HEADER VIRAL PROTEIN 28-OCT-21 7Q3R TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RBD IN COMPLEX WITH THE NEUTRALIZING TITLE 2 NANOBODIES VHH-F04 AND VHH-G09 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VHH-F04; COMPND 8 CHAIN: F; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: VHH-G09; COMPND 12 CHAIN: G; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 10 ORGANISM_TAXID: 30538; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 15 ORGANISM_TAXID: 30538; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS CORONAVIRUS, NANOBODY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.FERNANDEZ,R.PEDERZOLI,F.A.REY REVDAT 2 31-JAN-24 7Q3R 1 REMARK REVDAT 1 16-NOV-22 7Q3R 0 JRNL AUTH I.FERNANDEZ,F.A.REY JRNL TITL NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN JRNL TITL 2 AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 69177 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3502 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.9100 - 5.6000 1.00 2778 151 0.1698 0.1839 REMARK 3 2 5.6000 - 4.4500 1.00 2669 144 0.1381 0.1507 REMARK 3 3 4.4500 - 3.8800 1.00 2695 140 0.1349 0.1406 REMARK 3 4 3.8800 - 3.5300 1.00 2641 143 0.1626 0.1871 REMARK 3 5 3.5300 - 3.2800 1.00 2627 154 0.1765 0.2145 REMARK 3 6 3.2800 - 3.0800 1.00 2672 119 0.1972 0.2410 REMARK 3 7 3.0800 - 2.9300 1.00 2622 146 0.2123 0.2893 REMARK 3 8 2.9300 - 2.8000 1.00 2610 148 0.2345 0.2888 REMARK 3 9 2.8000 - 2.6900 1.00 2636 141 0.2173 0.2219 REMARK 3 10 2.6900 - 2.6000 1.00 2635 142 0.2122 0.2490 REMARK 3 11 2.6000 - 2.5200 1.00 2608 134 0.2024 0.2168 REMARK 3 12 2.5200 - 2.4500 1.00 2614 157 0.1967 0.2260 REMARK 3 13 2.4500 - 2.3800 1.00 2616 138 0.2008 0.2578 REMARK 3 14 2.3800 - 2.3200 1.00 2602 165 0.2154 0.2733 REMARK 3 15 2.3200 - 2.2700 1.00 2615 121 0.2056 0.2677 REMARK 3 16 2.2700 - 2.2200 1.00 2617 130 0.2216 0.2500 REMARK 3 17 2.2200 - 2.1800 1.00 2570 156 0.2078 0.2410 REMARK 3 18 2.1800 - 2.1400 1.00 2668 135 0.1979 0.1983 REMARK 3 19 2.1400 - 2.1000 1.00 2569 145 0.1844 0.2109 REMARK 3 20 2.1000 - 2.0600 1.00 2639 133 0.1810 0.2179 REMARK 3 21 2.0600 - 2.0300 1.00 2610 130 0.1855 0.2289 REMARK 3 22 2.0300 - 2.0000 1.00 2591 139 0.2099 0.2296 REMARK 3 23 2.0000 - 1.9700 1.00 2660 125 0.2400 0.2384 REMARK 3 24 1.9700 - 1.9400 1.00 2576 133 0.2845 0.3119 REMARK 3 25 1.9400 - 1.9200 0.97 2535 133 0.3617 0.3766 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 57.0235 56.8455 18.1546 REMARK 3 T TENSOR REMARK 3 T11: 0.2279 T22: 0.3605 REMARK 3 T33: 0.2820 T12: 0.0028 REMARK 3 T13: -0.0060 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.8026 L22: 0.7848 REMARK 3 L33: 0.8544 L12: -0.4642 REMARK 3 L13: 0.0193 L23: -0.0834 REMARK 3 S TENSOR REMARK 3 S11: 0.0058 S12: -0.0434 S13: -0.0646 REMARK 3 S21: 0.0074 S22: 0.0161 S23: 0.1750 REMARK 3 S31: 0.0096 S32: -0.2525 S33: -0.0256 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7Q3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292118928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978565 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69234 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 48.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 20.70 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 20.30 REMARK 200 R MERGE FOR SHELL (I) : 1.45600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6YM0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NAAC/HAC (PH 4.5), 0.2 M LI2SO4, REMARK 280 2.2 M NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 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 24.01250 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 24.01250 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 24.01250 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, G, 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 