HEADER PEPTIDE BINDING PROTEIN/INHIBITOR 27-FEB-22 7U3L TITLE GID4 IN COMPLEX WITH COMPOUND 91 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 7U3L 1 REMARK REVDAT 2 26-OCT-22 7U3L 1 JRNL REVDAT 1 05-OCT-22 7U3L 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 7014 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 352 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 35.6490 - 3.3098 0.99 2263 120 0.1975 0.2192 REMARK 3 2 3.3098 - 2.6273 0.99 2201 115 0.2742 0.2655 REMARK 3 3 2.6273 - 2.2953 0.99 2198 117 0.3269 0.3670 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.77 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): 3.2942 7.1881 -16.3328 REMARK 3 T TENSOR REMARK 3 T11: 0.2689 T22: 0.2364 REMARK 3 T33: 0.3519 T12: -0.0652 REMARK 3 T13: -0.0460 T23: -0.0453 REMARK 3 L TENSOR REMARK 3 L11: 6.2151 L22: 3.6514 REMARK 3 L33: 4.1008 L12: -1.8814 REMARK 3 L13: -3.0361 L23: -1.4253 REMARK 3 S TENSOR REMARK 3 S11: 0.1727 S12: 0.2543 S13: 0.4163 REMARK 3 S21: -0.1369 S22: -0.0972 S23: -0.2859 REMARK 3 S31: -0.1044 S32: 0.0403 S33: -0.0975 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.6258 -0.8687 -4.1658 REMARK 3 T TENSOR REMARK 3 T11: 0.4786 T22: 0.2021 REMARK 3 T33: 0.4265 T12: 0.0090 REMARK 3 T13: 0.0633 T23: 0.0931 REMARK 3 L TENSOR REMARK 3 L11: 5.7852 L22: 4.4004 REMARK 3 L33: 2.2888 L12: -3.7752 REMARK 3 L13: 1.7845 L23: -0.3450 REMARK 3 S TENSOR REMARK 3 S11: -0.1027 S12: -0.2518 S13: -0.1230 REMARK 3 S21: 0.4694 S22: 0.3762 S23: 0.7105 REMARK 3 S31: 0.0793 S32: -0.2097 S33: -0.3003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 215 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9897 2.6174 -10.4834 REMARK 3 T TENSOR REMARK 3 T11: 0.3932 T22: 0.1611 REMARK 3 T33: 0.3865 T12: -0.0217 REMARK 3 T13: 0.0163 T23: 0.0406 REMARK 3 L TENSOR REMARK 3 L11: 2.4846 L22: 3.0740 REMARK 3 L33: 5.1651 L12: -0.7914 REMARK 3 L13: 1.5080 L23: 1.3900 REMARK 3 S TENSOR REMARK 3 S11: -0.0005 S12: 0.0342 S13: 0.0361 REMARK 3 S21: 0.0311 S22: -0.0632 S23: -0.1221 REMARK 3 S31: 0.1857 S32: -0.0273 S33: 0.1001 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 7U3L 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_1000263399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.97911 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 20210322 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20210322 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7057 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 35.649 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.370 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.41 REMARK 200 R MERGE FOR SHELL (I) : 0.96800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 (%): 38.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M SODIUM FLUORIDE, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, 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 20.27900 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 LEU A 164 REMARK 465 LYS A 247 REMARK 465 ASP A 248 REMARK 465 ILE A 249 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 CD CE NZ REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 SER A 134 OG REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 GLN A 146 CD OE1 NE2 REMARK 470 HIS A 147 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 160 CE NZ REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 470 TYR A 168 CE1 CE2 CZ OH REMARK 470 LEU A 171 CD1 CD2 REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 LYS A 190 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 200 CD CE NZ REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 SER A 214 OG REMARK 470 ASN A 216 CG OD1 ND2 REMARK 470 SER A 217 OG REMARK 470 ASP A 219 CG OD1 OD2 REMARK 470 ASP A 221 CG OD1 OD2 REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 ILE A 246 CG1 CG2 CD1 REMARK 470 SER A 250 OG REMARK 470 ARG A 276 CD NE CZ NH1 NH2 REMARK 470 TRP A 280 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 280 CZ3 CH2 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 ASN A 216 -4.00 72.27 REMARK 500 HIS A 244 -168.98 -161.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 7U3L A 124 289 UNP Q8IVV7 GID4_HUMAN 124 289 SEQADV 7U3L 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 L4X A 301 38 HET GOL A 302 6 HETNAM L4X NALPHA-{(2R,4E)-2-[(N-BENZYLGLYCYL)AMINO]-5-PHENYLPENT- HETNAM 2 L4X 4-ENOYL}-N,4-DIMETHYL-L-PHENYLALANINAMIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 L4X C31 H36 N4 O3 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *30(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 PHE A 215 5 12 HELIX 4 AA4 ASP A 221 LYS A 226 1 6 HELIX 5 AA5 SER A 250 ALA A 255 5 6 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 LYS A 162 -1 O LYS A 160 N GLU A 142 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 TYR A 274 N PHE A 257 SHEET 8 AA1 9 SER A 283 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 37.914 40.558 54.257 90.00 109.90 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 0.026375 0.000000 0.009549 0.00000 SCALE2 0.000000 0.024656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019602 0.00000