HEADER HYDROLASE 08-AUG-25 9PYT TITLE NMR RDC REFINEMENT OF THE CATALYTIC DOMAIN OF THE SARS-COV-2 MONOMERIC TITLE 2 MAIN PROTEASE (MPROH41Q,10-306) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 5 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEASE, CATALYTIC, NSP5, SARS-COV-2, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.J.SMITH,J.YING,Y.SHEN,J.M.LOUIS,A.BAX REVDAT 2 18-FEB-26 9PYT 1 JRNL REVDAT 1 17-SEP-25 9PYT 0 JRNL AUTH M.J.SMITH,J.YING,Y.SHEN,J.M.LOUIS,A.BAX JRNL TITL SOLUTION DOMAIN DYNAMICS OF MONOMERIC SARS-COV‐2 MAIN JRNL TITL 2 PROTEASE REVEALED BY OPTIMIZED NMR RESIDUAL DIPOLAR COUPLING JRNL TITL 3 MEASUREMENTS. JRNL REF ACS PHYS CHEM AU V. 6 81 2026 JRNL REFN ISSN 2694-2445 JRNL PMID 41624715 JRNL DOI 10.1021/ACSPHYSCHEMAU.5C00081 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9PYT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1000298534. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298 REMARK 210 PH : 6.9; 6.9 REMARK 210 IONIC STRENGTH : 20; 20 REMARK 210 PRESSURE : 1 BAR; 1 BAR REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM CHLORIDE, 0.02 % REMARK 210 SODIUM AZIDE, 25 MM HEPES, 1 MM REMARK 210 TCEP, 500 UM [U-13C; U-15N; U-2H] REMARK 210 MPRO(10,306,H41Q), 97% H2O / 3% REMARK 210 D2O; 20 MM SODIUM CHLORIDE, 0.02 REMARK 210 % SODIUM AZIDE, 25 MM HEPES, 1 REMARK 210 MM TCEP, 430 UM [U-13C; U-15N; U- REMARK 210 2H] MPRO(10,306,H41Q), 13 MG/ML REMARK 210 PF1 PHAGE, 97% H2O / 3% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N TROSY-HSQC; 3D HNCA; REMARK 210 3D HNCO; 3D HNCB; 3D HN(COCA)CB; REMARK 210 4D 1H-15N TROSY-NOESY-TROSY; 2D REMARK 210 1H-15N ARTSY; 2D 15-15N QJNC' REMARK 210 TROSY; 3D TATER-HNCO; 3D QJC'CA REMARK 210 HNCO; 3D ARTSY-HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CCPNMR ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 SER A 1 REMARK 465 GLY A 2 REMARK 465 PHE A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 MET A 6 REMARK 465 ALA A 7 REMARK 465 PHE A 8 REMARK 465 PRO A 9 REMARK 465 PHE A 185 REMARK 465 VAL A 186 REMARK 465 ASP A 187 REMARK 465 ARG A 188 REMARK 465 GLN A 189 REMARK 465 THR A 190 REMARK 465 ALA A 191 REMARK 465 GLN A 192 REMARK 465 ALA A 193 REMARK 465 ALA A 194 REMARK 465 GLY A 195 REMARK 465 THR A 196 REMARK 465 ASP A 197 REMARK 465 THR A 198 REMARK 465 THR A 199 REMARK 465 ILE A 200 REMARK 465 THR A 201 REMARK 465 VAL A 202 REMARK 465 ASN A 203 REMARK 465 VAL A 204 REMARK 465 LEU A 205 REMARK 465 ALA A 206 REMARK 465 TRP A 207 REMARK 465 LEU A 208 REMARK 465 TYR A 209 REMARK 465 ALA A 210 REMARK 465 ALA A 211 REMARK 465 VAL A 212 REMARK 465 ILE A 213 REMARK 465 ASN A 214 REMARK 465 GLY A 215 REMARK 465 ASP A 216 REMARK 465 ARG A 217 REMARK 465 TRP A 218 REMARK 465 PHE A 219 REMARK 465 LEU A 220 REMARK 465 ASN A 221 REMARK 465 ARG A 222 REMARK 465 PHE A 223 REMARK 465 THR A 224 REMARK 465 THR A 225 REMARK 465 THR A 226 REMARK 465 LEU A 227 REMARK 465 ASN A 228 REMARK 465 ASP A 229 REMARK 465 PHE A 230 REMARK 465 ASN A 231 REMARK 465 LEU A 232 REMARK 465 VAL A 233 REMARK 465 ALA A 234 REMARK 465 MET A 235 REMARK 465 LYS A 236 REMARK 465 TYR A 237 REMARK 465 ASN A 238 REMARK 465 TYR A 239 REMARK 465 GLU A 240 REMARK 465 PRO A 241 REMARK 465 LEU A 242 REMARK 465 THR A 243 REMARK 465 GLN A 244 REMARK 465 ASP A 245 REMARK 465 HIS A 246 REMARK 465 VAL A 247 REMARK 465 ASP A 248 REMARK 465 ILE A 249 REMARK 465 LEU A 250 REMARK 465 GLY A 251 REMARK 465 PRO A 252 REMARK 465 LEU A 253 REMARK 465 SER A 254 REMARK 465 ALA A 255 REMARK 465 GLN A 256 