HEADER VIRAL PROTEIN 08-MAY-24 8ZFV TITLE CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF NUCLEOCAPSID PROTEIN FROM TITLE 2 SARS-COV-2 IN COMPLEX WITH CEFTRIAXONE CAVEAT 8ZFV 9F2 A 502 HAS WRONG CHIRALITY AT ATOM C11 9F2 A 503 HAS CAVEAT 2 8ZFV WRONG CHIRALITY AT ATOM C11 9F2 D 502 HAS WRONG CHIRALITY CAVEAT 3 8ZFV AT ATOM C11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A, C, B, D; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: N,NUCLEOCAPSID PROTEIN,NC,PROTEIN N; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, NUCLEOCAPSID PROTEIN, RNA BINDING C-TERMINAL DOMAIN, KEYWDS 2 DRUGS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.DHAKA,J.K.MAHTO,S.TOMAR,P.KUMAR REVDAT 1 02-APR-25 8ZFV 0 JRNL AUTH P.DHAKA,J.K.MAHTO,A.SINGH,P.KUMAR,S.TOMAR JRNL TITL STRUCTURAL INSIGHTS INTO THE RNA BINDING INHIBITORS OF THE JRNL TITL 2 C-TERMINAL DOMAIN OF THE SARS-COV-2 NUCLEOCAPSID. JRNL REF J.STRUCT.BIOL. V. 217 08197 2025 JRNL REFN ESSN 1095-8657 JRNL PMID 40113149 JRNL DOI 10.1016/J.JSB.2025.108197 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 33047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1752 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2444 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.1940 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3548 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 669 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.28000 REMARK 3 B22 (A**2) : 1.07000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.03000 REMARK 3 B13 (A**2) : -0.12000 REMARK 3 B23 (A**2) : 0.34000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.161 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.392 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3856 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3545 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5230 ; 1.844 ; 1.838 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8169 ; 0.662 ; 1.797 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 459 ; 7.341 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 55 ;21.586 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;14.035 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 522 ; 0.551 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4664 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 953 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1821 ; 1.295 ; 1.321 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1821 ; 1.290 ; 1.321 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2285 ; 2.086 ; 2.362 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2286 ; 2.086 ; 2.363 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2035 ; 2.365 ; 1.769 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2036 ; 2.365 ; 1.769 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2940 ; 3.835 ; 3.093 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4866 ; 6.470 ;21.920 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4867 ; 6.470 ;21.920 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 251 A 794 REMARK 3 ORIGIN FOR THE GROUP (A): 16.8053 -9.7322 6.5349 REMARK 3 T TENSOR REMARK 3 T11: 0.0204 T22: 0.0020 REMARK 3 T33: 0.0222 T12: -0.0027 REMARK 3 T13: 0.0010 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.4696 L22: 0.1381 REMARK 3 L33: 0.3189 L12: -0.2084 REMARK 3 L13: 0.0152 L23: -0.0616 REMARK 3 S TENSOR REMARK 3 S11: -0.0426 S12: -0.0160 S13: -0.0069 REMARK 3 S21: 0.0011 S22: 0.0123 S23: -0.0195 REMARK 3 S31: -0.0116 S32: 0.0064 S33: 0.0303 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 257 C 652 REMARK 3 ORIGIN FOR THE GROUP (A): -5.1667 9.3060 -8.1763 REMARK 3 T TENSOR REMARK 3 T11: 0.0077 T22: 0.0197 REMARK 3 T33: 0.0163 T12: 0.0057 REMARK 3 T13: 0.0054 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.7079 L22: 0.2569 REMARK 3 L33: 0.0396 L12: 0.1263 REMARK 3 L13: -0.0652 L23: -0.0686 REMARK 3 S TENSOR REMARK 3 S11: -0.0550 S12: -0.0584 S13: 0.0239 REMARK 3 S21: -0.0206 S22: 0.0362 S23: -0.0163 REMARK 3 S31: 0.0147 S32: 0.0044 S33: 0.0188 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 253 B 656 REMARK 3 ORIGIN FOR THE GROUP (A): 4.9242 -16.8943 18.9813 REMARK 3 T TENSOR REMARK 3 T11: 0.0167 T22: 0.0298 REMARK 3 T33: 0.0240 T12: 0.0078 REMARK 3 T13: 0.0042 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.5991 L22: 0.0847 REMARK 3 L33: 0.4942 L12: 0.1821 REMARK 3 L13: -0.1295 L23: 0.0001 REMARK 3 S TENSOR REMARK 3 S11: -0.0325 S12: -0.0944 S13: -0.0945 REMARK 3 S21: -0.0262 S22: -0.0442 S23: -0.0305 REMARK 3 S31: -0.0156 S32: -0.0230 S33: 0.0767 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 254 D 771 REMARK 3 ORIGIN FOR THE GROUP (A): -16.8327 17.4623 -18.3235 REMARK 3 T TENSOR REMARK 3 T11: 0.0083 T22: 0.0106 REMARK 3 T33: 0.0279 T12: -0.0043 REMARK 3 T13: 0.0033 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 0.4869 L22: 0.2389 REMARK 3 L33: 0.4341 L12: -0.2606 REMARK 3 L13: -0.0738 L23: 0.0386 REMARK 3 S TENSOR REMARK 3 S11: -0.0178 S12: 0.0675 S13: 0.0665 REMARK 3 S21: 0.0227 S22: -0.0357 S23: -0.0196 REMARK 3 S31: -0.0134 S32: 0.0105 S33: 0.0534 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8ZFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1300047594. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34801 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 26.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 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 <I/SIGMA(I)> FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6YUN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, 0.2 M LITHIUM SULFATE, 50 REMARK 280 MM TRIS PH 8.0, VAPOR DIFFUSION, SITTING DROP, 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 5330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 245 REMARK 465 GLY A 246 REMARK 465 THR A 247 REMARK 465 LYS A 248 REMARK 465 LYS A 249 REMARK 465 SER A 250 REMARK 465 PRO A 365 REMARK 465 THR A 366 REMARK 465 GLU A 367 REMARK 465 PRO