HEADER VIRAL PROTEIN 22-JUN-21 7F5H TITLE THE CRYSTAL STRUCTURE OF RBD-NANOBODY COMPLEX, DL28 (SC4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SARS-COV-2 SPIKE RECEPTOR-BINDING DOMAIN (RBD); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN (RBD); COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NANOBODY DL28; COMPND 9 CHAIN: C, D; COMPND 10 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: S, 2; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 11 ORGANISM_TAXID: 30538; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOBODY, RBD, NEUTRALIZING ANTIBODY, SARS-COV-2, RECEPTOR-BINDING KEYWDS 2 DOMAIN, RECEPTOR-BINDING MOTIF, RBM DISTORTION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.P.LUO,T.LI,Y.LAI,Y.ZHOU,J.TAN,D.LI REVDAT 3 29-NOV-23 7F5H 1 REMARK REVDAT 2 11-JAN-23 7F5H 1 JRNL REVDAT 1 29-JUN-22 7F5H 0 JRNL AUTH T.LI,B.ZHOU,Z.LUO,Y.LAI,S.HUANG,Y.ZHOU,Y.LI,A.GAUTAM, JRNL AUTH 2 S.BOURGEAU,S.WANG,J.BAO,J.TAN,D.LAVILLETTE,D.LI JRNL TITL STRUCTURAL CHARACTERIZATION OF A NEUTRALIZING NANOBODY WITH JRNL TITL 2 BROAD ACTIVITY AGAINST SARS-COV-2 VARIANTS. JRNL REF FRONT MICROBIOL V. 13 75840 2022 JRNL REFN ESSN 1664-302X JRNL PMID 35722331 JRNL DOI 10.3389/FMICB.2022.875840 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 24003 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1307 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1689 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.3740 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.4260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4878 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 127 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.26000 REMARK 3 B22 (A**2) : 1.26000 REMARK 3 B33 (A**2) : -4.08000 REMARK 3 B12 (A**2) : 0.63000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.785 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.346 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.293 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.886 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5140 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4571 ; 0.003 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6975 ; 1.582 ; 1.672 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10497 ; 1.570 ; 1.605 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 622 ; 8.056 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 276 ;26.715 ;22.246 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 749 ;13.003 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;14.164 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 652 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5913 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1311 ; 0.003 ; 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): 2500 ; 7.969 ; 9.347 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2499 ; 7.946 ; 9.346 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3118 ;12.121 ;14.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3119 ;12.123 ;14.002 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2640 ; 8.443 ;10.099 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2641 ; 8.442 ;10.099 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3858 ;12.933 ;14.918 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 334 527 B 334 527 5324 0.20 0.05 REMARK 3 2 C 1 113 D 1 113 3086 0.18 0.05 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 REMARK 4 REMARK 4 7F5H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-DEC-20 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) : 0.97853 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25343 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.17400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 1.56500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.350 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6M0J, 5M13 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM PHOSPHATE DIBASIC, 20% REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.75333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.37667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.56500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.18833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 110.94167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 