HEADER HYDROLASE 08-AUG-25 9PYS TITLE NMR RDC REFINEMENT OF THE HELICAL 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_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEASE, HELICAL, 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 9PYS 1 JRNL REVDAT 1 17-SEP-25 9PYS 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 9PYS 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_1000298772. 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, 500 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 HNCB; 3D HN(COCA)CB; 3D HNCO; REMARK 210 4D 1H-15N TROSY-NOESY-TROSY; 2D REMARK 210 1H-15N ARTSY; 2D 1H-15N QJNC'; REMARK 210 3D TATER-HNCO; 3D QJCAC' HNCO; REMARK 210 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 SER A 10 REMARK 465 GLY A 11 REMARK 465 LYS A 12 REMARK 465 VAL A 13 REMARK 465 GLU A 14 REMARK 465 GLY A 15 REMARK 465 CYS A 16 REMARK 465 MET A 17 REMARK 465 VAL A 18 REMARK 465 GLN A 19 REMARK 465 VAL A 20 REMARK 465 THR A 21 REMARK 465 CYS A 22 REMARK 465 GLY A 23 REMARK 465 THR A 24 REMARK 465 THR A 25 REMARK 465 THR A 26 REMARK 465 LEU A 27 REMARK 465 ASN A 28 REMARK 465 GLY A 29 REMARK 465 LEU A 30 REMARK 465 TRP A 31 REMARK 465 LEU A 32 REMARK 465 ASP A 33 REMARK 465 ASP A 34 REMARK 465 VAL A 35 REMARK 465 VAL A 36 REMARK 465 TYR A 37 REMARK 465 CYS A 38 REMARK 465 PRO A 39 REMARK 465 ARG A 40 REMARK 465 GLN A 41 REMARK 465 VAL A 42 REMARK 465 ILE A 43 REMARK 465 CYS A 44 REMARK 465 THR A 45 REMARK 465 SER A 46 REMARK 465 GLU A 47 REMARK 465 ASP A 48 REMARK 465 MET A 49 REMARK 465 LEU A 50 REMARK 465 ASN A 51 REMARK 465 PRO A 52 REMARK 465 ASN A 53 REMARK 465 TYR A 54 REMARK 465 GLU A 55 REMARK 465 ASP A 56 REMARK 465 LEU A 57 REMARK 465 LEU A 58 REMARK 465 ILE A 59 REMARK 465 ARG A 60 REMARK 465 LYS A 61 REMARK 465 SER A 62 REMARK 465 ASN A 63 REMARK 465 HIS A 64 REMARK 465 ASN A 65 REMARK 465 PHE A 66 REMARK 465 LEU A 67 REMARK 465 VAL A 68 REMARK 465 GLN A 69 REMARK 465 ALA A 70 REMARK 465 GLY A 71 REMARK 465 ASN A 72 REMARK 465 VAL A 73 REMARK 465 GLN A 74 REMARK 465 LEU A 75 REMARK 465 ARG A 76 REMARK 465 VAL A 77 REMARK 465 ILE A 78 REMARK 465 GLY A 79 REMARK 465 HIS A 80 REMARK 465 SER A 81 REMARK 465 MET A 82 REMARK 465 GLN A 83 REMARK 465 ASN A 84 REMARK 465 CYS A 85 REMARK 465 VAL A 86 REMARK 465 LEU A 87 REMARK 465 LYS A 88 REMARK 465 LEU A 89 REMARK 465 LYS A 90 REMARK 465 VAL A 91 REMARK 465 ASP A 92 REMARK 465 THR A 93 REMARK 465 ALA A 94 REMARK 465 ASN A 95 REMARK 465 PRO A 96 REMARK 465 LYS A 97 REMARK 465 THR A 98 REMARK 465 PRO A 99 REMARK 465 LYS A 100 REMARK 465 TYR A 101 REMARK 465 LYS A 102 REMARK 465 PHE A 103 REMARK 465 VAL A 104 REMARK 465 ARG A 105 REMARK 465 ILE A 106 REMARK 465 GLN A 107 REMARK 465 PRO A 108 REMARK 465 GLY A 109 