A 368 REMARK 465 LYS A 369 REMARK 465 LYS A 370 REMARK 465 ASP A 371 REMARK 465 LYS A 372 REMARK 465 LYS A 373 REMARK 465 LYS A 374 REMARK 465 LYS A 375 REMARK 465 ALA A 376 REMARK 465 ASP A 377 REMARK 465 GLU A 378 REMARK 465 THR A 379 REMARK 465 GLN A 380 REMARK 465 ALA A 381 REMARK 465 LEU A 382 REMARK 465 PRO A 383 REMARK 465 GLN A 384 REMARK 465 ARG A 385 REMARK 465 GLN A 386 REMARK 465 LYS A 387 REMARK 465 LYS A 388 REMARK 465 GLN A 389 REMARK 465 GLN A 390 REMARK 465 THR A 391 REMARK 465 VAL A 392 REMARK 465 THR A 393 REMARK 465 LEU A 394 REMARK 465 LEU A 395 REMARK 465 PRO A 396 REMARK 465 ALA A 397 REMARK 465 ALA A 398 REMARK 465 ASP A 399 REMARK 465 LEU A 400 REMARK 465 ASP A 401 REMARK 465 ASP A 402 REMARK 465 PHE A 403 REMARK 465 SER A 404 REMARK 465 LYS A 405 REMARK 465 GLN A 406 REMARK 465 LEU A 407 REMARK 465 GLN A 408 REMARK 465 GLN A 409 REMARK 465 SER A 410 REMARK 465 MET A 411 REMARK 465 SER A 412 REMARK 465 SER A 413 REMARK 465 ALA A 414 REMARK 465 ASP A 415 REMARK 465 SER A 416 REMARK 465 THR A 417 REMARK 465 GLN A 418 REMARK 465 ALA A 419 REMARK 465 MET C 245 REMARK 465 GLY C 246 REMARK 465 THR C 247 REMARK 465 LYS C 248 REMARK 465 LYS C 249 REMARK 465 SER C 250 REMARK 465 ALA C 251 REMARK 465 ALA C 252 REMARK 465 GLU C 253 REMARK 465 ALA C 254 REMARK 465 SER C 255 REMARK 465 LYS C 256 REMARK 465 PRO C 365 REMARK 465 THR C 366 REMARK 465 GLU C 367 REMARK 465 PRO C 368 REMARK 465 LYS C 369 REMARK 465 LYS C 370 REMARK 465 ASP C 371 REMARK 465 LYS C 372 REMARK 465 LYS C 373 REMARK 465 LYS C 374 REMARK 465 LYS C 375 REMARK 465 ALA C 376 REMARK 465 ASP C 377 REMARK 465 GLU C 378 REMARK 465 THR C 379 REMARK 465 GLN C 380 REMARK 465 ALA C 381 REMARK 465 LEU C 382 REMARK 465 PRO C 383 REMARK 465 GLN C 384 REMARK 465 ARG C 385 REMARK 465 GLN C 386 REMARK 465 LYS C 387 REMARK 465 LYS C 388 REMARK 465 GLN C 389 REMARK 465 GLN C 390 REMARK 465 THR C 391 REMARK 465 VAL C 392 REMARK 465 THR C 393 REMARK 465 LEU C 394 REMARK 465 LEU C 395 REMARK 465 PRO C 396 REMARK 465 ALA C 397 REMARK 465 ALA C 398 REMARK 465 ASP C 399 REMARK 465 LEU C 400 REMARK 465 ASP C 401 REMARK 465 ASP C 402 REMARK 465 PHE C 403 REMARK 465 SER C 404 REMARK 465 LYS C 405 REMARK 465 GLN C 406 REMARK 465 LEU C 407 REMARK 465 GLN C 408 REMARK 465 GLN C 409 REMARK 465 SER C 410 REMARK 465 MET C 411 REMARK 465 SER C 412 REMARK 465 SER C 413 REMARK 465 ALA C 414 REMARK 465 ASP C 415 REMARK 465 SER C 416 REMARK 465 THR C 417 REMARK 465 GLN C 418 REMARK 465 ALA C 419 REMARK 465 MET B 245 REMARK 465 GLY B 246 REMARK 465 THR B 247 REMARK 465 LYS B 248 REMARK 465 LYS B 249 REMARK 465 SER B 250 REMARK 465 ALA B 251 REMARK 465 ALA B 252 REMARK 465 PRO B 365 REMARK 465 THR B 366 REMARK 465 GLU B 367 REMARK 465 PRO B 368 REMARK 465 LYS B 369 REMARK 465 LYS B 370 REMARK 465 ASP B 371 REMARK 465 LYS B 372 REMARK 465 LYS B 373 REMARK 465 LYS B 374 REMARK 465 LYS B 375 REMARK 465 ALA B 376 REMARK 465 ASP B 377 REMARK 465 GLU B 378 REMARK 465 THR B 379 REMARK 465 GLN