HEADER UNKNOWN FUNCTION 04-MAR-22 7Z4S TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MPRO IN COMPLEX WITH CYCLIC PEPTIDE TITLE 2 GM4 INCLUDING UNNATURAL AMINO ACIDS. CAVEAT 7Z4S CYS C 13 HAS WRONG CHIRALITY AT ATOM CA CYS D 13 HAS WRONG CAVEAT 2 7Z4S CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: A, B; 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 MOL_ID: 2; COMPND 9 MOLECULE: MACROCYCLIC PEPTIDE INHIBITOR; COMPND 10 CHAIN: C, D; COMPND 11 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS PROTEASE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.D.OWEN,T.MIURA,T.MALLA,L.LUKACIK,C.M.STRAIN-DAMERELL,A.TUMBER, AUTHOR 2 L.BREWITZ,M.A.MCDONOUGH,E.SALAH,N.TERASAKA,T.KATOH,A.KAWAMURA, AUTHOR 3 C.J.SCHOFIELD,H.SUGA,M.A.WALSH REVDAT 6 07-FEB-24 7Z4S 1 REMARK REVDAT 5 15-NOV-23 7Z4S 1 REMARK ATOM REVDAT 4 19-JUL-23 7Z4S 1 JRNL REMARK REVDAT 3 14-JUN-23 7Z4S 1 CAVEAT COMPND SOURCE JRNL REVDAT 3 2 1 REMARK DBREF SEQRES HET REVDAT 3 3 1 HETNAM HETSYN FORMUL SHEET REVDAT 3 4 1 LINK ATOM REVDAT 2 24-MAY-23 7Z4S 1 COMPND FORMUL LINK ATOM REVDAT 1 22-MAR-23 7Z4S 0 JRNL AUTH T.MIURA,T.R.MALLA,C.D.OWEN,A.TUMBER,L.BREWITZ,M.A.MCDONOUGH, JRNL AUTH 2 E.SALAH,N.TERASAKA,T.KATOH,P.LUKACIK,C.STRAIN-DAMERELL, JRNL AUTH 3 H.MIKOLAJEK,M.A.WALSH,A.KAWAMURA,C.J.SCHOFIELD,H.SUGA JRNL TITL IN VITRO SELECTION OF MACROCYCLIC PEPTIDE INHIBITORS JRNL TITL 2 CONTAINING CYCLIC GAMMA 2,4 -AMINO ACIDS TARGETING THE JRNL TITL 3 SARS-COV-2 MAIN PROTEASE. JRNL REF NAT.CHEM. V. 15 998 2023 JRNL REFN ESSN 1755-4349 JRNL PMID 37217786 JRNL DOI 10.1038/S41557-023-01205-1 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 65737 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3366 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4638 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.3700 REMARK 3 BIN FREE R VALUE SET COUNT : 257 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4926 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 292 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.35000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : 0.65000 REMARK 3 B12 (A**2) : -0.40000 REMARK 3 B13 (A**2) : -0.45000 REMARK 3 B23 (A**2) : 0.25000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.294 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5123 ; 0.008 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 4741 ; 0.001 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6956 ; 1.322 ; 1.855 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10896 ; 1.092 ; 2.698 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 636 ; 6.492 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 254 ;34.997 ;23.031 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 800 ;13.080 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;14.606 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 771 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5915 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1229 ; 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): 2544 ; 2.239 ; 1.611 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2542 ; 2.238 ; 1.611 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3180 ; 2.973 ; 2.409 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3180 ; 2.973 ; 2.409 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2579 ; 3.432 ; 1.953 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2579 ; 3.432 ; 1.953 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3773 ; 4.848 ; 2.791 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5623 ; 7.246 ;20.310 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5576 ; 7.239 ;20.005 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 1 A 402 REMARK 3 ORIGIN FOR THE GROUP (A): 12.9350 0.3340 0.6620 REMARK 3 T TENSOR REMARK 3 T11: 0.0887 T22: 0.1071 REMARK 3 T33: 0.1505 T12: -0.0881 REMARK 3 T13: -0.1121 T23: 0.1180 REMARK 3 L TENSOR REMARK 3 L11: 1.4095 L22: 2.0501 REMARK 3 L33: 1.3763 L12: -0.7110 REMARK 3 L13: -0.2731 L23: 0.6946 REMARK 3 S TENSOR REMARK 3 S11: 0.0359 S12: -0.0528 S13: 0.0341 REMARK 3 S21: 0.0242 S22: -0.0516 S23: -0.0535 REMARK 3 S31: -0.0151 S32: -0.0450 S33: 0.0157 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 : B 1 B 404 REMARK 3 ORIGIN FOR THE GROUP (A): -13.3280 0.2290 0.8080 REMARK 3 T TENSOR REMARK 3 T11: 0.0862 T22: 0.0760 REMARK 3 T33: 0.1552 T12: -0.0675 REMARK 3 T13: -0.1111 T23: 0.1012 REMARK 3 L TENSOR REMARK 3 L11: 1.6343 L22: 0.9215 REMARK 3 L33: 2.1112 L12: -0.5128 REMARK 3 L13: 0.7498 L23: -0.4310 REMARK 3 S TENSOR REMARK 3 S11: -0.0113 S12: -0.0066 S13: -0.0392 REMARK 3 S21: 0.0068 S22: -0.0053 S23: 0.0251 REMARK 3 S31: -0.0801 S32: 0.0467 S33: 0.0167 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 : C 0 C 14 REMARK 3 ORIGIN FOR THE GROUP (A): -15.3760 19.9060 -5.5180 REMARK 3 T TENSOR REMARK 3 T11: 0.2799 T22: 0.0666 REMARK 3 T33: 0.2684 T12: -0.0426 REMARK 3 T13: -0.0944 T23: 0.0985 REMARK 3 L TENSOR REMARK 3 L11: 3.1120 L22: 1.5077 REMARK 3 L33: 7.6469 L12: -0.9828 REMARK 3 L13: 1.2730 L23: -0.5650 REMARK 3 S TENSOR REMARK 3 S11: 0.0749 S12: 0.3142 S13: 0.5093 REMARK 3 S21: -0.0974 S22: -0.1188 S23: -0.1241 REMARK 3 S31: -1.0183 S32: 0.1419 S33: 0.0440 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 0 D 14 REMARK 3 ORIGIN FOR THE GROUP (A): 15.2720 -19.0020 8.6250 REMARK 3 T TENSOR REMARK 3 T11: 0.1563 T22: 0.0951 REMARK 3 T33: 0.1630 T12: -0.0430 REMARK 3 T13: -0.0941 T23: 0.1188 REMARK 3 L TENSOR REMARK 3 L11: 2.3221 L22: 6.4411 REMARK 3 L33: 2.2343 L12: -0.6181 REMARK 3 L13: -1.3351 L23: 3.3754 REMARK 3 S TENSOR REMARK 3 S11: -0.0375 S12: -0.2427 S13: -0.2646 REMARK 3 S21: 0.5153 S22: -0.0182 S23: -0.0748 REMARK 3 S31: 0.2715 S32: 0.0800 S33: 0.0557 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 7Z4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1292121322. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 407784 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 53.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 53.