 219 REMARK 465 HIS A 244 REMARK 465 THR A 245 REMARK 465 ILE A 246 REMARK 465 LYS A 247 REMARK 465 ASP A 248 REMARK 465 ILE A 249 REMARK 465 SER A 250 REMARK 465 GLY A 251 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 SER A 124 OG REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 LYS A 133 CD CE NZ REMARK 470 SER A 134 OG REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 SER A 138 OG REMARK 470 TYR A 139 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS A 147 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 470 GLU A 167 CG CD OE1 OE2 REMARK 470 TYR A 168 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 GLU A 195 CG CD OE1 OE2 REMARK 470 ASP A 196 CG OD1 OD2 REMARK 470 ARG A 199 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 PHE A 220 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 GLU A 224 CG CD OE1 OE2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 SER A 253 OG REMARK 470 ARG A 276 CD NE CZ NH1 NH2 REMARK 470 SER A 278 OG REMARK 470 GLU A 279 CG CD OE1 OE2 DBREF 7U3G A 124 289 UNP Q8IVV7 GID4_HUMAN 124 289 SEQADV 7U3G GLY A 123 UNP Q8IVV7 EXPRESSION TAG SEQRES 1 A 167 GLY SER GLY SER LYS PHE ARG GLY HIS GLN LYS SER LYS SEQRES 2 A 167 GLY ASN SER TYR ASP VAL GLU VAL VAL LEU GLN HIS VAL SEQRES 3 A 167 ASP THR GLY ASN SER TYR LEU CYS GLY TYR LEU LYS ILE SEQRES 4 A 167 LYS GLY LEU THR GLU GLU TYR PRO THR LEU THR THR PHE SEQRES 5 A 167 PHE GLU GLY GLU ILE ILE SER LYS LYS HIS PRO PHE LEU SEQRES 6 A 167 THR ARG LYS TRP ASP ALA ASP GLU ASP VAL ASP ARG LYS SEQRES 7 A 167 HIS TRP GLY LYS PHE LEU ALA PHE TYR GLN TYR ALA LYS SEQRES 8 A 167 SER PHE ASN SER ASP ASP PHE ASP TYR GLU GLU LEU LYS SEQRES 9 A 167 ASN GLY ASP TYR VAL PHE MET ARG TRP LYS GLU GLN PHE SEQRES 10 A 167 LEU VAL PRO ASP HIS THR ILE LYS ASP ILE SER GLY ALA SEQRES 11 A 167 SER PHE ALA GLY PHE TYR TYR ILE CYS PHE GLN LYS SER SEQRES 12 A 167 ALA ALA SER ILE GLU GLY TYR TYR TYR HIS ARG SER SER SEQRES 13 A 167 GLU TRP TYR GLN SER LEU ASN LEU THR HIS VAL HET L6F A 301 17 HETNAM L6F (1R)-1-PHENYL-1,2,3,4-TETRAHYDROISOQUINOLIN-5-AMINE FORMUL 2 L6F C15 H16 N2 FORMUL 3 HOH *20(H2 O) HELIX 1 AA1 THR A 150 ASN A 152 5 3 HELIX 2 AA2 ASP A 194 GLY A 203 1 10 HELIX 3 AA3 LYS A 204 TYR A 211 5 8 HELIX 4 AA4 ASP A 221 ASN A 227 1 7 SHEET 1 AA1 9 LYS A 127 LYS A 133 0 SHEET 2 AA1 9 SER A 138 ASP A 149 -1 O VAL A 143 N PHE A 128 SHEET 3 AA1 9 TYR A 154 ILE A 161 -1 O TYR A 154 N ASP A 149 SHEET 4 AA1 9 LEU A 171 ILE A 179 -1 O GLY A 177 N LEU A 155 SHEET 5 AA1 9 TYR A 230 LEU A 240 -1 O GLN A 238 N PHE A 174 SHEET 6 AA1 9 PHE A 257 GLN A 263 -1 O ILE A 260 N MET A 233 SHEET 7 AA1 9 SER A 268 TYR A 274 -1 O GLU A 270 N CYS A 261 SHEET 8 AA1 9 GLN A 282 HIS A 288 -1 O LEU A 284 N GLY A 271 SHEET 9 AA1 9 LYS A 127 LYS A 133 -1 N HIS A 131 O ASN A 285 CRYST1 38.390 40.260 51.700 90.00 107.61 90.00 P 1 21 1 2 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 0.026048 0.000000 0.008267 0.00000 SCALE2 0.000000 0.024839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020293 0.00000