B 380 REMARK 465 ALA B 381 REMARK 465 LEU B 382 REMARK 465 PRO B 383 REMARK 465 GLN B 384 REMARK 465 ARG B 385 REMARK 465 GLN B 386 REMARK 465 LYS B 387 REMARK 465 LYS B 388 REMARK 465 GLN B 389 REMARK 465 GLN B 390 REMARK 465 THR B 391 REMARK 465 VAL B 392 REMARK 465 THR B 393 REMARK 465 LEU B 394 REMARK 465 LEU B 395 REMARK 465 PRO B 396 REMARK 465 ALA B 397 REMARK 465 ALA B 398 REMARK 465 ASP B 399 REMARK 465 LEU B 400 REMARK 465 ASP B 401 REMARK 465 ASP B 402 REMARK 465 PHE B 403 REMARK 465 SER B 404 REMARK 465 LYS B 405 REMARK 465 GLN B 406 REMARK 465 LEU B 407 REMARK 465 GLN B 408 REMARK 465 GLN B 409 REMARK 465 SER B 410 REMARK 465 MET B 411 REMARK 465 SER B 412 REMARK 465 SER B 413 REMARK 465 ALA B 414 REMARK 465 ASP B 415 REMARK 465 SER B 416 REMARK 465 THR B 417 REMARK 465 GLN B 418 REMARK 465 ALA B 419 REMARK 465 MET D 245 REMARK 465 GLY D 246 REMARK 465 THR D 247 REMARK 465 LYS D 248 REMARK 465 LYS D 249 REMARK 465 SER D 250 REMARK 465 ALA D 251 REMARK 465 ALA D 252 REMARK 465 GLU D 253 REMARK 465 PRO D 365 REMARK 465 THR D 366 REMARK 465 GLU D 367 REMARK 465 PRO D 368 REMARK 465 LYS D 369 REMARK 465 LYS D 370 REMARK 465 ASP D 371 REMARK 465 LYS D 372 REMARK 465 LYS D 373 REMARK 465 LYS D 374 REMARK 465 LYS D 375 REMARK 465 ALA D 376 REMARK 465 ASP D 377 REMARK 465 GLU D 378 REMARK 465 THR D 379 REMARK 465 GLN D 380 REMARK 465 ALA D 381 REMARK 465 LEU D 382 REMARK 465 PRO D 383 REMARK 465 GLN D 384 REMARK 465 ARG D 385 REMARK 465 GLN D 386 REMARK 465 LYS D 387 REMARK 465 LYS D 388 REMARK 465 GLN D 389 REMARK 465 GLN D 390 REMARK 465 THR D 391 REMARK 465 VAL D 392 REMARK 465 THR D 393 REMARK 465 LEU D 394 REMARK 465 LEU D 395 REMARK 465 PRO D 396 REMARK 465 ALA D 397 REMARK 465 ALA D 398 REMARK 465 ASP D 399 REMARK 465 LEU D 400 REMARK 465 ASP D 401 REMARK 465 ASP D 402 REMARK 465 PHE D 403 REMARK 465 SER D 404 REMARK 465 LYS D 405 REMARK 465 GLN D 406 REMARK 465 LEU D 407 REMARK 465 GLN D 408 REMARK 465 GLN D 409 REMARK 465 SER D 410 REMARK 465 MET D 411 REMARK 465 SER D 412 REMARK 465 SER D 413 REMARK 465 ALA D 414 REMARK 465 ASP D 415 REMARK 465 SER D 416 REMARK 465 THR D 417 REMARK 465 GLN D 418 REMARK 465 ALA D 419 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 TYR C 268 89.04 -158.89 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 ARG A 262 0.13 SIDE CHAIN REMARK 500 ARG B 259 0.23 SIDE CHAIN REMARK 500 ARG B 276 0.22 SIDE CHAIN REMARK 500 ARG D 276 0.21 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8ZFV A 247 419 UNP P0DTC9 NCAP_SARS2 247 419 DBREF 8ZFV C 247 419 UNP P0DTC9 NCAP_SARS2 247 419 DBREF 8ZFV B 247 419 UNP P0DTC9 NCAP_SARS2 247 419 DBREF 8ZFV D 247 419 UNP P0DTC9 NCAP_SARS2 247 419 SEQADV 8ZFV MET A 245 UNP P0DTC9 INITIATING METHIONINE SEQADV 8ZFV GLY A 246 UNP P0DTC9 EXPRESSION TAG SEQADV 8ZFV MET C 245 UNP P0DTC9 INITIATING METHIONINE SEQADV 8ZFV GLY C 246 UNP P0DTC9 EXPRESSION TAG SEQADV 8ZFV MET B 245 UNP P0DTC9 INITIATING METHIONINE SEQADV 8ZFV GLY B 246 UNP P0DTC9 EXPRESSION