HEADER VIRAL PROTEIN 04-MAR-24 8YK4 TITLE STRUCTURE OF SARS-COV-2 RBD AND ANTIBODY NT-108 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIBODY NT-108, SINGLE CHAIN FV FRAGMENT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE PROTEIN S1; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 8 2; SOURCE 9 ORGANISM_TAXID: 2697049; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, SPIKE, RBD, ANTIBODY, IGG, SCFV, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ANRAKU,S.KITA,T.ONODERA,A.SATO,T.TADOKORO,Y.ADACHI,S.ITO,T.SUZUKI, AUTHOR 2 J.SASAKI,N.SHIWA,N.IWATA,N.NAGATA,Y.KAZUKI,M.OSHIMURA,M.SASAKI, AUTHOR 3 Y.ORBA,T.SUZUKI,H.SAWA,T.HASHIGUCHI,H.FUKUHARA,Y.TAKAHASHI,K.MAENAKA REVDAT 1 12-MAR-25 8YK4 0 JRNL AUTH Y.ANRAKU,T.TADOKORO,T.SUZUKI,J.SASAKI,T.HASHIGUCHI,S.KITA, JRNL AUTH 2 N.SHIWA,N.IWATA,N.NAGATA,T.SUZUKI,Y.KAZUKI,H.FUKUHARA, JRNL AUTH 3 M.OSHIMURA,A.SATO,M.SASAKI,Y.ORBA,H.SAWA,K.MAENAKA JRNL TITL STRUCTURAL BASIS FOR POTENT NEUTRALIZATION ACTIVITY OF JRNL TITL 2 SARS-COV-2 ANTIBODY, NT-108 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 17738 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 861 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 48.3500 - 5.8100 0.99 2990 135 0.2427 0.2487 REMARK 3 2 5.8100 - 4.6100 0.99 2817 146 0.2006 0.2324 REMARK 3 3 4.6100 - 4.0300 1.00 2810 133 0.2035 0.2083 REMARK 3 4 4.0300 - 3.6600 0.99 2761 138 0.2637 0.3033 REMARK 3 5 3.6600 - 3.4000 0.99 2764 158 0.2886 0.3301 REMARK 3 6 3.4000 - 3.2000 0.99 2735 151 0.3223 0.3472 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) : 0.456 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.294 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.12 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 : 0.001 3258 REMARK 3 ANGLE : 0.401 4426 REMARK 3 CHIRALITY : 0.042 476 REMARK 3 PLANARITY : 0.003 570 REMARK 3 DIHEDRAL : 14.985 1151 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6857 11.1378 74.6014 REMARK 3 T TENSOR REMARK 3 T11: 0.4419 T22: 0.3526 REMARK 3 T33: 0.9580 T12: 0.0761 REMARK 3 T13: -0.0322 T23: 0.1165 REMARK 3 L TENSOR REMARK 3 L11: 2.4206 L22: 4.3404 REMARK 3 L33: 1.9056 L12: 3.0701 REMARK 3 L13: -0.6195 L23: 0.0980 REMARK 3 S TENSOR REMARK 3 S11: 0.0792 S12: -0.4071 S13: -1.4789 REMARK 3 S21: 0.6187 S22: 0.1179 S23: 0.2250 REMARK 3 S31: 0.3288 S32: 0.1309 S33: -0.1512 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0470 16.4963 76.6268 REMARK 3 T TENSOR REMARK 3 T11: 0.5245 T22: 0.3015 REMARK 3 T33: 0.6627 T12: -0.0566 REMARK 3 T13: 0.0950 T23: 0.0454 REMARK 3 L TENSOR REMARK 3 L11: 4.1487 L22: 5.1789 REMARK 3 L33: 4.9832 L12: 0.8821 REMARK 3 L13: 1.3166 L23: 0.3033 REMARK 3 S TENSOR REMARK 3 S11: 0.2236 S12: -0.3084 S13: -0.4961 REMARK 3 S21: 0.5501 S22: 0.0616 S23: 0.9998 REMARK 3 S31: 0.2446 S32: -0.2989 S33: -0.3550 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 78 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2702 13.4730 70.1908 REMARK 3 T TENSOR REMARK 3 T11: 0.3938 T22: 0.3474 REMARK 3 T33: 1.0420 T12: 0.0840 REMARK 3 T13: -0.1013 T23: 0.1227 REMARK 3 L TENSOR REMARK 3 L11: 6.8535 L22: 