HEADER PEPTIDE BINDING PROTEIN/INHIBITOR 27-FEB-22 7U3I TITLE GID4 IN COMPLEX WITH COMPOUND 16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSE-INDUCED DEGRADATION PROTEIN 4 HOMOLOG; COMPND 3 CHAIN: A, B; 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 7U3I 1 REMARK REVDAT 2 26-OCT-22 7U3I 1 JRNL REVDAT 1 05-OCT-22 7U3I 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. 1.99 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 18720 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 943 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 49.1160 - 3.8073 0.95 2620 144 0.1626 0.1995 REMARK 3 2 3.8073 - 3.0221 0.95 2614 137 0.1762 0.1927 REMARK 3 3 3.0221 - 2.6401 0.93 2562 133 0.2018 0.2300 REMARK 3 4 2.6401 - 2.3987 0.95 2589 138 0.2362 0.3121 REMARK 3 5 2.3987 - 2.2268 0.95 2602 141 0.2513 0.3008 REMARK 3 6 2.2268 - 2.0955 0.89 2461 135 0.2870 0.3282 REMARK 3 7 2.0955 - 1.9910 0.85 2329 115 0.3220 0.3627 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.21 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 : 17 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.1935 -2.6540 -14.6583 REMARK 3 T TENSOR REMARK 3 T11: 0.3562 T22: 0.4195 REMARK 3 T33: 0.3670 T12: -0.0411 REMARK 3 T13: -0.1141 T23: 0.0344 REMARK 3 L TENSOR REMARK 3 L11: 4.4135 L22: 5.6124 REMARK 3 L33: 4.3384 L12: -3.3120 REMARK 3 L13: 1.4008 L23: -2.3496 REMARK 3 S TENSOR REMARK 3 S11: -0.3604 S12: 0.1385 S13: 0.2457 REMARK 3 S21: -0.4332 S22: 0.3336 S23: 0.2994 REMARK 3 S31: -0.3112 S32: -0.4582 S33: -0.0566 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.4217 -7.5913 -17.7162 REMARK 3 T TENSOR REMARK 3 T11: 0.4808 T22: 0.3180 REMARK 3 T33: 0.2963 T12: -0.0382 REMARK 3 T13: -0.0301 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 6.7035 L22: 6.1995 REMARK 3 L33: 7.4377 L12: -3.7981 REMARK 3 L13: 2.9375 L23: -1.8987 REMARK 3 S TENSOR REMARK 3 S11: 0.6376 S12: 0.8988 S13: -0.1497 REMARK 3 S21: -1.2347 S22: -0.3846 S23: 0.5215 REMARK 3 S31: 0.5351 S32: 0.1680 S33: -0.2169 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.5449 -2.3745 -9.6974 REMARK 3 T TENSOR REMARK 3 T11: 0.2866 T22: 0.4001 REMARK 3 T33: 0.7499 T12: 0.0310 REMARK 3 T13: 0.1709 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 3.9450 L22: 0.2422 REMARK 3 L33: 3.2732 L12: 0.7415 REMARK 3 L13: -0.6239 L23: 0.2205 REMARK 3 S TENSOR REMARK 3 S11: 0.0983 S12: 0.3178 S13: 0.1078 REMARK 3 S21: -0.7902 S22: 0.1021 S23: -1.2773 REMARK 3 S31: 0.2769 S32: 0.4395 S33: -0.0853 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 204 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4946 7.1633 -7.9022 REMARK 3 T TENSOR REMARK 3 T11: 0.5321 T22: 0.3593 REMARK 3 T33: 0.4893 T12: -0.0229 REMARK 3 T13: 0.0589 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 9.8926 L22: 2.3518 REMARK 3 L33: 2.1720 L12: 2.6659 REMARK 3 L13: -3.6279 L23: -1.2955 REMARK 3 S TENSOR REMARK 3 S11: -0.0628 S12: 0.5622 S13: 0.3923 REMARK 3 S21: 0.4678 S22: 0.1226 S23: -1.1007 REMARK 3 S31: -0.8748 S32: 0.0751 S33: -0.0173 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 205 THROUGH 221 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0011 3.0380 2.8263 REMARK 3 T TENSOR REMARK 3 T11: 0.4632 T22: 0.4759 REMARK 3 T33: 0.5354 T12: 0.0346 REMARK 3 T13: -0.0291 T23: -0.0687 REMARK 3 L TENSOR REMARK 3 L11: 5.4392 L22: 2.0383 REMARK 3 L33: 8.6685 L12: -2.7907 REMARK 3 L13: -2.1708 L23: -0.9490 REMARK 3 S TENSOR REMARK 3 S11: -0.2534 S12: -0.6065 S13: -0.0841 REMARK 3 S21: 0.2310 S22: 0.8712 S23: -0.9729 REMARK 3 S31: 0.2719 S32: 0.8787 S33: -0.5609 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 222 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.9626 -5.7907 4.9002 REMARK 3 T TENSOR REMARK 3 T11: 0.6922 T22: 0.6914 REMARK 3 T33: 0.5153 T12: 0.1087 REMARK 3 T13: -0.0324 T23: 0.0866 REMARK 3 L TENSOR REMARK 3 L11: 5.1590 L22: 5.2350 REMARK 3 L33: 8.1450 L12: -5.0596 REMARK 3 L13: -0.8708 L23: 2.4112 REMARK 3 S TENSOR REMARK 3 S11: -0.6516 S12: -2.5428 S13: -0.4066 REMARK 3 S21: 1.3089 S22: 1.2954 S23: -0.3217 REMARK 3 S31: 0.0653 S32: 1.4206 S33: -0.4804 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 230 THROUGH 240 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5991 -4.6591 -13.1193 REMARK 3 T TENSOR REMARK 3 T11: 0.3633 T22: 0.2829 REMARK 3 T33: 0.3175 T12: 0.0182 REMARK 3 T13: 0.0450 T23: 0.0308 REMARK 3 L TENSOR REMARK 3 L11: 2.9446 L22: 6.4788 REMARK 3 L33: 6.9082 L12: 1.2927 REMARK 3 L13: 0.6747 L23: 5.6597 REMARK 3 S TENSOR REMARK 3 S11: 0.0777 S12: 0.2152 S13: -0.3048 REMARK 3 S21: -0.6129 S22: 0.3425 S23: -0.3007 REMARK 3 S31: -0.9935 S32: 0.3534 S33: -0.4152 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 241 THROUGH 274 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.0286 -1.0120 -14.3691 REMARK 3 T TENSOR REMARK 3 T11: 0.3653 T22: 0.2973 REMARK 3 T33: 0.2971 T12: -0.0273 REMARK 3 T13: 0.0234 T23: 0.0528 REMARK 3 L TENSOR REMARK 3 L11: 3.1854 L22: 2.3936 REMARK 3 L33: 3.9409 L12: -0.1647 REMARK 3 L13: 0.0220 L23: -0.2355 REMARK 3 S TENSOR REMARK 3 S11: 0.1698 S12: 0.4310 S13: 0.2909 REMARK 3 S21: -0.4137 S22: 0.0035 S23: -0.0873 REMARK 3 S31: -0.5006 S32: -0.0978 S33: -0.1304 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9343 4.9601 -14.8379 REMARK 3 T TENSOR REMARK 3 T11: 0.4987 T22: 0.5018 REMARK 3 T33: 0.3721 T12: 0.0393 REMARK 3 T13: 0.0465 T23: 0.0760 REMARK 3 L TENSOR REMARK 3 L11: 7.6903 L22: 6.5256 REMARK 3 L33: 6.2394 L12: -1.7798 REMARK 3 L13: -1.8944 L23: 1.3249 REMARK 3 S TENSOR REMARK 3 S11: 0.1673 S12: 0.4328 S13: 1.6653 REMARK 3 S21: -0.9026 S22: 0.1195 S23: 0.0513 REMARK 3 S31: -0.8798 S32: 0.0627 S33: -0.2395 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 124 THROUGH 136 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9540 19.7621 12.4462 REMARK 3 T TENSOR REMARK 3 T11: 0.4494 T22: 0.4920 REMARK 3 T33: 0.5216 T12: -0.0109 REMARK 3 T13: -0.1045 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 5.9974 L22: 5.3937 REMARK 3 L33: 6.7321 L12: 2.7126 REMARK 3 L13: 2.7664 L23: 3.7214 REMARK 3 S TENSOR REMARK 3 S11: -0.1861 S12: -0.3468 S13: 0.4321 REMARK 3 S21: 0.5280 S22: 0.4787 S23: -0.1947 REMARK 3 S31: -0.3184 S32: 0.1612 S33: -0.2901 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 137 THROUGH 161 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2334 12.3506 12.5905 REMARK 3 T TENSOR REMARK 3 T11: 0.3680 T22: 0.4090 REMARK 3 T33: 0.3588 T12: 0.0560 REMARK 3 T13: -0.0264 T23: 0.0306 REMARK 3 L TENSOR REMARK 3 L11: 7.3110 L22: 9.0552 REMARK 3 L33: 5.6389 L12: 4.8466 REMARK 3 L13: 3.3749 L23: 3.3022 REMARK 3 S TENSOR REMARK 3 S11: 0.0237 S12: -0.5400 S13: -0.4267 REMARK 3 S21: 0.7476 S22: -0.0126 S23: -0.3951 REMARK 3 S31: 0.1293 S32: 0.1241 S33: -0.0534 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 162 THROUGH 170 