88.75333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 44.37667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 22.18833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 66.56500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 110.94167 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: 3320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E 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: 3210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, F 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 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 P PO4 B 602 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 ALA A 327 REMARK 465 GLY A 328 REMARK 465 SER A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 GLY A 532 REMARK 465 THR A 533 REMARK 465 LEU A 534 REMARK 465 GLU A 535 REMARK 465 VAL A 536 REMARK 465 LEU A 537 REMARK 465 PHE A 538 REMARK 465 GLN A 539 REMARK 465 ALA B 327 REMARK 465 GLY B 328 REMARK 465 SER B 329 REMARK 465 PRO B 330 REMARK 465 ASN B 331 REMARK 465 ILE B 332 REMARK 465 LYS B 529 REMARK 465 SER B 530 REMARK 465 THR B 531 REMARK 465 GLY B 532 REMARK 465 THR B 533 REMARK 465 LEU B 534 REMARK 465 GLU B 535 REMARK 465 VAL B 536 REMARK 465 LEU B 537 REMARK 465 PHE B 538 REMARK 465 GLN B 539 REMARK 465 GLY C -3 REMARK 465 SER C -2 REMARK 465 SER C -1 REMARK 465 SER C 0 REMARK 465 GLY C 115 REMARK 465 ARG C 116 REMARK 465 ALA C 117 REMARK 465 GLY C 118 REMARK 465 GLU C 119 REMARK 465 GLN C 120 REMARK 465 LYS C 121 REMARK 465 LEU C 122 REMARK 465 ILE C 123 REMARK 465 SER C 124 REMARK 465 GLU C 125 REMARK 465 GLU C 126 REMARK 465 ASP C 127 REMARK 465 LEU C 128 REMARK 465 ASN C 129 REMARK 465 SER C 130 REMARK 465 ALA C 131 REMARK 465 VAL C 132 REMARK 465 ASP C 133 REMARK 465 HIS C 134 REMARK 465 HIS C 135 REMARK 465 HIS C 136 REMARK 465 HIS C 137 REMARK 465 HIS C 138 REMARK 465 HIS C 139 REMARK 465 GLY D -3 REMARK 465 SER D -2 REMARK 465 SER D -1 REMARK 465 SER D 0 REMARK 465 LYS D 121 REMARK 465 LEU D 122 REMARK 465 ILE D 123 REMARK 465 SER D 124 REMARK 465 GLU D 125 REMARK 465 GLU D 126 REMARK 465 ASP D 127 REMARK 465 LEU D 128 REMARK 465 ASN D 129 REMARK 465 SER D 130 REMARK 465 ALA D 131 REMARK 465 VAL D 132 REMARK 465 ASP D 133 REMARK 465 HIS D 134 REMARK 465 HIS D 135 REMARK 465 HIS D 136 REMARK 465 HIS D 137 REMARK 465 HIS D 138 REMARK 465 HIS D 139 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 LYS A 529 CG CD CE NZ REMARK 470 THR B 333 OG1 CG2 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 428 33.79 -92.00 REMARK 500 ASN A 481 50.35 -118.53 REMARK 500 LEU A 518 -169.32 -126.06 REMARK 500 ALA B 411 143.03 -170.52 REMARK 500 TYR B 423 117.16 -162.42 REMARK 500 ASP B 428 36.07 -94.46 REMARK 500 ASP D 98 -162.56 -100.25 REMARK 500 REMARK 500 REMARK: NULL DBREF 7F5H A 330 531 UNP P0DTC2 SPIKE_SARS2 330 531 DBREF 7F5H B 330 531 UNP P0DTC2 SPIKE_SARS2 330 531 DBREF 7F5H C -3 139 PDB 7F5H 7F5H -3 139 DBREF 7F5H D -3 139 PDB 7F5H 7F5H -3 139 SEQADV 7F5H ALA A 327 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H GLY A 328 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H SER A 329 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H GLY A 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H THR A 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H LEU A 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H GLU A 535 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H VAL A 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H LEU A 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H PHE A 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H GLN A 539 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H ALA B 327 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H GLY B 328 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H SER B 329 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H GLY B 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H THR B 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H LEU B 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H GLU B 535 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H VAL B 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H LEU B 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H PHE B 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7F5H GLN B 539 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 