4.4913 REMARK 3 L33: 1.1815 L12: 5.0333 REMARK 3 L13: -0.3955 L23: 0.6579 REMARK 3 S TENSOR REMARK 3 S11: -0.4375 S12: -0.0234 S13: -0.6363 REMARK 3 S21: -0.6137 S22: 0.1686 S23: 0.5450 REMARK 3 S31: -0.1002 S32: 0.0772 S33: 0.2607 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 108 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4940 29.6337 54.9982 REMARK 3 T TENSOR REMARK 3 T11: 0.3685 T22: 0.4407 REMARK 3 T33: 0.3454 T12: 0.0623 REMARK 3 T13: -0.0492 T23: 0.0529 REMARK 3 L TENSOR REMARK 3 L11: 1.6031 L22: 5.8998 REMARK 3 L33: 1.2787 L12: -1.8338 REMARK 3 L13: 0.3092 L23: 1.7013 REMARK 3 S TENSOR REMARK 3 S11: -0.0998 S12: 0.5361 S13: 0.6349 REMARK 3 S21: -0.3737 S22: 0.1266 S23: -0.4924 REMARK 3 S31: 0.3820 S32: -0.3414 S33: 0.0676 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 141 THROUGH 209 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3351 34.3499 64.3077 REMARK 3 T TENSOR REMARK 3 T11: 0.3725 T22: 0.1613 REMARK 3 T33: 0.4424 T12: -0.0050 REMARK 3 T13: -0.0537 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 5.0267 L22: 1.0370 REMARK 3 L33: 4.4741 L12: 0.3773 REMARK 3 L13: -0.5804 L23: -0.4879 REMARK 3 S TENSOR REMARK 3 S11: 0.0149 S12: -0.0703 S13: 0.1316 REMARK 3 S21: -0.3131 S22: 0.0520 S23: 0.0232 REMARK 3 S31: -0.0496 S32: 0.1371 S33: -0.0872 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 210 THROUGH 246 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.4784 26.7251 60.8944 REMARK 3 T TENSOR REMARK 3 T11: 0.3444 T22: 0.1776 REMARK 3 T33: 0.5082 T12: -0.0034 REMARK 3 T13: 0.0140 T23: 0.0507 REMARK 3 L TENSOR REMARK 3 L11: 2.5397 L22: 2.4960 REMARK 3 L33: 9.3197 L12: -0.9206 REMARK 3 L13: -1.8222 L23: 3.8011 REMARK 3 S TENSOR REMARK 3 S11: 0.0263 S12: 0.0663 S13: -0.0750 REMARK 3 S21: -0.0293 S22: 0.1108 S23: -0.0853 REMARK 3 S31: 0.2748 S32: -0.0363 S33: -0.2220 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 338 THROUGH 353 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1047 36.5515 99.4294 REMARK 3 T TENSOR REMARK 3 T11: 0.7938 T22: 0.8654 REMARK 3 T33: 0.5074 T12: 0.1921 REMARK 3 T13: -0.0821 T23: -0.1233 REMARK 3 L TENSOR REMARK 3 L11: 6.0470 L22: 8.7519 REMARK 3 L33: 1.9972 L12: 1.1139 REMARK 3 L13: -0.1922 L23: -0.9906 REMARK 3 S TENSOR REMARK 3 S11: -0.2311 S12: -1.3714 S13: 0.5937 REMARK 3 S21: -0.3485 S22: 0.9484 S23: 0.6680 REMARK 3 S31: -0.4520 S32: 0.5306 S33: -0.7746 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 354 THROUGH 367 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.0781 38.7111 112.5431 REMARK 3 T TENSOR REMARK 3 T11: 1.0034 T22: 1.6744 REMARK 3 T33: 0.8406 T12: 0.0020 REMARK 3 T13: 0.3662 T23: -0.4440 REMARK 3 L TENSOR REMARK 3 L11: 2.7482 L22: 3.6351 REMARK 3 L33: 3.0726 L12: -1.3919 REMARK 3 L13: -0.8751 L23: -2.0514 REMARK 3 S TENSOR REMARK 3 S11: -0.5743 S12: -0.9767 S13: -1.3606 REMARK 3 S21: 1.1597 S22: -0.4008 S23: 0.8727 REMARK 3 S31: -0.4496 S32: 0.0145 S33: 0.7823 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 368 THROUGH 379 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.7892 23.7971 108.1562 REMARK 3 T TENSOR REMARK 3 T11: 