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0328 20.4627 25.9939 REMARK 3 T TENSOR REMARK 3 T11: 0.9022 T22: 0.9849 REMARK 3 T33: 0.6451 T12: -0.2876 REMARK 3 T13: -0.1959 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 2.5141 L22: 5.9080 REMARK 3 L33: 5.2088 L12: 0.1540 REMARK 3 L13: 0.4485 L23: 0.2977 REMARK 3 S TENSOR REMARK 3 S11: -0.0598 S12: -0.3187 S13: 1.6661 REMARK 3 S21: 2.5994 S22: -1.9655 S23: -0.3415 REMARK 3 S31: 0.9115 S32: -0.3615 S33: 1.3732 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 171 THROUGH 204 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.2288 19.0560 9.5934 REMARK 3 T TENSOR REMARK 3 T11: 0.3110 T22: 0.3564 REMARK 3 T33: 0.4135 T12: -0.0027 REMARK 3 T13: 0.1156 T23: 0.0257 REMARK 3 L TENSOR REMARK 3 L11: 1.8222 L22: 5.8512 REMARK 3 L33: 4.2645 L12: -0.6057 REMARK 3 L13: 2.3293 L23: -0.8361 REMARK 3 S TENSOR REMARK 3 S11: -0.1561 S12: -0.3453 S13: 0.1437 REMARK 3 S21: 0.2773 S22: 0.1524 S23: 0.7509 REMARK 3 S31: -0.4997 S32: -0.4241 S33: -0.0426 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 205 THROUGH 221 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2438 23.1022 -4.4671 REMARK 3 T TENSOR REMARK 3 T11: 0.5099 T22: 0.5582 REMARK 3 T33: 0.6237 T12: -0.0930 REMARK 3 T13: -0.0267 T23: 0.1560 REMARK 3 L TENSOR REMARK 3 L11: 2.6386 L22: 5.5573 REMARK 3 L33: 2.3451 L12: -2.9323 REMARK 3 L13: -1.6824 L23: 0.1567 REMARK 3 S TENSOR REMARK 3 S11: 0.1778 S12: 0.4407 S13: -0.5334 REMARK 3 S21: -0.7352 S22: 0.7829 S23: 1.4482 REMARK 3 S31: 0.0763 S32: -1.1534 S33: -0.9243 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 222 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3220 14.4519 -6.4366 REMARK 3 T TENSOR REMARK 3 T11: 0.6057 T22: 0.5507 REMARK 3 T33: 0.4775 T12: -0.1443 REMARK 3 T13: 0.0193 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 4.2112 L22: 4.1742 REMARK 3 L33: 6.1895 L12: 4.1790 REMARK 3 L13: -0.4357 L23: -0.9013 REMARK 3 S TENSOR REMARK 3 S11: -0.3638 S12: 2.5682 S13: 0.5881 REMARK 3 S21: -1.4780 S22: 0.8609 S23: 0.1665 REMARK 3 S31: -0.0654 S32: -0.5482 S33: -0.5184 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 230 THROUGH 251 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4074 14.5784 16.4563 REMARK 3 T TENSOR REMARK 3 T11: 0.4666 T22: 0.2405 REMARK 3 T33: 0.2861 T12: 0.0025 REMARK 3 T13: 0.0305 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 4.6416 L22: 2.9873 REMARK 3 L33: 8.1300 L12: 0.4000 REMARK 3 L13: 1.9817 L23: -0.3050 REMARK 3 S TENSOR REMARK 3 S11: 0.1748 S12: -0.6394 S13: -0.2341 REMARK 3 S21: 0.7320 S22: 0.1424 S23: 0.0319 REMARK 3 S31: 0.1132 S32: -0.4050 S33: -0.3147 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 252 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9410 22.3277 10.8408 REMARK 3 T TENSOR REMARK 3 T11: 0.4224 T22: 0.3014 REMARK 3 T33: 0.3106 T12: 0.0053 REMARK 3 T13: 0.0356 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 5.5662 L22: 5.2931 REMARK 3 L33: 4.4778 L12: -0.0606 REMARK 3 L13: -1.6159 L23: -0.0058 REMARK 3 S TENSOR REMARK 3 S11: 0.3251 S12: -0.6311 S13: 0.6157 REMARK 3 S21: 0.5575 S22: -0.0011 S23: 0.0560 REMARK 3 S31: -0.8049 S32: 0.0998 S33: -0.3847 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 124 THROUGH 128 OR REMARK 3 (RESID 129 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB OR NAME CG OR NAME REMARK 3 CD )) OR RESID 130 THROUGH 159 OR (RESID REMARK 3 