HEADER VIRAL PROTEIN 11-FEB-26 23LY
TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MAIN PROTEASE E166V MUTANT IN COMPLEX
TITLE 2 WITH LERITRELVIR
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
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, NSP5, MAIN PROTEASE, CORONAVIRUS, PROTEASE INHIBITOR,
KEYWDS 2 ALPHA-KETOAMIDE INHIBITOR, PEPTIDOMIMETIC INHIBITOR, VIRAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR X.HUANG,Q.LI,Z.YANG,N.ZHONG,X.XIONG
REVDAT 2 24-JUN-26 23LY 1 JRNL
REVDAT 1 03-JUN-26 23LY 0
JRNL AUTH X.HUANG,P.KUZMIC,S.ZHANG,C.A.RAMOS-GUZMAN,X.CHEN,J.GUI,Q.LI,
JRNL AUTH 2 S.YAN,B.ZOU,C.NIU,Y.ZHAO,H.LIN,N.WANG,J.CHEN,X.CHEN,
JRNL AUTH 3 J.SPENCER,A.J.MULHOLLAND,J.CHEN,N.ZHONG,Z.YANG,X.XIONG
JRNL TITL ENHANCED TARGET BINDING BY LERITRELVIR RESTORES DIMERIZATION
JRNL TITL 2 OF MPRO MUTANTS AND MITIGATES DRUG RESISTANCE
JRNL REF BIORXIV 2026
JRNL REFN ISSN 2692-8205
JRNL DOI 10.64898/2026.06.09.730104
REMARK 2
REMARK 2 RESOLUTION. 1.56 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0430
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.16
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 75840
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.148
REMARK 3 FREE R VALUE : 0.197
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.094
REMARK 3 FREE R VALUE TEST SET COUNT : 3863
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) : 1.56
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5313
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.54
REMARK 3 BIN R VALUE (WORKING SET) : 0.2320
REMARK 3 BIN FREE R VALUE SET COUNT : 298
REMARK 3 BIN FREE R VALUE : 0.2600
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4702
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 96
REMARK 3 SOLVENT ATOMS : 481
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.35
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.51600
REMARK 3 B22 (A**2) : 1.64100
REMARK 3 B33 (A**2) : -3.70400
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.09400
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.110
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.226
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4954 ; 0.009 ; 0.012
REMARK 3 BOND LENGTHS OTHERS (A): 4591 ; 0.001 ; 0.016
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6756 ; 1.800 ; 1.794
REMARK 3 BOND ANGLES OTHERS (DEGREES): 10568 ; 0.617 ; 1.728
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 624 ; 6.913 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 32 ;19.799 ; 6.875
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 768 ;13.928 ;10.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 773 ; 0.085 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5866 ; 0.009 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1158 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 899 ; 0.219 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 73 ; 0.214 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2493 ; 0.181 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 304 ; 0.179 ; 0.200
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): 2463 ; 5.956 ; 2.126
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2463 ; 5.938 ; 2.126
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3080 ; 8.871 ; 3.823
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3081 ; 8.870 ; 3.824
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2491 ; 7.151 ; 2.382
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2492 ; 7.149 ; 2.382
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3670 ;10.414 ; 4.253
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3671 ;10.412 ; 4.253
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): 9545 ; 3.609 ; 3.000
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 : 1
REMARK 3
REMARK 3 NCS GROUP NUMBER : 1
REMARK 3 CHAIN NAMES : A B
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 A 1 A 306 NULL
REMARK 3 1 B 1 B 306 NULL
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
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 BULK SOLVENT
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 THEIR
REMARK 3 RIDING POSITIONS
REMARK 4
REMARK 4 23LY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 14-FEB-26.