213 ALA GLY SER PRO ASN ILE THR ASN LEU CYS PRO PHE GLY SEQRES 2 A 213 GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA SEQRES 3 A 213 TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SEQRES 4 A 213 SER VAL LEU TYR ASN SER ALA SER PHE SER THR PHE LYS SEQRES 5 A 213 CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS SEQRES 6 A 213 PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY SEQRES 7 A 213 ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS SEQRES 8 A 213 ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR SEQRES 9 A 213 GLY CYS VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER SEQRES 10 A 213 LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE SEQRES 11 A 213 ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER SEQRES 12 A 213 THR GLU ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY SEQRES 13 A 213 VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR SEQRES 14 A 213 GLY PHE GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR SEQRES 15 A 213 ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO SEQRES 16 A 213 ALA THR VAL CYS GLY PRO LYS LYS SER THR GLY THR LEU SEQRES 17 A 213 GLU VAL LEU PHE GLN SEQRES 1 B 213 ALA GLY SER PRO ASN ILE THR ASN LEU CYS PRO PHE GLY SEQRES 2 B 213 GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA SEQRES 3 B 213 TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SEQRES 4 B 213 SER VAL LEU TYR ASN SER ALA SER PHE SER THR PHE LYS SEQRES 5 B 213 CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS SEQRES 6 B 213 PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY SEQRES 7 B 213 ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS SEQRES 8 B 213 ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR SEQRES 9 B 213 GLY CYS VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER SEQRES 10 B 213 LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE SEQRES 11 B 213 ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER SEQRES 12 B 213 THR GLU ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY SEQRES 13 B 213 VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR SEQRES 14 B 213 GLY PHE GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR SEQRES 15 B 213 ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO SEQRES 16 B 213 ALA THR VAL CYS GLY PRO LYS LYS SER THR GLY THR LEU SEQRES 17 B 213 GLU VAL LEU PHE GLN SEQRES 1 C 143 GLY SER SER SER GLN VAL GLN LEU GLN GLU SER GLY GLY SEQRES 2 C 143 GLY LEU VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS SEQRES 3 C 143 ALA ALA SER GLY SER ASP PHE SER SER SER THR MET GLY SEQRES 4 C 143 TRP TYR ARG GLN ALA PRO GLY LYS GLN ARG GLU PHE VAL SEQRES 5 C 143 ALA ILE SER SER GLU GLY SER THR SER TYR ALA GLY SER SEQRES 6 C 143 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS SEQRES 7 C 143 ASN THR VAL TYR LEU GLN MET ASN SER LEU GLU PRO GLU SEQRES 8 C 143 ASP THR ALA VAL TYR TYR CYS ASN VAL VAL ASP ARG TRP SEQRES 9 C 143 TYR ASP TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 10 C 143 ALA GLY ARG ALA GLY GLU GLN LYS LEU ILE SER GLU GLU SEQRES 11 C 143 ASP LEU ASN SER ALA VAL ASP HIS HIS HIS HIS HIS HIS SEQRES 1 D 143 GLY SER SER SER GLN VAL GLN LEU GLN GLU SER GLY GLY SEQRES 2 D 143 GLY LEU VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS SEQRES 3 D 143 ALA ALA SER GLY SER ASP PHE SER SER SER THR MET GLY SEQRES 4 D 143 TRP TYR ARG GLN ALA PRO GLY LYS GLN ARG GLU PHE VAL SEQRES 5 D 143 ALA ILE SER SER GLU GLY SER THR SER TYR ALA GLY SER SEQRES 6 D 143 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS SEQRES 7 D 143 ASN THR VAL TYR LEU GLN MET ASN SER LEU GLU PRO GLU SEQRES 8 D 143 ASP THR ALA VAL TYR TYR CYS ASN VAL VAL ASP ARG TRP SEQRES 9 D 143 TYR ASP TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 10 D 143 ALA GLY ARG ALA GLY GLU GLN LYS LEU ILE SER GLU GLU SEQRES 11 D 143 ASP LEU ASN SER ALA VAL ASP HIS HIS HIS HIS HIS HIS HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET FUC E 4 10 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET FUC F 4 10 HET GOL A 601 6 HET GOL B 601 6 HET PO4 B 602 5 HET GOL C 201 6 HET GOL D 201 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 NAG 4(C8 H15 N O6) FORMUL 5 BMA 2(C6 H12 O6) FORMUL 5 FUC 2(C6 H12 O5) FORMUL 7 GOL 4(C3 H8 O3) FORMUL 9 PO4 O4 P 3- FORMUL 12 HOH *21(H2 O) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 