160 AND (NAME N OR NAME CA OR NAME C OR REMARK 3 NAME O OR NAME CB OR NAME CG OR NAME CD )) REMARK 3 OR RESID 161 THROUGH 182 OR (RESID 183 REMARK 3 AND (NAME N OR NAME CA OR NAME C OR NAME REMARK 3 O OR NAME CB OR NAME CG )) OR RESID 184 REMARK 3 THROUGH 226 OR (RESID 227 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 228 THROUGH 244 OR (RESID 245 REMARK 3 AND (NAME N OR NAME CA OR NAME C OR NAME REMARK 3 O OR NAME CB )) OR RESID 251 THROUGH 289 REMARK 3 OR RESID 301 THROUGH 401)) REMARK 3 SELECTION : (CHAIN B AND (RESID 124 THROUGH 145 OR REMARK 3 (RESID 146 THROUGH 147 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB OR REMARK 3 NAME CG )) OR RESID 148 THROUGH 161 OR REMARK 3 (RESID 162 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 165 REMARK 3 THROUGH 199 OR (RESID 200 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB OR REMARK 3 NAME CG )) OR RESID 201 THROUGH 222 OR REMARK 3 (RESID 223 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 224 REMARK 3 THROUGH 245 OR RESID 251 THROUGH 289 OR REMARK 3 RESID 301 THROUGH 401)) REMARK 3 ATOM PAIRS NUMBER : 1333 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7U3I 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_1000263394. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-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-E 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20200417 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20200417 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18720 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 49.116 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.318 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.13 REMARK 200 R MERGE FOR SHELL (I) : 0.94800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.320 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 (%): 36.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG3350, 0.1 M BIS-TRIS, 0.2 M REMARK 280 AMMONIUM FORMATE, 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 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 GLY A 123 REMARK 465 GLY A 163 REMARK 465 LEU A 164 REMARK 465 LYS A 213 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 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 B 123 REMARK 465 LEU B 164 REMARK 465 LYS B 213 REMARK 465 SER B 214 REMARK 465 PHE B 215 REMARK 465 ASN B 216 REMARK 465 SER B 217 REMARK 465 ASP B 218 REMARK 465 LYS B 247 REMARK 465 ASP B 248 REMARK 465 ILE B 249 REMARK 465 SER B 250 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 CD CE NZ REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 GLN A 146 CD OE1 NE2 REMARK 470 HIS A 147 ND1 CD2 CE1 NE2 REMARK 470 ILE A 161 CD1 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 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 ASP A 219 CG OD1 OD2 REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 HIS A 244 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 278 OG REMARK 470 GLU A 279 CG CD OE1 OE2 REMARK 470 SER B 124 OG REMARK 470 LYS B 127 CD CE NZ REMARK 470 ARG B 129 NE CZ NH1 NH2 REMARK 470 LYS B 133 CD CE NZ REMARK 470 LYS B 135 CG CD CE NZ REMARK 470 HIS B 147 ND1 CD2 CE1 NE2 REMARK 470 LYS B 160 CE NZ REMARK 470 ILE B 161 CD1 REMARK 470 LYS B 162 CD CE NZ REMARK 470 GLU B 166 CG CD OE1 OE2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 TYR B 168 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 