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 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 SER A 371 REMARK 465 ALA A 372 REMARK 465 ALA F -2 REMARK 465 MET F -1 REMARK 465 ALA F 0 REMARK 465 GLU F 1 REMARK 465 ALA F 129 REMARK 465 ALA F 130 REMARK 465 ALA F 131 REMARK 465 HIS F 132 REMARK 465 HIS F 133 REMARK 465 HIS F 134 REMARK 465 HIS F 135 REMARK 465 HIS F 136 REMARK 465 HIS F 137 REMARK 465 HIS F 138 REMARK 465 HIS F 139 REMARK 465 ALA G -2 REMARK 465 MET G -1 REMARK 465 ALA G 0 REMARK 465 ALA G 122 REMARK 465 ALA G 123 REMARK 465 ALA G 124 REMARK 465 HIS G 125 REMARK 465 HIS G 126 REMARK 465 HIS G 127 REMARK 465 HIS G 128 REMARK 465 HIS G 129 REMARK 465 HIS G 130 REMARK 465 HIS G 131 REMARK 465 HIS G 132 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 LEU A 335 CG CD1 CD2 REMARK 470 ASN A 360 CG OD1 ND2 REMARK 470 ASN A 370 CG OD1 ND2 REMARK 470 HIS A 519 CG ND1 CD2 CE1 NE2 REMARK 470 GLN F 13 CG CD OE1 NE2 REMARK 470 ARG F 27 CG CD NE CZ NH1 NH2 REMARK 470 LYS F 43 CG CD CE NZ REMARK 470 LYS F 87 CG CD CE NZ REMARK 470 GLN G 113 CG CD OE1 NE2 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 NZ LYS G 86 OE1 GLU G 88 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS F 22 CB CYS F 22 SG -0.101 REMARK 500 CYS F 96 CB CYS F 96 SG -0.192 REMARK 500 GLU G 6 CG GLU G 6 CD 0.104 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 G 22 CA - CB - SG ANGL. DEV. = -11.0 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 PHE A 377 88.02 -160.07 REMARK 500 PHE A 400 175.04 178.83 REMARK 500 ASN A 422 -50.45 -126.37 REMARK 500 GLU F 89 -18.32 -47.60 REMARK 500 ALA F 92 166.76 179.45 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7Q3R A 331 528 UNP A0A6H2EIN2_SARS2 DBREF2 7Q3R A A0A6H2EIN2 331 528 DBREF 7Q3R F -2 139 PDB 7Q3R 7Q3R -2 139 DBREF 7Q3R G -2 132 PDB 7Q3R 7Q3R -2 132 SEQRES 1 A 198 ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN SEQRES 2 A 198 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 3 A 198 ARG ILE SER ASN CYS VAL ALA ASP TYR SER PHE LEU TYR SEQRES 4 A 198 ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SEQRES 5 A 198 SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL SEQRES 6 A 198 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 7 A 198 GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR SEQRES 8 A 198 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 9 A 198 ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY SEQRES 10 A 198 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 11 A 198 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 12 A 198 GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE SEQRES 13 A 198 ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO SEQRES 14 A 198 THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL SEQRES 15 A 198 LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS SEQRES 16 A 198 GLY PRO LYS SEQRES 1 F 142 ALA MET ALA GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SEQRES 2 F 142 LEU VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA SEQRES 3 F 142 ALA SER GLY ARG ALA PHE SER ARG TYR PHE MET GLY TRP SEQRES 4 F 142 PHE ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA SEQRES 5 F 142 GLY ILE SER ARG SER GLY GLY SER THR ASP TYR ALA ASN SEQRES 6 F 142 PHE VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA SEQRES 7 F 142 LYS ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO SEQRES 8 F 142 GLU ASP THR ALA VAL TYR TYR CYS ALA ALA THR VAL ASP SEQRES 9 F 142 TYR SER GLY THR LEU THR ALA ALA ARG GLY ARG GLU ASP SEQRES 10 F 142 TYR ASP ASP TRP GLY GLN GLY ILE GLN VAL THR VAL SER SEQRES 11 F 142 SER ALA ALA ALA HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 G 135 ALA MET ALA GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SEQRES 2 G 135 THR VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS GLU SEQRES 3 G 135 VAL SER GLY THR GLY PHE THR ILE ASN ALA MET GLY TRP SEQRES 4 G 135 ASP ARG GLN ALA PRO GLY LYS GLN ARG GLU LEU VAL ALA SEQRES 5 G 135 THR ILE THR ARG GLY ASP ARG ILE HIS TYR ALA ASP SER SEQRES 6 G 135 VAL LYS GLY ARG PHE ALA ILE SER ARG ASP LYS ASP LYS SEQRES 7 G 135 ASN THR VAL TYR LEU GLU MET ASN ASN LEU LYS PRO GLU SEQRES 8 G 135 ASP THR ALA VAL TYR TYR CYS ASP VAL ALA ALA PHE ASP SEQRES 9 G 135 SER SER ASP TYR GLU VAL LEU ASP SER TRP GLY GLN GLY SEQRES 10 G 135 THR GLN VAL THR VAL SER SER ALA ALA ALA HIS HIS HIS SEQRES 11 G 135 HIS HIS HIS HIS HIS HET NAG B 1 14 HET NAG B 2 14 HET CL A 601 1 HET CL A 602 1 HET CL A 603 1 HET CL F 201 1 HET CL F 202 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE 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 FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 5 CL 5(CL 1-) FORMUL 10 HOH *277(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 ASN A 370 5 6 HELIX 4 AA4 SER A 383 ASP A 389 5 7 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 ALA F 28 SER F 30 5 3 HELIX 10 AB1 ASN F 74 LYS F 76 5 3 HELIX 11 AB2 LYS F 87 THR F 91 5 5 HELIX 12 AB3 GLY F 111 TYR F 115 5 5 HELIX 13 AB4 ASP G 61 LYS G 64 5 4 HELIX 14 AB5 LYS G 86 THR G 90 5 5 SHEET 1 AA1 6 ASN A 354 ILE A 358 0 SHEET 2 AA1 6 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 6 PRO A 507 GLU A 516 -1 O GLU A 516 N ASN A 394 SHEET 4 AA1 6 GLY A 431 ASN A 437 -1 N CYS A 432 O LEU A 513 SHEET 5 AA1 6 THR A 376 TYR A 380 -1 N LYS A 378 O VAL A 433 SHEET 6 AA1 6 LEU F 106 ALA F 109 -1 O THR F 107 N CYS A 379 SHEET 1 AA2 3 CYS A 361 VAL A 362 0 SHEET 2 AA2 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA2 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 LEU F 4 GLY F 8 0 SHEET 2 AA5 4 LEU F 18 ALA F 24 -1 O ALA F 23 N VAL F 5 SHEET 3 AA5 4 THR F 78 MET F 83 -1 O MET F 83 N LEU F 18 SHEET 4 AA5 4 PHE F 68 ASP F 73 -1 N THR F 69 O GLN F 82 SHEET 1 AA6 6 GLY F 10 GLN F 13 0 SHEET 2 AA6 6 ILE F 122 SER F 127 1 O THR F 125 N GLY F 10 SHEET 3 AA6 6 ALA F 92 VAL F 100 -1 N TYR F 94 O ILE F 122 SHEET 4 AA6 6 TYR F 32 GLN F 39 -1 N GLY F 35 O ALA F 97 SHEET 5 AA6 6 GLU F 46 ILE F 51 -1 O VAL F 48 N TRP F 36 SHEET 6 AA6 6 THR F 58 TYR F 60 -1 O ASP F 59 N GLY F 50 SHEET 1 AA7 4 GLY F 10 GLN F 13 0 SHEET 2 AA7 4 ILE F 122 SER F 127 1 O THR F 125 N GLY F 10 SHEET 3 AA7 4 ALA F 92 VAL F 100 -1 N TYR F 94 O ILE F 122 SHEET 4 AA7 4 ASP F 117 TRP F 118 -1 O ASP F 117 N ALA F 98 SHEET 1 AA8 4 GLN G 3 SER G 7 0 SHEET 2 AA8 4 LEU G 18 SER G 25 -1 O GLU G 23 N VAL G 5 SHEET 3 AA8 4 THR G 77 MET G 82 -1 O MET G 82 N LEU G 18 SHEET 4 AA8 4 PHE G 67 ARG G 71 -1 N ALA G 68 O GLU G 81 SHEET 1 AA9 6 GLY G 10 VAL G 12 0 SHEET 2 AA9 6 THR G 115 VAL G 119 1 O GLN G 116 N GLY G 10 SHEET 3 AA9 6 ALA G 91 ASP G 101 -1 N TYR G 93 O THR G 115 SHEET 4 AA9 6 PHE G 29 GLN G 39 -1 N ASP G 37 O TYR G 94 SHEET 5 AA9 6 GLU G 46 THR G 52 -1 O ALA G 49 N TRP G 36 SHEET 6 AA9 6 ARG G 56 TYR G 59 -1 O HIS G 58 N THR G 50 SHEET 1 AB1 4 GLY G 10 VAL G 12 0 SHEET 2 AB1 4 THR G 115 VAL G 119 1 O GLN G 116 N GLY G 10 SHEET 3 AB1 4 ALA G 91 ASP G 101 -1 N TYR G 93 O THR G 115 SHEET 4 AB1 4 SER G 110 TRP G 111 -1 O SER G 110 N VAL G 97 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.04 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.08 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.06 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.13 SSBOND 5 CYS F 22 CYS F 96 1555 1555 2.01 SSBOND 6 CYS G 22 CYS G 95 1555 1555 1.96 LINK ND2 ASN A 343 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 CRYST1 180.578 180.578 48.025 90.00 90.00 120.00 P 63 6 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 0.005538 0.003197 0.000000 0.00000 SCALE2 0.000000 0.006394 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020822 0.00000