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.02700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 29.00 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: 6YB7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPRO WAS THAWED AND DILUTED TO 6 MG/ML REMARK 280 USING 20 MM HEPES PH 7.5, 50 MM NACL. GM4 WAS DILUTED INTO THE REMARK 280 PROTEIN SOLUTION TO A FINAL CONCENTRATION OF 10 MM AND ALLOWED REMARK 280 TO INCUBATE FOR TWO HOURS AT ROOM TEMPERATURE PRIOR TO REMARK 280 DISPENSING PLATES. THE DROP COMPOSITION WAS 0.15 UL PROTEIN REMARK 280 LIGAND SOLUTION, 0.3 UL 11% (V/V) PEG 4K, 0.1 M MES PH 6.5, AND REMARK 280 0.05 UL MPRO CRYSTAL SEED STOCK. THE MPRO CRYSTAL SEED STOCK WAS REMARK 280 PREPARED BY CRUSHING MPRO CRYSTALS WITH A PIPETTE TIP, REMARK 280 SUSPENDING THEM IN 30% PEG 4K, 5% (V/V) DMSO, 0.1 M MES PH 6.5, REMARK 280 AND VORTEXING FOR 60 S WITH APPROXIMATELY 10 GLASS BEADS (1.0 MM REMARK 280 DIAMETER, BIOSPEC PRODUCTS). RESERVOIR SOLUTION WAS 11% (V/V) REMARK 280 PEG 4K, 5% (V/V) DMSO, 0.1 M MES PH 6.5. CRYSTALS WERE GROWN REMARK 280 USING THE SITTING DROP VAPOR DIFFUSION METHOD AT 20 C AND REMARK 280 APPEARED WITHIN 24 HOURS, REACHING FULL SIZE WITHIN 36 HOURS. REMARK 280 CRYSTALS WERE LOOPED AFTER ONE WEEK., VAPOR DIFFUSION, SITTING REMARK 280 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 O HOH A 545 O HOH A 574 2.15 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 II7 C 4 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 II7 D 4 CA - C - N ANGL. DEV. = 16.7 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 -131.00 52.36 REMARK 500 ASN A 51 69.72 -152.55 REMARK 500 ASN A 84 -123.64 54.22 REMARK 500 TYR A 154 -101.34 52.32 REMARK 500 TYR A 154 -101.34 51.93 REMARK 500 THR A 224 108.07 -46.19 REMARK 500 ASP B 33 -130.67 53.14 REMARK 500 ASN B 51 68.73 -151.67 REMARK 500 ASN B 84 -124.00 54.61 REMARK 500 TYR B 154 -101.71 49.25 REMARK 500 HIS C 3 32.35 -90.82 REMARK 500 HIS D 3 36.37 -91.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 II7 C 4 LEU C 5 -135.03 REMARK 500 II7 D 4 LEU D 5 -137.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 II7 C 4 16.75 REMARK 500 II7 D 4 16.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Z4S A 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 7Z4S B 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 7Z4S C 0 14 PDB 7Z4S 7Z4S 0 14 DBREF 7Z4S D 0 14 PDB 7Z4S 7Z4S 0 14 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 CSO 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 CSO 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 SEQRES 1 C 15 ACE DTY PHE HIS II7 LEU ASN LEU GLY TYR ARG PRO GLY SEQRES 2 C 15 CYS NH2 SEQRES 1 D 15 ACE DTY PHE HIS II7 LEU ASN LEU GLY TYR ARG PRO GLY SEQRES 2 D 15 CYS NH2 MODRES 7Z4S CSO A 156 CYS MODIFIED RESIDUE MODRES 7Z4S CSO B 156 CYS MODIFIED RESIDUE HET CSO A 156 7 HET CSO B 156 7 HET ACE C 0 3 HET DTY C 1 12 HET II7 C 4 7 HET NH2 C 14 1 HET ACE D 0 3 HET DTY D 1 12 HET II7 D 4 7 HET NH2 D 14 1 HET PEG A 401 7 HET DMS A 402 4 HET PEG B 401 7 HET EDO B 402 4 HET PGE B 403 10 HET EDO B 404 4 HETNAM CSO S-HYDROXYCYSTEINE HETNAM ACE ACETYL GROUP HETNAM DTY D-TYROSINE HETNAM II7 CIS-3-AMINOCYCLOBUTANE CARBOXYLIC ACID HETNAM NH2 AMINO GROUP HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETSYN II7 