1.4688 T22: 1.3106 REMARK 3 T33: 1.5100 T12: -0.1397 REMARK 3 T13: 0.6071 T23: 0.4005 REMARK 3 L TENSOR REMARK 3 L11: 7.8097 L22: 4.0085 REMARK 3 L33: 0.8078 L12: -4.4719 REMARK 3 L13: 1.6040 L23: -0.0865 REMARK 3 S TENSOR REMARK 3 S11: 0.3964 S12: -1.6811 S13: 0.3335 REMARK 3 S21: 1.7656 S22: 0.7176 S23: 2.3606 REMARK 3 S31: 0.3278 S32: -1.2546 S33: -0.9519 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 380 THROUGH 394 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1134 27.0864 118.8785 REMARK 3 T TENSOR REMARK 3 T11: 1.3756 T22: 1.7346 REMARK 3 T33: 0.7327 T12: -0.1527 REMARK 3 T13: -0.1242 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 3.6466 L22: 0.4090 REMARK 3 L33: 5.6706 L12: -1.2072 REMARK 3 L13: -4.5350 L23: 1.4819 REMARK 3 S TENSOR REMARK 3 S11: -0.9764 S12: -1.6697 S13: 0.4828 REMARK 3 S21: 0.2122 S22: 0.7079 S23: 0.0159 REMARK 3 S31: 0.1302 S32: 1.5130 S33: 0.3091 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 395 THROUGH 409 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4413 27.5286 100.5565 REMARK 3 T TENSOR REMARK 3 T11: 0.9438 T22: 1.1440 REMARK 3 T33: 0.4847 T12: -0.0071 REMARK 3 T13: 0.0109 T23: 0.1531 REMARK 3 L TENSOR REMARK 3 L11: 6.6632 L22: 5.6356 REMARK 3 L33: 6.7758 L12: 0.9829 REMARK 3 L13: -0.4550 L23: 1.5194 REMARK 3 S TENSOR REMARK 3 S11: -0.4513 S12: -0.9421 S13: -0.2563 REMARK 3 S21: 0.7540 S22: -0.0751 S23: -0.2310 REMARK 3 S31: 0.1238 S32: 0.5446 S33: 0.4693 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 410 THROUGH 451 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.1985 27.4791 98.4701 REMARK 3 T TENSOR REMARK 3 T11: 0.7317 T22: 0.9825 REMARK 3 T33: 0.4389 T12: 0.0420 REMARK 3 T13: 0.1218 T23: 0.1175 REMARK 3 L TENSOR REMARK 3 L11: 2.4303 L22: 3.8184 REMARK 3 L33: 0.6858 L12: 0.6648 REMARK 3 L13: -0.8404 L23: 0.9646 REMARK 3 S TENSOR REMARK 3 S11: -0.1920 S12: -0.8351 S13: -0.1925 REMARK 3 S21: 0.8900 S22: -0.0112 S23: 0.2218 REMARK 3 S31: 0.2421 S32: -0.3640 S33: 0.1723 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 452 THROUGH 502 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8379 31.9286 88.9695 REMARK 3 T TENSOR REMARK 3 T11: 0.5598 T22: 0.5076 REMARK 3 T33: 0.5835 T12: 0.0810 REMARK 3 T13: -0.1552 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 3.7568 L22: 3.2893 REMARK 3 L33: 6.1184 L12: 0.3288 REMARK 3 L13: -2.5543 L23: -0.5046 REMARK 3 S TENSOR REMARK 3 S11: -0.2177 S12: -0.6870 S13: 0.0790 REMARK 3 S21: 0.5343 S22: 0.1940 S23: 0.0309 REMARK 3 S31: -0.5297 S32: 0.4926 S33: 0.0152 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 503 THROUGH 525 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.9138 29.8363 104.9472 REMARK 3 T TENSOR REMARK 3 T11: 1.2669 T22: 1.0402 REMARK 3 T33: 0.3686 T12: -0.0220 REMARK 3 T13: 0.0362 T23: -0.0913 REMARK 3 L TENSOR REMARK 3 L11: 2.3175 L22: 0.0305 REMARK 3 L33: 2.9753 L12: -0.0860 REMARK 3 L13: -0.6172 L23: 0.3144 REMARK 3 S TENSOR REMARK 3 S11: 0.1771 S12: -0.6150 S13: 0.1512 REMARK 3 S21: 1.2956 S22: 0.0374 S23: -0.1089 REMARK 3 S31: -0.1407 S32: -0.0252 S33: -0.1491 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 8YK4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300045268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 1.18_3845 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 1.18_3845 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17765 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 48.