TYR A 365 SER A 371 1 7 HELIX 4 AA4 PRO A 384 ASN A 388 5 5 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 SER A 438 SER A 443 1 6 HELIX 8 AA8 GLY A 502 TYR A 505 5 4 HELIX 9 AA9 PHE B 338 ASN B 343 1 6 HELIX 10 AB1 SER B 349 TRP B 353 5 5 HELIX 11 AB2 ASP B 364 SER B 371 1 8 HELIX 12 AB3 ASP B 405 ILE B 410 5 6 HELIX 13 AB4 LYS B 417 ASN B 422 1 6 HELIX 14 AB5 SER B 438 SER B 443 1 6 HELIX 15 AB6 GLY B 502 TYR B 505 5 4 HELIX 16 AB7 GLY C 60 LYS C 63 5 4 HELIX 17 AB8 GLU C 85 THR C 89 5 5 HELIX 18 AB9 GLY D 60 LYS D 63 5 4 HELIX 19 AC1 GLU D 85 THR D 89 5 5 SHEET 1 AA110 ASN A 354 ILE A 358 0 SHEET 2 AA110 ASN A 394 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA110 PRO A 507 GLU A 516 -1 O VAL A 512 N ASP A 398 SHEET 4 AA110 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA110 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 6 AA110 THR D 108 ARG D 116 -1 O ALA D 114 N CYS A 379 SHEET 7 AA110 ALA D 90 VAL D 97 -1 N ALA D 90 O VAL D 110 SHEET 8 AA110 THR D 33 GLN D 39 -1 N GLY D 35 O ASN D 95 SHEET 9 AA110 GLU D 46 SER D 51 -1 O SER D 51 N MET D 34 SHEET 10 AA110 THR D 56 TYR D 58 -1 O SER D 57 N ILE D 50 SHEET 1 AA2 4 GLY D 10 GLN D 13 0 SHEET 2 AA2 4 THR D 108 ARG D 116 1 O SER D 113 N VAL D 12 SHEET 3 AA2 4 ALA D 90 VAL D 97 -1 N ALA D 90 O VAL D 110 SHEET 4 AA2 4 ASP D 102 TRP D 104 -1 O TYR D 103 N VAL D 96 SHEET 1 AA3 2 CYS A 391 PHE A 392 0 SHEET 2 AA3 2 VAL A 524 CYS A 525 -1 O VAL A 524 N PHE A 392 SHEET 1 AA4 2 LEU A 452 ARG A 454 0 SHEET 2 AA4 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA5 2 TYR A 473 GLN A 474 0 SHEET 2 AA5 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA6 5 ARG B 357 ILE B 358 0 SHEET 2 AA6 5 ASN B 394 ARG B 403 -1 O VAL B 395 N ILE B 358 SHEET 3 AA6 5 PRO B 507 GLU B 516 -1 O TYR B 508 N ILE B 402 SHEET 4 AA6 5 GLY B 431 ASN B 437 -1 N ILE B 434 O VAL B 511 SHEET 5 AA6 5 THR B 376 TYR B 380 -1 N LYS B 378 O VAL B 433 SHEET 1 AA7 2 CYS B 391 PHE B 392 0 SHEET 2 AA7 2 VAL B 524 CYS B 525 -1 O VAL B 524 N PHE B 392 SHEET 1 AA8 2 LEU B 452 ARG B 454 0 SHEET 2 AA8 2 LEU B 492 SER B 494 -1 O GLN B 493 N TYR B 453 SHEET 1 AA9 2 TYR B 473 GLN B 474 0 SHEET 2 AA9 2 CYS B 488 TYR B 489 -1 O TYR B 489 N TYR B 473 SHEET 1 AB1 4 GLN C 3 SER C 7 0 SHEET 2 AB1 4 ARG C 19 SER C 25 -1 O SER C 25 N GLN C 3 SHEET 3 AB1 4 THR C 76 MET C 81 -1 O LEU C 79 N LEU C 20 SHEET 4 AB1 4 PHE C 66 ASP C 71 -1 N SER C 69 O TYR C 78 SHEET 1 AB2 6 GLY C 10 GLN C 13 0 SHEET 2 AB2 6 THR C 108 SER C 113 1 O THR C 111 N GLY C 10 SHEET 3 AB2 6 ALA C 90 VAL C 97 -1 N TYR C 92 O THR C 108 SHEET 4 AB2 6 THR C 33 GLN C 39 -1 N GLY C 35 O ASN C 95 SHEET 5 AB2 6 GLU C 46 SER C 51 -1 O ALA C 49 N TRP C 36 SHEET 6 AB2 6 THR C 56 TYR C 58 -1 O SER C 57 N ILE C 50 SHEET 1 AB3 4 GLY C 10 GLN C 13 0 SHEET 2 AB3 4 THR C 108 SER C 113 1 O THR C 111 N GLY C 10 SHEET 3 AB3 4 ALA C 90 VAL C 97 -1 N TYR C 92 O THR C 108 SHEET 4 AB3 4 ASP C 102 TRP C 104 -1 O TYR C 103 N VAL C 96 SHEET 1 AB4 4 GLN D 3 GLY D 8 0 SHEET 2 AB4 4 LEU D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AB4 4 THR D 76 MET D 81 -1 O MET D 81 N LEU D 18 SHEET 4 AB4 4 PHE D 66 ASP D 71 -1 N THR D 67 O GLN D 80 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.05 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.06 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.02 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.08 SSBOND 5 CYS B 336 CYS B 361 1555 1555 2.03 SSBOND 6 CYS B 379 CYS B 432 1555 1555 2.06 SSBOND 7 CYS B 391 CYS B 525 1555 1555 2.04 SSBOND 8 CYS B 480 CYS B 488 1555 1555 2.05 SSBOND 9 CYS C 22 CYS C 94 1555 1555 2.09 SSBOND 10 CYS D 22 CYS D 94 1555 1555 2.08 LINK ND2 ASN A 343 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN B 343 C1 NAG F 1 1555 1555 1.42 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.37 LINK O6 NAG E 1 C1 FUC E 4 1555 1555 1.36 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.35 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.37 LINK O6 NAG F 1 C1 FUC F 4 1555 1555 1.37 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.37 CRYST1 177.463 177.463 133.130 90.00 90.00 120.00 P 65 2 2 24 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 0.005635 0.003253 0.000000 0.00000 SCALE2 0.000000 0.006507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007511 0.00000