PDB Short entry for 5RGL HEADER HYDROLASE/HYDROLASE INHIBITOR 07-APR-20 5RGL TITLE PANDDA ANALYSIS GROUP DEPOSITION SARS-COV-2 MAIN PROTEASE FRAGMENT TITLE 2 SCREEN -- CRYSTAL STRUCTURE OF SARS-COV-2 MAIN PROTEASE IN COMPLEX TITLE 3 WITH PCM-0102962 (MPRO-X0705) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SARS-COV-2 MAIN PROTEASE,3CL-PRO,3CLP,MAIN PROTEASE,MPRO, COMPND 5 NON-STRUCTURAL PROTEIN 5,NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 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 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.FEARON,C.D.OWEN,A.DOUANGAMATH,P.LUKACIK,A.J.POWELL,C.M.STRAIN- AUTHOR 2 DAMERELL,E.RESNICK,T.KROJER,P.GEHRTZ,C.WILD,A.AIMON,J.BRANDAO-NETO, AUTHOR 3 A.CARBERY,L.DUNNETT,R.SKYNER,M.SNEE,N.LONDON,M.A.WALSH,F.VON DELFT REVDAT 4 24-FEB-21 5RGL 1 JRNL REVDAT 3 27-JAN-21 5RGL 1 COMPND REVDAT 2 06-MAY-20 5RGL 1 COMPND SOURCE DBREF REVDAT 1 15-APR-20 5RGL 0 JRNL AUTH A.DOUANGAMATH,D.FEARON,P.GEHRTZ,T.KROJER,P.LUKACIK,C.D.OWEN, JRNL AUTH 2 E.RESNICK,C.STRAIN-DAMERELL,A.AIMON,P.ABRANYI-BALOGH, JRNL AUTH 3 J.BRANDAO-NETO,A.CARBERY,G.DAVISON,A.DIAS,T.D.DOWNES, JRNL AUTH 4 L.DUNNETT,M.FAIRHEAD,J.D.FIRTH,S.P.JONES,A.KEELEY, JRNL AUTH 5 G.M.KESERU,H.F.KLEIN,M.P.MARTIN,M.E.M.NOBLE,P.O'BRIEN, JRNL AUTH 6 A.POWELL,R.N.REDDI,R.SKYNER,M.SNEE,M.J.WARING,C.WILD, JRNL AUTH 7 N.LONDON,F.VON DELFT,M.A.WALSH JRNL TITL CRYSTALLOGRAPHIC AND ELECTROPHILIC FRAGMENT SCREENING OF THE JRNL TITL 2 SARS-COV-2 MAIN PROTEASE. JRNL REF NAT COMMUN V. 11 5047 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 33028810 JRNL DOI 10.1038/S41467-020-18709-W REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24105 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1262 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1735 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2347 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 337 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.26000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.64000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.733 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2778 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2371 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3608 ; 1.503 ; 1.639 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5518 ; 1.378 ; 1.568 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 7.917 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;32.171 ;23.101 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 421 ;13.871 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;11.587 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 334 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3078 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 551 ; 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): 1396 ; 1.406 ; 2.070 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1380 ; 1.414 ; 2.061 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1687 ; 2.248 ; 3.079 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5RGL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-20. REMARK 100 THE DEPOSITION ID IS D_1001403192. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9126 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25397 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 55.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.21500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 1.51800 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 6LU7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4K, 5% DMSO, 0.1M MES PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.43900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.43350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.43900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.43350 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: 4720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 747 LIES ON A SPECIAL POSITION. 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 PHE A 305 REMARK 465 GLN A 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 751 O HOH A 765 2.02 REMARK 500 O HOH A 655 O HOH A 744 2.17 REMARK 500 OE1 GLU A 288 O HOH A 501 2.18 REMARK 500 O HOH A 715 O HOH A 719 2.19 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 O HOH A 723 O HOH A 732 4545 1.99 REMARK 500 O HOH A 828 O HOH A 828 2554 2.04 REMARK 500 O HOH A 615 O HOH A 729 1554 2.14 REMARK 500 O HOH A 547 O HOH A 557 2554 2.19 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 -134.66 58.22 REMARK 500 ASN A 51 61.92 -162.45 REMARK 500 ASN A 84 -119.57 51.68 REMARK 500 TYR A 154 -79.68 55.85 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 A 837 DISTANCE = 6.53 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U0Y A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 405 DBREF 5RGL A 1 306 UNP P0DTD1 R1AB_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 HET DMS A 401 4 HET DMS A 402 4 HET DMS A 403 4 HET U0Y A 404 18 HET DMS A 405 4 HETNAM DMS DIMETHYL SULFOXIDE HETNAM U0Y 1-[4-(4-METHYLBENZENE-1-CARBONYL)PIPERAZIN-1-YL]ETHAN- HETNAM 2 U0Y 1-ONE FORMUL 2 DMS 4(C2 H6 O S) FORMUL 5 U0Y C14 H18 N2 O2 FORMUL 7 HOH *337(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 GLU A 47 ASN A 51 5 5 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 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 GLY A 258 1 16 HELIX 9 AA9 ALA A 260 GLY A 275 1 16 HELIX 10 AB1 THR A 292 GLY A 302 1 11 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 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 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 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 PHE A 159 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O THR A 175 N MET A 162 LINK SG CYS A 145 C13 U0Y A 404 1555 1555 1.81 SITE 1 AC1 8 GLN A 74 LEU A 75 ARG A 76 PHE A 223 SITE 2 AC1 8 THR A 224 ASP A 263 HOH A 541 HOH A 597 SITE 1 AC2 5 MET A 6 PHE A 8 SER A 123 GLN A 127 SITE 2 AC2 5 ARG A 298 SITE 1 AC3 3 GLY A 15 MET A 17 LYS A 97 SITE 1 AC4 13 LEU A 27 HIS A 41 ASN A 142 GLY A 143 SITE 2 AC4 13 CYS A 145 HIS A 164 VAL A 297 SER A 301 SITE 3 AC4 13 VAL A 303 DMS A 405 HOH A 508 HOH A 599 SITE 4 AC4 13 HOH A 802 SITE 1 AC5 6 PHE A 140 LEU A 141 ASN A 142 HIS A 163 SITE 2 AC5 6 GLU A 166 U0Y A 404 CRYST1 112.878 52.867 44.455 90.00 102.97 90.00 C 1 2 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 0.008859 0.000000 0.002040 0.00000 SCALE2 0.000000 0.018915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023083 0.00000