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CHES PH9.5, 20% PEG8000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+1/2 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 0.00000 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 0.00000 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 27.57600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 74.82050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 126.71450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.57600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 74.82050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 126.71450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.57600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.82050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 126.71450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.57600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 74.82050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 126.71450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 MET A -29 REMARK 465 GLY A -28 REMARK 465 ILE A -27 REMARK 465 LEU A -26 REMARK 465 PRO A -25 REMARK 465 SER A -24 REMARK 465 PRO A -23 REMARK 465 GLY A -22 REMARK 465 MET A -21 REMARK 465 PRO A -20 REMARK 465 ALA A -19 REMARK 465 LEU A -18 REMARK 465 LEU A -17 REMARK 465 SER A -16 REMARK 465 LEU A -15 REMARK 465 VAL A -14 REMARK 465 SER A -13 REMARK 465 LEU A -12 REMARK 465 LEU A -11 REMARK 465 SER A -10 REMARK 465 VAL A -9 REMARK 465 LEU A -8 REMARK 465 LEU A -7 REMARK 465 MET A -6 REMARK 465 GLY A -5 REMARK 465 CYS A -4 REMARK 465 VAL A -3 REMARK 465 ALA A -2 REMARK 465 GLU A -1 REMARK 465 THR A 0 REMARK 465 GLY A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 109 REMARK 465 GLY A 110 REMARK 465 GLY A 111 REMARK 465 GLY A 112 REMARK 465 SER A 113 REMARK 465 GLY A 114 REMARK 465 GLY A 115 REMARK 465 GLY A 116 REMARK 465 GLY A 117 REMARK 465 SER A 118 REMARK 465 GLY A 119 REMARK 465 GLY A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 122 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 HIS A 252 REMARK 465 PRO C 322 REMARK 465 THR C 323 REMARK 465 GLU C 324 REMARK 465 SER C 325 REMARK 465 ILE C 326 REMARK 465 VAL C 327 REMARK 465 ARG C 328 REMARK 465 PHE C 329 REMARK 465 PRO C 330 REMARK 465 ASN C 331 REMARK 465 ILE C 332 REMARK 465 THR C 333 REMARK 465 ASN C 334 REMARK 465 LEU C 335 REMARK 465 CYS C 336 REMARK 465 PRO C 337 REMARK 465 ASP C 389 REMARK 465 LEU C 390 REMARK 465 CYS C 391 REMARK 465 PHE C 392 REMARK 465 THR C 393 REMARK 465 LEU C 517 REMARK 465 LEU C 518 REMARK 465 HIS C 519 REMARK 465 ALA C 520 REMARK 465 PRO C 521 REMARK 465 GLY C 526 REMARK 465 PRO C 527 REMARK 465 LYS C 528 REMARK 465 LYS C 529 REMARK 465 SER C 530 REMARK 465 THR C 531 REMARK 465 ASN C 532 REMARK 