3-AZANYLCYCLOBUTANE-1-CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 DTY 2(C9 H11 N O3) FORMUL 3 II7 2(C5 H9 N O2) FORMUL 3 NH2 2(H2 N) FORMUL 5 PEG 2(C4 H10 O3) FORMUL 6 DMS C2 H6 O S FORMUL 8 EDO 2(C2 H6 O2) FORMUL 9 PGE C6 H14 O4 FORMUL 11 HOH *292(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 THR A 45 LEU A 50 1 6 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 SER A 62 HIS A 64 5 3 HELIX 6 AA6 ILE A 200 ASN A 214 1 15 HELIX 7 AA7 THR A 226 TYR A 237 1 12 HELIX 8 AA8 THR A 243 LEU A 250 1 8 HELIX 9 AA9 LEU A 250 GLY A 258 1 9 HELIX 10 AB1 ALA A 260 GLY A 275 1 16 HELIX 11 AB2 THR A 292 GLY A 302 1 11 HELIX 12 AB3 SER B 10 GLY B 15 1 6 HELIX 13 AB4 HIS B 41 CYS B 44 5 4 HELIX 14 AB5 THR B 45 LEU B 50 1 6 HELIX 15 AB6 ASN B 53 ARG B 60 1 8 HELIX 16 AB7 SER B 62 HIS B 64 5 3 HELIX 17 AB8 ILE B 200 ASN B 214 1 15 HELIX 18 AB9 THR B 226 TYR B 237 1 12 HELIX 19 AC1 THR B 243 LEU B 250 1 8 HELIX 20 AC2 LEU B 250 GLY B 258 1 9 HELIX 21 AC3 ALA B 260 GLY B 275 1 16 HELIX 22 AC4 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 ALA A 70 O VAL A 73 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 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 ILE A 78 O LYS A 90 SHEET 1 AA2 3 LYS A 100 PHE A 103 0 SHEET 2 AA2 3 CSO A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 3 HIS A 172 THR A 175 -1 O THR A 175 N MET A 162 SHEET 1 AA3 5 SER A 121 ALA A 129 0 SHEET 2 AA3 5 THR A 111 TYR A 118 -1 N ALA A 116 O SER A 123 SHEET 3 AA3 5 VAL A 148 ASP A 153 -1 O PHE A 150 N SER A 113 SHEET 4 AA3 5 CSO A 156 GLU A 166 -1 O CSO A 156 N ASP A 153 SHEET 5 AA3 5 DTY D 1 PHE D 2 -1 O DTY D 1 N GLU A 166 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 GLY B 29 N VAL B 18 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 SER B 81 O LYS B 88 SHEET 1 AA5 3 LYS B 100 PHE B 103 0 SHEET 2 AA5 3 CSO B 156 GLU B 166 1 O VAL B 157 N LYS B 100 SHEET 3 AA5 3 HIS B 172 THR B 175 -1 O THR B 175 N MET B 162 SHEET 1 AA6 5 SER B 121 ALA B 129 0 SHEET 2 AA6 5 THR B 111 TYR B 118 -1 N ALA B 116 O SER B 123 SHEET 3 AA6 5 VAL B 148 ASP B 153 -1 O PHE B 150 N SER B 113 SHEET 4 AA6 5 CSO B 156 GLU B 166 -1 O SER B 158 N ASN B 151 SHEET 5 AA6 5 DTY C 1 PHE C 2 -1 O DTY C 1 N GLU B 166 LINK C ASP A 155 N CSO A 156 1555 1555 1.34 LINK C CSO A 156 N VAL A 157 1555 1555 1.33 LINK C ASP B 155 N CSO B 156 1555 1555 1.34 LINK C CSO B 156 N VAL B 157 1555 1555 1.34 LINK C ACE C 0 N DTY C 1 1555 1555 1.33 LINK CH3 ACE C 0 SG CYS C 13 1555 1555 1.81 LINK C DTY C 1 N PHE C 2 1555 1555 1.33 LINK C HIS C 3 N II7 C 4 1555 1555 1.34 LINK C II7 C 4 N LEU C 5 1555 1555 1.34 LINK C CYS C 13 N NH2 C 14 1555 1555 1.32 LINK C ACE D 0 N DTY D 1 1555 1555 1.33 LINK CH3 ACE D 0 SG CYS D 13 1555 1555 1.82 LINK C DTY D 1 N PHE D 2 1555 1555 1.33 LINK C HIS D 3 N II7 D 4 1555 1555 1.34 LINK C II7 D 4 N LEU D 5 1555 1555 1.34 LINK C CYS D 13 N NH2 D 14 1555 1555 1.33 CRYST1 54.515 56.112 63.238 113.87 110.53 90.92 P 1 2 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 0.018344 0.000295 0.007786 0.00000 SCALE2 0.000000 0.017824 0.008688 0.00000 SCALE3 0.000000 0.000000 0.018785 0.00000