HEADER IMMUNE SYSTEM 27-MAY-21 7N1A TITLE SARS-COV-2 YLQ PEPTIDE BINDS TO HLA-A2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MHC CLASS I ANTIGEN, A-2 ALPHA CHAIN; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 7 CHAIN: B, E; COMPND 8 FRAGMENT: UNP RESIDUES 21-119; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: SPIKE PROTEIN S1; COMPND 12 CHAIN: C, F; COMPND 13 FRAGMENT: EPITOPE YLQPRTFLL (UNP RESIDUES 269-277); COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HLA-A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: B2M, CDABP0092, HDCMA22P; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 18 2; SOURCE 19 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 20 ORGANISM_TAXID: 2697049 KEYWDS PMHC, SARS-COV-2, SPIKE, YLQ, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.WU,R.A.MARIUZZA REVDAT 4 18-OCT-23 7N1A 1 JRNL REVDAT 3 02-FEB-22 7N1A 1 JRNL REVDAT 2 18-AUG-21 7N1A 1 JRNL REVDAT 1 28-JUL-21 7N1A 0 JRNL AUTH D.WU,A.KOLESNIKOV,R.YIN,J.D.GUEST,R.GOWTHAMAN,A.SHMELEV, JRNL AUTH 2 Y.SERDYUK,D.V.DIANOV,G.A.EFIMOV,B.G.PIERCE,R.A.MARIUZZA JRNL TITL STRUCTURAL ASSESSMENT OF HLA-A2-RESTRICTED SARS-COV-2 SPIKE JRNL TITL 2 EPITOPES RECOGNIZED BY PUBLIC AND PRIVATE T-CELL RECEPTORS. JRNL REF NAT COMMUN V. 13 19 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35013235 JRNL DOI 10.1038/S41467-021-27669-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.WU,A.KOLESNIKOV,R.YIN,J.D.GUEST,R.GOWTHAMAN,A.SHMELEV, REMARK 1 AUTH 2 Y.SERDYUK,G.A.EFIMOV,B.G.PIERCE,R.A.MARIUZZA REMARK 1 TITL STRUCTURAL BASIS FOR RECOGNITION OF TWO HLA-A2-RESTRICTED REMARK 1 TITL 2 SARS-COV-2 SPIKE EPITOPES BY PUBLIC AND PRIVATE T CELL REMARK 1 TITL 3 RECEPTORS REMARK 1 REF BIORXIV 2021 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2021.07.28.454232 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 54879 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 2682 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 43.3000 - 5.5067 1.00 2863 159 0.1808 0.2250 REMARK 3 2 5.5067 - 4.3722 1.00 2777 165 0.1608 0.1927 REMARK 3 3 4.3722 - 3.8199 1.00 2758 156 0.1689 0.2039 REMARK 3 4 3.8199 - 3.4708 1.00 2791 121 0.1765 0.2062 REMARK 3 5 3.4708 - 3.2221 1.00 2739 148 0.1984 0.2347 REMARK 3 6 3.2221 - 3.0322 1.00 2731 148 0.2112 0.2396 REMARK 3 7 3.0322 - 2.8804 1.00 2727 168 0.2134 0.2750 REMARK 3 8 2.8804 - 2.7550 1.00 2754 138 0.2234 0.2627 REMARK 3 9 2.7550 - 2.6490 1.00 2706 142 0.2323 0.2886 REMARK 3 10 2.6490 - 2.5576 1.00 2766 109 0.2270 0.2955 REMARK 3 11 2.5576 - 2.4776 1.00 2760 139 0.2257 0.3157 REMARK 3 12 2.4776 - 2.4068 1.00 2719 136 0.2179 0.2738 REMARK 3 13 2.4068 - 2.3434 1.00 2744 136 0.2230 0.3001 REMARK 3 14 2.3434 - 2.2863 1.00 2740 134 0.2215 0.2827 REMARK 3 15 2.2863 - 2.2343 1.00 2683 134 0.2089 0.2722 REMARK 3 16 2.2343 - 2.1867 1.00 2754 126 0.2110 0.2655 REMARK 3 17 2.1867 - 2.1430 1.00 2742 128 0.2229 0.2691 REMARK 3 18 2.1430 - 2.1026 1.00 2696 181 0.2258 0.2823 REMARK 3 19 2.1026 - 2.0650 1.00 2747 114 0.2242 0.2884 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.41 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 : NULL 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 7N1A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000257130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 558646 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.065 REMARK 200 RESOLUTION RANGE LOW (A) : 43.318 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 6VR5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM THIOCYANATE (PH 7.0), REMARK 280 22% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 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 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,X-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 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 142.80867 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 71.40433 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 71.40433 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 142.80867 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 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, 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 HOH B 185 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 MET A 0 REMARK 465 MET D 0 REMARK 465 GLU D 89 REMARK 465 GLU D 275 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 B 48 CG CD CE NZ REMARK 470 LYS B 58 CG CD CE NZ REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 LYS E 48 CG CD CE NZ REMARK 470 LYS E 58 CG CD CE NZ REMARK 470 LYS E 75 CG 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 CE MET E 0 O HOH D 493 1.75 REMARK 500 OH TYR D 27 O HOH D 401 1.80 REMARK 500 OG SER D 251 O HOH D 402 1.84 REMARK 500 O HOH