HEADER VIRAL PROTEIN 29-SEP-21 7VK5 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MPRO AT 2.10 A RESOLUTION-8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MAIN PROTEASE; COMPND 5 EC: 3.4.22.69; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, MAIN PROTEASE, SFX, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.DEMIRCI,O.GOCENLER REVDAT 2 29-NOV-23 7VK5 1 REMARK REVDAT 1 26-JAN-22 7VK5 0 JRNL AUTH O.GUVEN,M.GUL,E.AYAN,J.A.JOHNSON,B.CAKILKAYA,G.USTA, JRNL AUTH 2 F.B.ERTEM,N.TOKAY,B.YUKSEL,O.GOCENLER,C.BUYUKDAG,S.BOTHA, JRNL AUTH 3 G.KETAWALA,Z.SU,B.HAYES,F.POITEVIN,A.BATYUK,C.H.YOON, JRNL AUTH 4 C.KUPITZ,S.DURDAGI,R.G.SIERRA,H.DEMIRCI JRNL TITL CASE STUDY OF HIGH-THROUGHPUT DRUG SCREENING AND REMOTE DATA JRNL TITL 2 COLLECTION FOR SARS-COV-2 MAIN PROTEASE BY USING SERIAL JRNL TITL 3 FEMTOSECOND X-RAY CRYSTALLOGRAPHY JRNL REF CRYSTALS V. 11 2021 JRNL REFN ESSN 2073-4352 JRNL DOI 10.3390/CRYST11121579 REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 41092 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.410 REMARK 3 FREE R VALUE TEST SET COUNT : 1811 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 47.1100 - 5.1000 0.99 3200 151 0.2288 0.2388 REMARK 3 2 5.1000 - 4.0500 1.00 3085 141 0.1860 0.2107 REMARK 3 3 4.0500 - 3.5400 1.00 3052 143 0.1892 0.2275 REMARK 3 4 3.5400 - 3.2100 1.00 3022 139 0.2178 0.2328 REMARK 3 5 3.2100 - 2.9800 1.00 3012 141 0.2417 0.2932 REMARK 3 6 2.9800 - 2.8100 1.00 3013 142 0.2490 0.3199 REMARK 3 7 2.8100 - 2.6700 1.00 3002 137 0.2720 0.3142 REMARK 3 8 2.6700 - 2.5500 1.00 2990 134 0.3243 0.3847 REMARK 3 9 2.5500 - 2.4500 1.00 2996 136 0.4443 0.4979 REMARK 3 10 2.4500 - 2.3700 1.00 2974 139 0.3365 0.3809 REMARK 3 11 2.3700 - 2.2900 1.00 2992 134 0.3269 0.3681 REMARK 3 12 2.2900 - 2.2300 1.00 2972 140 0.3963 0.3944 REMARK 3 13 2.2300 - 2.1700 0.99 2971 134 0.4404 0.4495 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.49 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 : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.5796 8.5434 -21.9913 REMARK 3 T TENSOR REMARK 3 T11: 0.3095 T22: 0.3258 REMARK 3 T33: 0.3235 T12: 0.0304 REMARK 3 T13: 0.0118 T23: 0.0438 REMARK 3 L TENSOR REMARK 3 L11: 2.6825 L22: 1.1145 REMARK 3 L33: 3.3292 L12: 0.2896 REMARK 3 L13: 1.3998 L23: 0.9368 REMARK 3 S TENSOR REMARK 3 S11: 0.0118 S12: -0.2919 S13: -0.0596 REMARK 3 S21: 0.0757 S22: -0.0558 S23: 0.1392 REMARK 3 S31: -0.0191 S32: -0.4058 S33: 0.0539 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.8334 5.9134 -30.1547 REMARK 3 T TENSOR REMARK 3 T11: 0.3033 T22: 0.2679 REMARK 3 T33: 0.3312 T12: 0.0316 REMARK 3 T13: -0.0186 T23: 0.0321 REMARK 3 L TENSOR REMARK 3 L11: 5.9334 L22: 0.4708 REMARK 3 L33: 2.5128 L12: 0.2627 REMARK 3 L13: -0.6079 L23: 0.5932 REMARK 3 S TENSOR REMARK 3 S11: 0.0077 S12: 0.2370 S13: -0.4306 REMARK 3 S21: 0.0733 S22: -0.0652 S23: -0.0769 REMARK 3 S31: 0.2752 S32: 0.0491 S33: 0.0439 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 236 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.0785 7.2878 -39.5996 REMARK 3 T TENSOR REMARK 3 T11: 0.4062 T22: 0.4385 REMARK 3 T33: 0.4612 T12: 0.0269 REMARK 3 T13: 0.1013 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 3.7747 L22: 2.1569 REMARK 3 L33: 5.3636 L12: -0.1524 REMARK 3 L13: 1.4737 L23: -1.0294 REMARK 3 S TENSOR REMARK 3 S11: 0.0535 S12: 0.0777 S13: 0.0922 REMARK 3 S21: -0.1137 S22: 0.0483 S23: -0.0645 REMARK 3 S31: 0.0595 S32: 0.2613 S33: 0.0982 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 237 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0356 9.0924 -32.9726 REMARK 3 T TENSOR REMARK 3 T11: 0.2849 T22: 0.4015 REMARK 3 T33: 0.3844 T12: -0.0001 REMARK 3 T13: 0.0536 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 5.2018 L22: 3.1032 REMARK 3 L33: 2.1884 L12: -0.1415 REMARK 3 L13: -0.9667 L23: -0.3950 REMARK 