REMARK 100 THE DEPOSITION ID IS D_1300069463.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-SEP-24
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL19U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97923
REMARK 200 MONOCHROMATOR : DOUBLE MIRROR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS BUILT 20240630
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76106
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560
REMARK 200 RESOLUTION RANGE LOW (A) : 53.160
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 5.200
REMARK 200 R MERGE (I) : 0.07600
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 12.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.85900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 2.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER 2.8.3
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.71
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM CITRATE TRIBASIC PH
REMARK 280 6.0, 14% W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 53.15850
REMARK 290 SMTRY3 2 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: 3410 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 24680 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 TYR A 154 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2
REMARK 470 MET A 235 CG SD CE
REMARK 470 ARG B 222 CG CD NE CZ NH1 NH2
REMARK 470 MET B 235 CG SD CE
REMARK 470 LYS B 236 CD CE NZ
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 NE2 GLN B 306 O HOH B 501 1.80
REMARK 500 O HOH A 679 O HOH A 747 2.16
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 OE1 GLN A 107 OD1 ASN B 180 1556 1.92
REMARK 500 NE2 GLN A 107 OD1 ASN B 84 1556 2.07
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 CYS A 22 CB - CA - C ANGL. DEV. = -12.2 DEGREES
REMARK 500 MET A 49 CA - CB - CG ANGL. DEV. = -11.2 DEGREES
REMARK 500 MET A 49 CG - SD - CE ANGL. DEV. = -20.6 DEGREES
REMARK 500 ARG A 76 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES
REMARK 500 ARG A 217 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES
REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES
REMARK 500 GLU A 288 CG - CD - OE1 ANGL. DEV. = 12.1 DEGREES
REMARK 500 ARG A 298 CG - CD - NE ANGL. DEV. = 14.4 DEGREES
REMARK 500 ARG B 4 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES
REMARK 500 GLU B 55 CG - CD - OE1 ANGL. DEV. = -13.7 DEGREES
REMARK 500 ARG B 76 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES
REMARK 500 ARG B 76 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES
REMARK 500 MET B 82 CG - SD - CE ANGL. DEV. = 10.3 DEGREES
REMARK 500 GLN B 127 CB - CA - C ANGL. DEV. = -12.5 DEGREES
REMARK 500 ARG B 217 NE - CZ - NH2 ANGL. DEV. = 5.5 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 -133.47 53.37
REMARK 500 ASN A 51 62.62 -160.16
REMARK 500 ASN A 84 -123.77 53.18
REMARK 500 ASP A 153 77.21 -117.70
REMARK 500 TYR A 154 -110.96 94.91
REMARK 500 ASP B 33 -126.61 50.68
REMARK 500 ASN B 51 64.16 -160.75
REMARK 500 ASN B 84 -122.22 56.32
REMARK 500 TYR B 154 -98.04 69.33
REMARK 500 PRO B 184 38.05 -87.06
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 279 0.21 SIDE CHAIN
REMARK 500 ARG B 4 0.11 SIDE CHAIN
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 753 DISTANCE = 6.00 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 8IGN RELATED DB: PDB
DBREF 23LY A 1 306 UNP P0DTC1 R1A_SARS2 3264 3569
DBREF 23LY B 1 306 UNP P0DTC1 R1A_SARS2 3264 3569
SEQADV 23LY VAL A 166 UNP P0DTC1 GLU 3429 ENGINEERED MUTATION
SEQADV 23LY VAL B 166 UNP P0DTC1 GLU 3429 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 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 VAL 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 CYS
SEQRES 13 B 306 VAL SER PHE CYS TYR MET HIS HIS MET VAL 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
HET 7ON A 401 45
HET GOL A 402 6
HET 7ON B 401 45
HETNAM 7ON LERITRELVIR BOUND FORM
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 7ON 2(C31 H46 F3 N5 O6)
FORMUL 4 GOL C3 H8 O3