465 LEU C 533 REMARK 465 VAL C 534 REMARK 465 LYS C 535 REMARK 465 ASN C 536 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 ALA A 53 -63.41 65.16 REMARK 500 SER A 153 30.59 -96.72 REMARK 500 SER A 156 53.28 -112.90 REMARK 500 LEU A 173 -61.74 -100.89 REMARK 500 ARG A 179 -90.33 -113.85 REMARK 500 LYS A 181 -165.58 -127.78 REMARK 500 ARG A 193 13.54 -159.30 REMARK 500 ASN A 210 -74.94 -61.11 REMARK 500 ALA A 229 43.59 -99.59 REMARK 500 ASN C 343 38.95 -83.31 REMARK 500 ALA C 352 47.95 -101.74 REMARK 500 ASN C 422 -62.78 -123.21 REMARK 500 SER C 443 100.04 -161.62 REMARK 500 PHE C 497 80.61 60.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YK4 A -29 252 PDB 8YK4 8YK4 -29 252 DBREF1 8YK4 C 322 536 UNP A0A7U3DZD0_SARS2 DBREF2 8YK4 C A0A7U3DZD0 322 536 SEQRES 1 A 282 MET GLY ILE LEU PRO SER PRO GLY MET PRO ALA LEU LEU SEQRES 2 A 282 SER LEU VAL SER LEU LEU SER VAL LEU LEU MET GLY CYS SEQRES 3 A 282 VAL ALA GLU THR GLY GLU ILE VAL LEU THR GLN SER PRO SEQRES 4 A 282 GLY THR LEU SER LEU SER PRO GLY GLU ARG ALA THR LEU SEQRES 5 A 282 SER CYS ARG ALA SER GLN SER VAL SER SER THR PHE LEU SEQRES 6 A 282 ALA TRP TYR GLN GLN LYS PRO GLY GLN ALA PRO ARG LEU SEQRES 7 A 282 LEU ILE TYR GLY ALA SER TYR MET ALA THR GLY ILE PRO SEQRES 8 A 282 ASP ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR SEQRES 9 A 282 LEU THR ILE SER ARG LEU GLU PRO GLU ASP PHE ALA VAL SEQRES 10 A 282 TYR TYR CYS GLN GLN TYR GLY SER SER LEU THR PHE GLY SEQRES 11 A 282 GLY GLY THR LYS LEU GLU ILE LYS GLY GLY GLY GLY SER SEQRES 12 A 282 GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLN VAL GLN SEQRES 13 A 282 LEU GLN GLN SER GLY PRO GLY LEU VAL LYS PRO SER GLN SEQRES 14 A 282 THR LEU SER LEU THR CYS SER ILE SER GLY ASP SER VAL SEQRES 15 A 282 SER SER ASN SER ALA ALA TRP ASN TRP ILE ARG GLN SER SEQRES 16 A 282 PRO SER ARG GLY LEU GLU TRP LEU GLY ARG THR TYR TYR SEQRES 17 A 282 ARG SER LYS TRP TYR ASN ASP TYR ALA GLY THR VAL LYS SEQRES 18 A 282 SER ARG ILE ALA ILE ASN PRO ASP THR SER LYS ASN GLN SEQRES 19 A 282 PHE SER LEU HIS LEU ASN SER VAL THR PRO GLU ASP THR SEQRES 20 A 282 ALA VAL TYR PHE CYS ALA ARG VAL ILE SER VAL ALA GLY SEQRES 21 A 282 TYR ALA PHE ASP ILE TRP GLY GLN GLY THR MET VAL THR SEQRES 22 A 282 VAL SER SER HIS HIS HIS HIS HIS HIS SEQRES 1 C 215 PRO THR GLU SER ILE VAL ARG PHE PRO ASN ILE THR ASN SEQRES 2 C 215 LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG PHE SEQRES 3 C 215 ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER ASN SEQRES 4 C 215 CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SER SEQRES 5 C 215 PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR LYS SEQRES 6 C 215 LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SER SEQRES 7 C 215 PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA PRO SEQRES 8 C 215 GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS LEU SEQRES 9 C 215 PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SER SEQRES 10 C 215 ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN TYR SEQRES 11 C 215 LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO PHE SEQRES 12 C 215 GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SER SEQRES 13 C 215 THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR PHE SEQRES 14 C 215 PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY VAL SEQRES 15 C 215 GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE GLU SEQRES 16 C 215 LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS LYS SEQRES 17 C 215 SER THR ASN LEU VAL LYS ASN HELIX 1 AA1 GLU A 81 PHE A 85 5 5 HELIX 2 AA2 VAL A 190 SER A 192 5 3 HELIX 3 AA3 THR A 213 THR A 217 5 5 HELIX 4 AA4 GLY C 339 ASN C 343 1 5 HELIX 5 AA5 GLY C 404 ILE C 410 5 7 HELIX 6 AA6 GLY C 416 ASN C 422 1 7 HELIX 7 AA7 GLY C 502 GLN C 506 5 5 SHEET 1 AA1 4 LEU A 5 SER A 8 0 SHEET 2 AA1 4 ALA A 20 ALA A 26 -1 O ARG A 25 N THR A 6 SHEET 3 AA1 4 ASP A 72 ILE A 77 -1 O LEU A 75 N LEU A 22 SHEET 4 AA1 4 PHE A 64 SER A 69 -1 N SER A 67 O THR A 74 SHEET 1 AA2 6 THR A 11 LEU A 14 0 SHEET 2 AA2 6 THR A 103 ILE A 107 1 O GLU A 106 N LEU A 12 SHEET 3 AA2 6 ALA A 86 TYR A 93 -1 N TYR A 88 O THR A 103 SHEET 4 AA2 6 ALA A 36 GLN A 40 -1 N ALA A 36 O GLN A 91 SHEET 5 AA2 6 ARG A 47 TYR A 51 -1 O ARG A 47 N GLN A 39 SHEET 6 AA2 6 TYR A 55 MET A 56 -1 O TYR A 55 N TYR A 51 SHEET 1 AA3 4 THR A 11 LEU A 14 0 SHEET 2 AA3 4 THR A 103 ILE A 107 1 O GLU A 106 N LEU A 12 SHEET 3 AA3 4 ALA A 86 TYR A 93 -1 N TYR A 88 O THR A 103 SHEET 4 AA3 4 LEU A 97 PHE A 99 -1 O THR A 98 N GLN A 92 SHEET 1 AA4 4 GLN A 126 SER A 130 0 SHEET 2 AA4 4 LEU A 141 SER A 148 -1 O SER A 146 N GLN A 128 SHEET 3 AA4 4 GLN A 204 LEU A 209 -1 O LEU A 207 N LEU A 143 SHEET 4 AA4 4 ILE A 194 ASP A 199 -1 N ASP A 199 O GLN A 204 SHEET 1 AA5 6 LEU A 134 VAL A 135 0 SHEET 2 AA5 6 THR A 240 VAL A 244 1 O THR A 243 N VAL A 135 SHEET 3 AA5 6 ALA A 218 VAL A 225 -1 N ALA A 218 O VAL A 242 SHEET 4 AA5 6 ALA A 158 SER A 165 -1 N ILE A 162 O PHE A 221 SHEET 5 AA5 6 GLY A 169 TYR A 178 -1 O GLY A 169 N SER A 165 SHEET 6 AA5 6 TRP A 182 TYR A 186 -1 O TYR A 183 N TYR A 177 SHEET 1 AA6 4 LEU A 134 VAL A 135 0 SHEET 2 AA6 4 THR A 240 VAL A 244 1 O THR A 243 N VAL A 135 SHEET 3 AA6 4 ALA A 218 VAL A 225 -1 N ALA A 218 O VAL A 242 SHEET 4 AA6 4 PHE A 233 TRP A 236 -1 O ILE A 235 N ARG A 224 SHEET 1 AA7 5 ASN C 354 ILE C 358 0 SHEET 2 AA7 5 VAL C 395 ILE C 402 -1 O VAL C 395 N ILE C 358 SHEET 3 AA7 5 TYR C 508 PHE C 515 -1 O VAL C 512 N ASP C 398 SHEET 4 AA7 5 GLY C 431 ASN C 437 -1 N ILE C 434 O VAL C 511 SHEET 5 AA7 5 THR C 376 CYS C 379 -1 N THR C 376 O ALA C 435 SHEET 1 AA8 2 CYS C 361 VAL C 362 0 SHEET 2 AA8 2 VAL C 524 CYS C 525 1 N CYS C 525 O CYS C 361 SHEET 1 AA9 2 LEU C 452 ARG C 454 0 SHEET 2 AA9 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AB1 2 TYR C 473 GLN C 474 0 SHEET 2 AB1 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SSBOND 1 CYS A 24 CYS A 90 1555 1555 2.03 SSBOND 2 CYS A 145 CYS A 222 1555 1555 2.04 SSBOND 3 CYS C 379 CYS C 432 1555 1555 2.03 SSBOND 4 CYS C 480 CYS C 488 1555 1555 2.03 CISPEP 1 SER A 8 PRO A 9 0 -0.36 CRYST1 55.152 149.641 253.429 90.00 90.00 90.00 I 2 2 2 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 0.018132 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003946 0.00000