REMARK 465 THR A 257 REMARK 465 GLY A 258 REMARK 465 ILE A 259 REMARK 465 ALA A 260 REMARK 465 VAL A 261 REMARK 465 LEU A 262 REMARK 465 ASP A 263 REMARK 465 MET A 264 REMARK 465 CYS A 265 REMARK 465 ALA A 266 REMARK 465 SER A 267 REMARK 465 LEU A 268 REMARK 465 LYS A 269 REMARK 465 GLU A 270 REMARK 465 LEU A 271 REMARK 465 LEU A 272 REMARK 465 GLN A 273 REMARK 465 ASN A 274 REMARK 465 GLY A 275 REMARK 465 MET A 276 REMARK 465 ASN A 277 REMARK 465 GLY A 278 REMARK 465 ARG A 279 REMARK 465 THR A 280 REMARK 465 ILE A 281 REMARK 465 LEU A 282 REMARK 465 GLY A 283 REMARK 465 SER A 284 REMARK 465 ALA A 285 REMARK 465 LEU A 286 REMARK 465 LEU A 287 REMARK 465 GLU A 288 REMARK 465 ASP A 289 REMARK 465 GLU A 290 REMARK 465 PHE A 291 REMARK 465 THR A 292 REMARK 465 PRO A 293 REMARK 465 PHE A 294 REMARK 465 ASP A 295 REMARK 465 VAL A 296 REMARK 465 VAL A 297 REMARK 465 ARG A 298 REMARK 465 GLN A 299 REMARK 465 CYS A 300 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 ASP A 33 -130.03 57.26 REMARK 500 1 ASN A 51 72.49 -156.47 REMARK 500 1 ASN A 84 -129.28 58.07 REMARK 500 1 TYR A 154 -116.58 55.71 REMARK 500 2 ASP A 33 -128.58 56.13 REMARK 500 2 ASN A 51 72.09 -157.94 REMARK 500 2 ASN A 84 -128.59 57.82 REMARK 500 2 TYR A 154 -116.41 55.95 REMARK 500 3 ASP A 33 -127.61 56.99 REMARK 500 3 ASN A 51 71.28 -158.92 REMARK 500 3 ASN A 84 -129.27 58.09 REMARK 500 3 TYR A 154 -116.07 55.78 REMARK 500 4 ASP A 33 -128.33 56.59 REMARK 500 4 ASN A 51 72.07 -158.41 REMARK 500 4 ASN A 84 -127.03 58.31 REMARK 500 4 TYR A 154 -116.77 55.94 REMARK 500 5 ASP A 33 -128.33 57.03 REMARK 500 5 ASN A 51 72.55 -157.19 REMARK 500 5 ASN A 84 -129.58 57.75 REMARK 500 5 PHE A 134 30.21 71.28 REMARK 500 5 TYR A 154 -116.67 55.45 REMARK 500 6 ASP A 33 -128.36 56.87 REMARK 500 6 ASN A 51 72.45 -158.07 REMARK 500 6 ASN A 84 -128.54 57.69 REMARK 500 6 TYR A 154 -115.64 55.81 REMARK 500 7 ASP A 33 -129.96 57.53 REMARK 500 7 ASN A 51 72.47 -157.13 REMARK 500 7 ASN A 84 -128.65 57.52 REMARK 500 7 TYR A 154 -117.01 55.83 REMARK 500 8 ASP A 33 -130.10 57.44 REMARK 500 8 ASN A 51 72.45 -157.90 REMARK 500 8 ASN A 84 -128.85 57.68 REMARK 500 8 TYR A 154 -117.05 56.39 REMARK 500 9 ASP A 33 -128.99 56.83 REMARK 500 9 ASN A 51 72.50 -158.00 REMARK 500 9 ASN A 84 -127.67 58.12 REMARK 500 9 TYR A 154 -116.24 55.63 REMARK 500 10 ASP A 33 -129.62 56.94 REMARK 500 10 ASN A 51 72.18 -157.00 REMARK 500 10 ASN A 84 -127.42 58.25 REMARK 500 10 TYR A 154 -117.31 55.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31264 RELATED DB: BMRB REMARK 900 NMR RDC REFINEMENT OF THE CATALYTIC DOMAIN OF THE SARS-COV-2 REMARK 900 MONOMERIC MAIN PROTEASE (MPROH41Q,10-306) DBREF 9PYT A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 9PYT GLN A 41 UNP P0DTD1 HIS 3304 ENGINEERED MUTATION 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 GLN 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 HELIX 1 AA1 LYS A 12 GLY A 15 5 4 HELIX 2 AA2 GLN A 41 CYS A 44 5 4 HELIX 3 AA3 THR A 45 ASN A 51 1 7 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 LYS A 61 HIS A 64 5 4 HELIX 6 AA6 GLY A 138 ASN A 142 5 5 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 THR A 25 N CYS A 22 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 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 SER A 81 O LYS A 88 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 CYS A 128 N PHE A 112 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 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MASTER 289 0 0 6 15 0 0 6 1346 1 0 24 END