TAG SEQADV 8ZFV MET D 245 UNP P0DTC9 INITIATING METHIONINE SEQADV 8ZFV GLY D 246 UNP P0DTC9 EXPRESSION TAG SEQRES 1 A 175 MET GLY THR LYS LYS SER ALA ALA GLU ALA SER LYS LYS SEQRES 2 A 175 PRO ARG GLN LYS ARG THR ALA THR LYS ALA TYR ASN VAL SEQRES 3 A 175 THR GLN ALA PHE GLY ARG ARG GLY PRO GLU GLN THR GLN SEQRES 4 A 175 GLY ASN PHE GLY ASP GLN GLU LEU ILE ARG GLN GLY THR SEQRES 5 A 175 ASP TYR LYS HIS TRP PRO GLN ILE ALA GLN PHE ALA PRO SEQRES 6 A 175 SER ALA SER ALA PHE PHE GLY MET SER ARG ILE GLY MET SEQRES 7 A 175 GLU VAL THR PRO SER GLY THR TRP LEU THR TYR THR GLY SEQRES 8 A 175 ALA ILE LYS LEU ASP ASP LYS ASP PRO ASN PHE LYS ASP SEQRES 9 A 175 GLN VAL ILE LEU LEU ASN LYS HIS ILE ASP ALA TYR LYS SEQRES 10 A 175 THR PHE PRO PRO THR GLU PRO LYS LYS ASP LYS LYS LYS SEQRES 11 A 175 LYS ALA ASP GLU THR GLN ALA LEU PRO GLN ARG GLN LYS SEQRES 12 A 175 LYS GLN GLN THR VAL THR LEU LEU PRO ALA ALA ASP LEU SEQRES 13 A 175 ASP ASP PHE SER LYS GLN LEU GLN GLN SER MET SER SER SEQRES 14 A 175 ALA ASP SER THR GLN ALA SEQRES 1 C 175 MET GLY THR LYS LYS SER ALA ALA GLU ALA SER LYS LYS SEQRES 2 C 175 PRO ARG GLN LYS ARG THR ALA THR LYS ALA TYR ASN VAL SEQRES 3 C 175 THR GLN ALA PHE GLY ARG ARG GLY PRO GLU GLN THR GLN SEQRES 4 C 175 GLY ASN PHE GLY ASP GLN GLU LEU ILE ARG GLN GLY THR SEQRES 5 C 175 ASP TYR LYS HIS TRP PRO GLN ILE ALA GLN PHE ALA PRO SEQRES 6 C 175 SER ALA SER ALA PHE PHE GLY MET SER ARG ILE GLY MET SEQRES 7 C 175 GLU VAL THR PRO SER GLY THR TRP LEU THR TYR THR GLY SEQRES 8 C 175 ALA ILE LYS LEU ASP ASP LYS ASP PRO ASN PHE LYS ASP SEQRES 9 C 175 GLN VAL ILE LEU LEU ASN LYS HIS ILE ASP ALA TYR LYS SEQRES 10 C 175 THR PHE PRO PRO THR GLU PRO LYS LYS ASP LYS LYS LYS SEQRES 11 C 175 LYS ALA ASP GLU THR GLN ALA LEU PRO GLN ARG GLN LYS SEQRES 12 C 175 LYS GLN GLN THR VAL THR LEU LEU PRO ALA ALA ASP LEU SEQRES 13 C 175 ASP ASP PHE SER LYS GLN LEU GLN GLN SER MET SER SER SEQRES 14 C 175 ALA ASP SER THR GLN ALA SEQRES 1 B 175 MET GLY THR LYS LYS SER ALA ALA GLU ALA SER LYS LYS SEQRES 2 B 175 PRO ARG GLN LYS ARG THR ALA THR LYS ALA TYR ASN VAL SEQRES 3 B 175 THR GLN ALA PHE GLY ARG ARG GLY PRO GLU GLN THR GLN SEQRES 4 B 175 GLY ASN PHE GLY ASP GLN GLU LEU ILE ARG GLN GLY THR SEQRES 5 B 175 ASP TYR LYS HIS TRP PRO GLN ILE ALA GLN PHE ALA PRO SEQRES 6 B 175 SER ALA SER ALA PHE PHE GLY MET SER ARG ILE GLY MET SEQRES 7 B 175 GLU VAL THR PRO SER GLY THR TRP LEU THR TYR THR GLY SEQRES 8 B 175 ALA ILE LYS LEU ASP ASP LYS ASP PRO ASN PHE LYS ASP SEQRES 9 B 175 GLN VAL ILE LEU LEU ASN LYS HIS ILE ASP ALA TYR LYS SEQRES 10 B 175 THR PHE PRO PRO THR GLU PRO LYS LYS ASP LYS LYS LYS SEQRES 11 B 175 LYS ALA ASP GLU THR GLN ALA LEU PRO GLN ARG GLN LYS SEQRES 12 B 175 LYS GLN GLN THR VAL THR LEU LEU PRO ALA ALA ASP LEU SEQRES 13 B 175 ASP ASP PHE SER LYS GLN LEU GLN GLN SER MET SER SER SEQRES 14 B 175 ALA ASP SER THR GLN ALA SEQRES 1 D 175 MET GLY THR LYS LYS SER ALA ALA GLU ALA SER LYS LYS SEQRES 2 D 175 PRO ARG GLN LYS ARG THR ALA THR LYS ALA TYR