REMARK 465 GLN A 110 REMARK 465 THR A 111 REMARK 465 PHE A 112 REMARK 465 SER A 113 REMARK 465 VAL A 114 REMARK 465 LEU A 115 REMARK 465 ALA A 116 REMARK 465 CYS A 117 REMARK 465 TYR A 118 REMARK 465 ASN A 119 REMARK 465 GLY A 120 REMARK 465 SER A 121 REMARK 465 PRO A 122 REMARK 465 SER A 123 REMARK 465 GLY A 124 REMARK 465 VAL A 125 REMARK 465 TYR A 126 REMARK 465 GLN A 127 REMARK 465 CYS A 128 REMARK 465 ALA A 129 REMARK 465 MET A 130 REMARK 465 ARG A 131 REMARK 465 PRO A 132 REMARK 465 ASN A 133 REMARK 465 PHE A 134 REMARK 465 THR A 135 REMARK 465 ILE A 136 REMARK 465 LYS A 137 REMARK 465 GLY A 138 REMARK 465 SER A 139 REMARK 465 PHE A 140 REMARK 465 LEU A 141 REMARK 465 ASN A 142 REMARK 465 GLY A 143 REMARK 465 SER A 144 REMARK 465 CYS A 145 REMARK 465 GLY A 146 REMARK 465 SER A 147 REMARK 465 VAL A 148 REMARK 465 GLY A 149 REMARK 465 PHE A 150 REMARK 465 ASN A 151 REMARK 465 ILE A 152 REMARK 465 ASP A 153 REMARK 465 TYR A 154 REMARK 465 ASP A 155 REMARK 465 CYS A 156 REMARK 465 VAL A 157 REMARK 465 SER A 158 REMARK 465 PHE A 159 REMARK 465 CYS A 160 REMARK 465 TYR A 161 REMARK 465 MET A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 MET A 165 REMARK 465 GLU A 166 REMARK 465 LEU A 167 REMARK 465 PRO A 168 REMARK 465 THR A 169 REMARK 465 GLY A 170 REMARK 465 VAL A 171 REMARK 465 HIS A 172 REMARK 465 ALA A 173 REMARK 465 GLY A 174 REMARK 465 THR A 175 REMARK 465 ASP A 176 REMARK 465 LEU A 177 REMARK 465 GLU A 178 REMARK 465 GLY A 179 REMARK 465 ASN A 180 REMARK 465 PHE A 181 REMARK 465 TYR A 182 REMARK 465 GLY A 183 REMARK 465 PRO A 184 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 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 HH TYR A 209 HG SER A 254 1.04 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 ARG A 217 -15.25 -148.74 REMARK 500 2 ARG A 217 -13.91 -152.75 REMARK 500 3 ARG A 217 -15.16 -148.56 REMARK 500 4 ARG A 217 -15.02 -151.43 REMARK 500 5 ARG A 217 -11.68 -151.46 REMARK 500 6 ARG A 217 -11.33 -151.72 REMARK 500 7 ARG A 217 -15.83 -148.54 REMARK 500 8 ARG A 217 -10.50 -155.05 REMARK 500 9 ARG A 217 -17.58 -150.86 REMARK 500 10 ARG A 217 -14.76 -151.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31263 RELATED DB: BMRB REMARK 900 NMR RDC REFINEMENT OF THE HELICAL DOMAIN OF THE SARS-COV-2 REMARK 900 MONOMERIC MAIN PROTEASE (MPROH41Q,10-306) DBREF 9PYS A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 9PYS 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 ILE A 200 GLY A 215 1 16 HELIX 2 AA2 THR A 226 TYR A 237 1 12 HELIX 3 AA3 THR A 243 LEU A 250 1 8 HELIX 4 AA4 LEU A 250 GLY A 258 1 9 HELIX 5 AA5 ALA A 260 GLY A 275 1 16 HELIX 6 AA6 THR A 292 SER A 301 1 10 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 327 0 0 6 0 0 0 6 839 1 0 24 END