3 S TENSOR REMARK 3 S11: 0.0267 S12: -0.3951 S13: 0.3798 REMARK 3 S21: 0.2536 S22: 0.0813 S23: 0.1570 REMARK 3 S31: -0.1474 S32: 0.0626 S33: -0.1266 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.3063 11.6342 3.2689 REMARK 3 T TENSOR REMARK 3 T11: 0.3163 T22: 0.2612 REMARK 3 T33: 0.3786 T12: -0.0382 REMARK 3 T13: -0.0437 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 2.6755 L22: 2.8613 REMARK 3 L33: 3.7961 L12: -0.8807 REMARK 3 L13: 1.2640 L23: -0.1335 REMARK 3 S TENSOR REMARK 3 S11: -0.1465 S12: -0.1732 S13: 0.4797 REMARK 3 S21: 0.1638 S22: -0.0748 S23: -0.4325 REMARK 3 S31: -0.5725 S32: 0.3067 S33: 0.1488 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 130 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5712 -1.0779 -5.3001 REMARK 3 T TENSOR REMARK 3 T11: 0.2884 T22: 0.2944 REMARK 3 T33: 0.2826 T12: -0.0152 REMARK 3 T13: 0.0122 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 2.0177 L22: 3.3318 REMARK 3 L33: 4.7264 L12: -0.0443 REMARK 3 L13: 1.3806 L23: 2.6068 REMARK 3 S TENSOR REMARK 3 S11: -0.2025 S12: 0.1655 S13: 0.0979 REMARK 3 S21: -0.2300 S22: 0.2793 S23: -0.1478 REMARK 3 S31: -0.1171 S32: 0.4075 S33: -0.1071 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 214 THROUGH 236 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.1904 -25.1735 -19.8964 REMARK 3 T TENSOR REMARK 3 T11: 0.7855 T22: 0.5355 REMARK 3 T33: 0.5169 T12: 0.2285 REMARK 3 T13: -0.1841 T23: -0.1448 REMARK 3 L TENSOR REMARK 3 L11: 4.6530 L22: 3.5288 REMARK 3 L33: 2.9565 L12: 0.0551 REMARK 3 L13: -1.0380 L23: 0.6697 REMARK 3 S TENSOR REMARK 3 S11: -0.5423 S12: -0.3756 S13: -0.6500 REMARK 3 S21: 1.0500 S22: 0.5824 S23: -0.5729 REMARK 3 S31: 0.0987 S32: 0.4090 S33: 0.2246 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 237 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4980 -18.0465 -17.1956 REMARK 3 T TENSOR REMARK 3 T11: 0.6806 T22: 0.3727 REMARK 3 T33: 0.3907 T12: -0.0341 REMARK 3 T13: 0.0001 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 7.1021 L22: 7.3363 REMARK 3 L33: 5.7135 L12: 0.0046 REMARK 3 L13: 0.2191 L23: 4.4510 REMARK 3 S TENSOR REMARK 3 S11: -0.0391 S12: -0.2267 S13: 0.4791 REMARK 3 S21: 0.4722 S22: 0.0166 S23: 0.0850 REMARK 3 S31: 0.2900 S32: 0.2097 S33: 0.0132 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 7VK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 294 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : MFX REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE MFX REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.25 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : SLAC EPIX10K 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45382 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 7CWC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM ACETATE TRIHYDRATE, 0.1M REMARK 280 TRIS 8.5, 30% W/V PEG 4000, PH 8.5, BATCH MODE, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 34.60000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.80000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.80000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.60000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.15000 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A 301 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 GLY B 302 REMARK 465 VAL B 303 REMARK 465 THR B 304 REMARK 465 PHE B 305 REMARK 465 GLN B 306 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 176 O HOH A 401 1.89 REMARK 500 NH1 ARG A 222 O HOH A 402 1.98 REMARK 500 OH TYR A 118 O HOH A 403 2.05 REMARK 500 OE1 GLN B 110 O HOH B 401 2.08 REMARK 500 O LYS B 61 O HOH B 402 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 56 NH2 ARG A 222 1455 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 76 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 MET B 130 CB - CG - SD ANGL. DEV. = -18.4 DEGREES REMARK 500 PHE B 181 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 33 -107.09 46.65 REMARK 500 ASN A 84 -109.25 59.88 REMARK 500 ASN A 119 57.74 35.74 REMARK 500 ASN A 119 57.74 35.39 REMARK 500 TYR A 154 -96.39 63.59 REMARK 500 PRO A 184 46.99 -88.15 REMARK 500 ASP B 33 -106.69 45.51 REMARK 500 ASN B 84 -42.35 68.64 REMARK 500 TYR B 154 -93.71 63.