ASN VAL SEQRES 3 D 175 THR GLN ALA PHE GLY ARG ARG GLY PRO GLU GLN THR GLN SEQRES 4 D 175 GLY ASN PHE GLY ASP GLN GLU LEU ILE ARG GLN GLY THR SEQRES 5 D 175 ASP TYR LYS HIS TRP PRO GLN ILE ALA GLN PHE ALA PRO SEQRES 6 D 175 SER ALA SER ALA PHE PHE GLY MET SER ARG ILE GLY MET SEQRES 7 D 175 GLU VAL THR PRO SER GLY THR TRP LEU THR TYR THR GLY SEQRES 8 D 175 ALA ILE LYS LEU ASP ASP LYS ASP PRO ASN PHE LYS ASP SEQRES 9 D 175 GLN VAL ILE LEU LEU ASN LYS HIS ILE ASP ALA TYR LYS SEQRES 10 D 175 THR PHE PRO PRO THR GLU PRO LYS LYS ASP LYS LYS LYS SEQRES 11 D 175 LYS ALA ASP GLU THR GLN ALA LEU PRO GLN ARG GLN LYS SEQRES 12 D 175 LYS GLN GLN THR VAL THR LEU LEU PRO ALA ALA ASP LEU SEQRES 13 D 175 ASP ASP PHE SER LYS GLN LEU GLN GLN SER MET SER SER SEQRES 14 D 175 ALA ASP SER THR GLN ALA HET SO4 A 501 5 HET 9F2 A 502 36 HET 9F2 A 503 36 HET PEG D 501 7 HET 9F2 D 502 36 HETNAM SO4 SULFATE ION HETNAM 9F2 CEFTRIAXONE HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 5 SO4 O4 S 2- FORMUL 6 9F2 3(C18 H18 N8 O7 S3) FORMUL 8 PEG C4 H10 O3 FORMUL 10 HOH *669(H2 O) HELIX 1 AA1 ALA A 252 LYS A 256 5 5 HELIX 2 AA2 PRO A 258 ARG A 262 5 5 HELIX 3 AA3 ASN A 269 GLY A 275 1 7 HELIX 4 AA4 ASP A 288 GLY A 295 1 8 HELIX 5 AA5 THR A 296 TYR A 298 5 3 HELIX 6 AA6 HIS A 300 GLN A 306 1 7 HELIX 7 AA7 SER A 310 SER A 318 1 9 HELIX 8 AA8 ASN A 345 ILE A 357 1 13 HELIX 9 AA9 ASP A 358 PHE A 363 5 6 HELIX 10 AB1 PRO C 258 ARG C 262 5 5 HELIX 11 AB2 ASN C 269 GLY C 275 1 7 HELIX 12 AB3 ASP C 288 GLY C 295 1 8 HELIX 13 AB4 THR C 296 TYR C 298 5 3 HELIX 14 AB5 HIS C 300 GLN C 306 1 7 HELIX 15 AB6 SER C 310 SER C 318 1 9 HELIX 16 AB7 ASN C 345 ILE C 357 1 13 HELIX 17 AB8 ASP C 358 PHE C 363 5 6 HELIX 18 AB9 GLU B 253 LYS B 257 5 5 HELIX 19 AC1 PRO B 258 ARG B 262 5 5 HELIX 20 AC2 ASN B 269 GLY B 275 1 7 HELIX 21 AC3 ASP B 288 GLY B 295 1 8 HELIX 22 AC4 THR B 296 TYR B 298 5 3 HELIX 23 AC5 HIS B 300 GLN B 306 1 7 HELIX 24 AC6 SER B 310 SER B 318 1 9 HELIX 25 AC7 ASN B 345 ILE B 357 1 13 HELIX 26 AC8 ASP B 358 PHE B 363 5 6 HELIX 27 AC9 PRO D 258 ARG D 262 5 5 HELIX 28 AD1 ASN D 269 GLY D 275 1 7 HELIX 29 AD2 ASP D 288 GLY D 295 1 8 HELIX 30 AD3 THR D 296 TYR D 298 5 3 HELIX 31 AD4 HIS D 300 GLN D 306 1 7 HELIX 32 AD5 SER D 310 SER D 318 1 9 HELIX 33 AD6 ASN D 345 ILE D 357 1 13 HELIX 34 AD7 ASP D 358 PHE D 363 5 6 SHEET 1 AA1 4 ARG A 319 THR A 325 0 SHEET 2 AA1 4 GLY A 328 LYS A 338 -1 O GLY A 328 N THR A 325 SHEET 3 AA1 4 GLY B 328 LYS B 338 -1 O ILE B 337 N LEU A 331 SHEET 4 AA1 4 ARG B 319 THR B 325 -1 N THR B 325 O GLY B 328 SHEET 1 AA2 4 ARG C 319 THR C 325 0 SHEET 2 AA2 4 GLY C 328 LYS C 338 -1 O THR C 334 N ARG C 319 SHEET 3 AA2 4 GLY D 328 LYS D 338 -1 O ILE D 337 N LEU C 331 SHEET 4 AA2 4 ARG D 319 THR D 325 -1 N ARG D 319 O THR D 334 CRYST1 43.539 46.643 69.021 106.66 90.11 93.46 P 1 4 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 0.022968 0.001388 0.000464 0.00000 SCALE2 0.000000 0.021479 0.006441 0.00000 SCALE3 0.000000 0.000000 0.015126 0.00000