182 CG CD CE NZ REMARK 470 LYS B 183 CD CE NZ REMARK 470 ASP B 196 CG OD1 OD2 REMARK 470 ARG B 199 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 200 CE NZ REMARK 470 ASP B 219 CG OD1 OD2 REMARK 470 GLU B 223 CD OE1 OE2 REMARK 470 LYS B 226 CG CD CE NZ REMARK 470 ASN B 227 CG OD1 ND2 REMARK 470 HIS B 244 CG ND1 CD2 CE1 NE2 REMARK 470 THR B 245 OG1 CG2 REMARK 470 ILE B 246 CG1 CG2 CD1 REMARK 470 SER B 278 OG REMARK 470 GLU B 279 CG CD OE1 OE2 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 SER A 181 -179.01 -173.16 REMARK 500 PRO A 242 49.75 -84.91 REMARK 500 SER B 181 -177.84 -172.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 7U3I A 124 289 UNP Q8IVV7 GID4_HUMAN 124 289 DBREF 7U3I B 124 289 UNP Q8IVV7 GID4_HUMAN 124 289 SEQADV 7U3I GLY A 123 UNP Q8IVV7 EXPRESSION TAG SEQADV 7U3I GLY B 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 SEQRES 1 B 167 GLY SER GLY SER LYS PHE ARG GLY HIS GLN LYS SER LYS SEQRES 2 B 167 GLY ASN SER TYR ASP VAL GLU VAL VAL LEU GLN HIS VAL SEQRES 3 B 167 ASP THR GLY ASN SER TYR LEU CYS GLY TYR LEU LYS ILE SEQRES 4 B 167 LYS GLY LEU THR GLU GLU TYR PRO THR LEU THR THR PHE SEQRES 5 B 167 PHE GLU GLY GLU ILE ILE SER LYS LYS HIS PRO PHE LEU SEQRES 6 B 167 THR ARG LYS TRP ASP ALA ASP GLU ASP VAL ASP ARG LYS SEQRES 7 B 167 HIS TRP GLY LYS PHE LEU ALA PHE TYR GLN TYR ALA LYS SEQRES 8 B 167 SER PHE ASN SER ASP ASP PHE ASP TYR GLU GLU LEU LYS SEQRES 9 B 167 ASN GLY ASP TYR VAL PHE MET ARG TRP LYS GLU GLN PHE SEQRES 10 B 167 LEU VAL PRO ASP HIS THR ILE LYS ASP ILE SER GLY ALA SEQRES 11 B 167 SER PHE ALA GLY PHE TYR TYR ILE CYS PHE GLN LYS SER SEQRES 12 B 167 ALA ALA SER ILE GLU GLY TYR TYR TYR HIS ARG SER SER SEQRES 13 B 167 GLU TRP TYR GLN SER LEU ASN LEU THR HIS VAL HET L5X A 301 14 HET GOL A 302 6 HET L5X B 301 14 HET GOL B 302 6 HETNAM L5X 3-{[(5S)-5-METHYL-4,5-DIHYDRO-1,3-THIAZOL-2- HETNAM 2 L5X YL]AMINO}PHENOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 L5X 2(C10 H12 N2 O S) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *66(H2 O) HELIX 1 AA1 ASP A 194 GLY A 203 1 10 HELIX 2 AA2 LYS A 204 TYR A 211 5 8 HELIX 3 AA3 ASP A 221 GLY A 228 1 8 HELIX 4 AA4 GLY A 251 ALA A 255 5 5 HELIX 5 AA5 ASP B 194 GLY B 203 1 10 HELIX 6 AA6 LYS B 204 TYR B 211 5 8 HELIX 7 AA7 ASP B 221 GLY B 228 1 8 HELIX 8 AA8 GLY B 251 ALA B 255 5 5 SHEET 1 AA1 9 SER A 126 SER A 134 0 SHEET 2 AA1 9 ASN A 137 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 PHE A 262 N VAL A 231 SHEET 7 AA1 9 SER A 268 TYR A 274 -1 O TYR A 274 N PHE A 257 SHEET 8 AA1 9 GLN A 282 HIS A 288 -1 O LEU A 284 N GLY A 271 SHEET 9 AA1 9 SER A 126 SER A 134 -1 N ARG A 129 O THR A 287 SHEET 1 AA2 9 LYS B 127 SER B 134 0 SHEET 2 AA2 9 ASN B 137 ASP B 149 -1 O VAL B 143 N PHE B 128 SHEET 3 AA2 9 TYR B 154 ILE B 161 -1 O LYS B 160 N GLU B 142 SHEET 4 AA2 9 LEU B 171 ILE B 179 -1 O LEU B 171 N ILE B 161 SHEET 5 AA2 9 TYR B 230 LEU B 240 -1 O GLN B 238 N PHE B 174 SHEET 6 AA2 9 PHE B 257 GLN B 263 -1 O TYR B 258 N TRP B 235 SHEET 7 AA2 9 SER B 268 TYR B 274 -1 O GLU B 270 N CYS B 261 SHEET 8 AA2 9 GLN B 282 HIS B 288 -1 O LEU B 286 N ILE B 269 SHEET 9 AA2 9 LYS B 127 SER B 134 -1 N LYS B 133 O SER B 283 CRYST1 38.651 40.141 51.614 89.99 107.90 89.97 P 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 0.025873 -0.000011 0.008356 0.00000 SCALE2 0.000000 0.024912 -0.000008 0.00000 SCALE3 0.000000 0.000000 0.020360 0.00000