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE B 181 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 430 DISTANCE = 8.08 ANGSTROMS REMARK 525 HOH B 431 DISTANCE = 8.95 ANGSTROMS DBREF 7VK5 A 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 7VK5 B 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN SEQRES 1 B 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 B 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 B 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 B 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 B 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 B 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 B 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 B 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 B 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 B 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 B 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 B 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 B 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 B 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 B 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 B 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 B 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 B 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 B 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 B 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 B 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 B 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 B 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 B 306 CYS SER GLY VAL THR PHE GLN FORMUL 3 HOH *79(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 ASN A 53 ARG A 60 1 8 HELIX 4 AA4 LYS A 61 HIS A 64 5 4 HELIX 5 AA5 ILE A 200 GLY A 215 1 16 HELIX 6 AA6 THR A 226 TYR A 237 1 12 HELIX 7 AA7 THR A 243 LEU A 250 1 8 HELIX 8 AA8 LEU A 250 THR A 257 1 8 HELIX 9 AA9 ALA A 260 GLY A 275 1 16 HELIX 10 AB1 THR A 292 GLN A 299 1 8 HELIX 11 AB2 SER B 10 GLY B 15 1 6 HELIX 12 AB3 HIS B 41 CYS B 44 5 4 HELIX 13 AB4 ASN B 53 LYS B 61 1 9 HELIX 14 AB5 SER B 62 HIS B 64 5 3 HELIX 15 AB6 ILE B 200 GLY B 215 1 16 HELIX 16 AB7 THR B 226 TYR B 237 1 12 HELIX 17 AB8 THR B 243 LEU B 250 1 8 HELIX 18 AB9 LEU B 250 GLY B 258 1 9 HELIX 19 AC1 ALA B 260 ASN B 274 1 15 HELIX 20 AC2 THR B 292 SER B 301 1 10 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O VAL A 35 N LEU A 32 SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 87 N CYS A 38 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N ILE A 78 O LYS A 90 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 AA3 3 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 PHE B 66 ALA B 70 -1 N ALA B 70 O VAL B 73 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N THR B 21 O LEU B 67 SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O LEU B 27 N VAL B 20 SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N ILE B 78 O LYS B 90 SHEET 1 AA5 5 TYR B 101 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASP B 153 O CYS B 156 SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O TYR B 126 N VAL B 114 SHEET 1 AA6 3 TYR B 101 PHE B 103 0 SHEET 2 AA6 3 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O THR B 175 N MET B 162 CRYST1 69.200 104.300 105.600 90.00 90.00 90.00 P 21 21 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 0.014451 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009470 0.00000