FORMUL 6 HOH *481(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 SER A 62 PHE A 66 5 5
HELIX 6 AA6 ILE A 200 ASN A 214 1 15
HELIX 7 AA7 THR A 226 LYS A 236 1 11
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 GLU B 47 ASN B 51 5 5
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 GLY B 302 1 11
SHEET 1 AA1 7 VAL A 73 LEU A 75 0
SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73
SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69
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 TYR A 101 PHE A 103 0
SHEET 2 AA2 5 CYS A 156 VAL 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 SER A 123 N ALA A 116
SHEET 1 AA3 3 TYR A 101 PHE A 103 0
SHEET 2 AA3 3 CYS A 156 VAL A 166 1 O PHE A 159 N LYS A 102
SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
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 LEU B 27 N VAL B 20
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 GLN B 83 O VAL B 86
SHEET 1 AA5 5 TYR B 101 PHE B 103 0
SHEET 2 AA5 5 CYS B 156 VAL B 166 1 O PHE B 159 N LYS B 102
SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASP B 153 O CYS B 156
SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150
SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O SER B 123 N ALA B 116
SHEET 1 AA6 3 TYR B 101 PHE B 103 0
SHEET 2 AA6 3 CYS B 156 VAL B 166 1 O PHE B 159 N LYS B 102
SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165
LINK SG CYS A 145 C7 7ON A 401 1555 1555 1.90
LINK SG CYS B 145 C7 7ON B 401 1555 1555 1.88
CRYST1 48.837 106.317 54.145 90.00 103.22 90.00 P 1 21 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 0.020476 0.000000 0.004809 0.00000
SCALE2 0.000000 0.009406 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018972 0.00000
CONECT 1132 4755
CONECT 3499 4806
CONECT 4740 4746
CONECT 4741 4769
CONECT 4742 4780
CONECT 4743 4756 4775
CONECT 4744 4746 4747 4753
CONECT 4745 4753 4754
CONECT 4746 4740 4744 4754
CONECT 4747 4744 4748
CONECT 4748 4747 4755 4758
CONECT 4749 4750 4772
CONECT 4750 4749 4751
CONECT 4751 4750 4773
CONECT 4752 4780 4781 4782 4783
CONECT 4753 4744 4745
CONECT 4754 4745 4746
CONECT 4755 1132 4748 4756 4784
CONECT 4756 4743 4755 4757
CONECT 4757 4756
CONECT 4758 4748 4759
CONECT 4759 4758 4760 4761
CONECT 4760 4759 4762 4765
CONECT 4761 4759
CONECT 4762 4760 4763 4769
CONECT 4763 4762 4764
CONECT 4764 4763 4765 4766
CONECT 4765 4760 4764 4768
CONECT 4766 4764 4767
CONECT 4767 4766 4768
CONECT 4768 4765 4767
CONECT 4769 4741 4762 4770
CONECT 4770 4769 4771 4774
CONECT 4771 4770 4772 4773
CONECT 4772 4749 4771
CONECT 4773 4751 4771
CONECT 4774 4770 4780
CONECT 4775 4743 4776 4779
CONECT 4776 4775 4777
CONECT 4777 4776 4778
CONECT 4778 4777 4779
CONECT 4779 4775 4778
CONECT 4780 4742 4752 4774
CONECT 4781 4752
CONECT 4782 4752
CONECT 4783 4752
CONECT 4784 4755
CONECT 4785 4786 4787
CONECT 4786 4785
CONECT 4787 4785 4788 4789
CONECT 4788 4787
CONECT 4789 4787 4790
CONECT 4790 4789
CONECT 4791 4797
CONECT 4792 4820
CONECT 4793 4831
CONECT 4794 4807 4826
CONECT 4795 4797 4798 4804
CONECT 4796 4804 4805
CONECT 4797 4791 4795 4805
CONECT 4798 4795 4799
CONECT 4799 4798 4806 4809
CONECT 4800 4801 4823
CONECT 4801 4800 4802
CONECT 4802 4801 4824
CONECT 4803 4831 4832 4833 4834
CONECT 4804 4795 4796
CONECT 4805 4796 4797
CONECT 4806 3499 4799 4807 4835
CONECT 4807 4794 4806 4808
CONECT 4808 4807
CONECT 4809 4799 4810
CONECT 4810 4809 4811 4812
CONECT 4811 4810 4813 4816
CONECT 4812 4810
CONECT 4813 4811 4814 4820
CONECT 4814 4813 4815
CONECT 4815 4814 4816 4817
CONECT 4816 4811 4815 4819
CONECT 4817 4815 4818
CONECT 4818 4817 4819
CONECT 4819 4816 4818
CONECT 4820 4792 4813 4821
CONECT 4821 4820 4822 4825
CONECT 4822 4821 4823 4824
CONECT 4823 4800 4822
CONECT 4824 4802 4822
CONECT 4825 4821 4831
CONECT 4826 4794 4827 4830
CONECT 4827 4826 4828
CONECT 4828 4827 4829
CONECT 4829 4828 4830
CONECT 4830 4826 4829
CONECT 4831 4793 4803 4825
CONECT 4832 4803
CONECT 4833 4803
CONECT 4834 4803
CONECT 4835 4806
MASTER 376 0 3 22 30 0 0 6 5279 2 98 48
END