B 168 O HOH B 176 1.85 REMARK 500 O1 PG4 A 301 O HOH A 401 1.90 REMARK 500 O HOH B 183 O HOH B 184 1.92 REMARK 500 O HOH A 503 O HOH A 544 1.94 REMARK 500 O HOH A 567 O HOH C 109 1.97 REMARK 500 OG1 THR A 200 O HOH A 402 1.98 REMARK 500 OD2 ASP A 61 O HOH A 403 1.99 REMARK 500 O HOH D 542 O HOH F 112 2.02 REMARK 500 OE1 GLN D 180 O HOH D 403 2.03 REMARK 500 O HOH B 105 O HOH B 106 2.03 REMARK 500 O HOH B 166 O HOH B 170 2.04 REMARK 500 O HOH E 128 O HOH E 132 2.05 REMARK 500 O HOH B 159 O HOH B 169 2.06 REMARK 500 O HOH D 530 O HOH D 531 2.06 REMARK 500 OE1 GLN C 3 O HOH C 101 2.09 REMARK 500 O HOH C 104 O HOH C 111 2.10 REMARK 500 O HOH F 102 O HOH F 109 2.11 REMARK 500 OG SER A 11 O HOH A 404 2.12 REMARK 500 O1 PG4 D 301 O HOH D 404 2.12 REMARK 500 NH2 ARG D 97 O HOH D 405 2.13 REMARK 500 OG1 THR D 178 O HOH D 406 2.15 REMARK 500 O ARG E 12 O HOH E 101 2.16 REMARK 500 OE1 GLU A 148 O HOH A 405 2.16 REMARK 500 O HOH A 489 O HOH B 107 2.17 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 NH2 ARG A 17 O GLY D 18 5444 1.25 REMARK 500 NH2 ARG A 17 C GLY D 18 5444 1.55 REMARK 500 CZ ARG A 17 O GLY D 18 5444 2.15 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 GLU A 161 CD GLU A 161 OE1 -0.070 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 ARG E 45 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG E 45 NE - CZ - NH2 ANGL. DEV. = 5.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 29 -121.35 50.93 REMARK 500 HIS A 114 101.81 -166.33 REMARK 500 TYR A 123 -61.71 -120.50 REMARK 500 TRP B 60 -1.47 73.54 REMARK 500 ASP B 98 30.50 -94.59 REMARK 500 ASP D 29 -123.94 51.78 REMARK 500 ASN D 86 28.27 47.45 REMARK 500 LEU D 110 -50.53 -126.10 REMARK 500 HIS D 114 102.51 -166.61 REMARK 500 SER D 195 -159.86 -130.01 REMARK 500 TRP E 60 -2.51 74.78 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 B 185 DISTANCE = 5.90 ANGSTROMS DBREF1 7N1A A 1 275 UNP A0A5B8RNS7_HUMAN DBREF2 7N1A A A0A5B8RNS7 25 299 DBREF 7N1A B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 7N1A C 1 9 UNP P0DTC2 SPIKE_SARS2 269 277 DBREF1 7N1A D 1 275 UNP A0A5B8RNS7_HUMAN DBREF2 7N1A D A0A5B8RNS7 25 299 DBREF 7N1A E 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 7N1A F 1 9 UNP P0DTC2 SPIKE_SARS2 269 277 SEQADV 7N1A MET A 0 UNP A0A5B8RNS INITIATING METHIONINE SEQADV 7N1A MET B 0 UNP P61769 INITIATING METHIONINE SEQADV 7N1A MET D 0 UNP A0A5B8RNS INITIATING METHIONINE SEQADV 7N1A MET E 0 UNP P61769 INITIATING METHIONINE SEQRES 1 A 276 MET GLY SER HIS SER MET ARG TYR PHE PHE THR SER VAL SEQRES 2 A 276 SER ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL SEQRES 3 A 276 GLY TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER SEQRES 4 A 276 ASP ALA ALA SER GLN ARG MET GLU PRO ARG ALA PRO TRP SEQRES 5 A 276 ILE GLU GLN GLU GLY PRO GLU TYR TRP ASP GLY GLU THR SEQRES 6 A 276 ARG LYS VAL LYS ALA HIS SER GLN THR HIS ARG VAL ASP SEQRES 7 A 276 LEU GLY THR LEU ARG GLY TYR TYR ASN GLN SER GLU ALA SEQRES 8 A 276 GLY SER HIS THR VAL GLN ARG MET TYR GLY CYS ASP VAL SEQRES 9 A 276 GLY SER ASP TRP ARG PHE LEU ARG GLY TYR HIS GLN TYR SEQRES 10 A 276 ALA TYR ASP GLY LYS ASP TYR ILE ALA LEU LYS GLU ASP SEQRES 11 A 276 LEU ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN THR SEQRES 12 A 276 THR LYS HIS LYS TRP GLU ALA ALA HIS VAL ALA GLU GLN SEQRES 13 A 276 LEU ARG ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU SEQRES 14 A 276 ARG ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG SEQRES 15 A 276 THR ASP ALA PRO LYS THR HIS MET THR HIS HIS ALA VAL SEQRES 16 A 276 SER ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU SER SEQRES 17 A 276 PHE TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP SEQRES 18 A 276 GLY GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR SEQRES 19 A 276 ARG PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA SEQRES 20 A 276 VAL VAL VAL PRO SER GLY GLN GLU GLN ARG TYR THR CYS SEQRES 21 A 276 HIS VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU SEQRES 22 A 276 ARG TRP GLU SEQRES 1 B 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 B 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 B 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 B 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 B 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 B 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 B 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 C 9 TYR LEU GLN PRO ARG THR PHE LEU LEU SEQRES 1 D 276 MET GLY SER HIS SER MET ARG TYR PHE PHE THR SER VAL SEQRES 2 D 276 SER ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL SEQRES 3 D 276 GLY TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER SEQRES 4 D 276 ASP ALA ALA SER GLN ARG MET GLU PRO ARG ALA PRO TRP SEQRES 5 D 276 ILE GLU GLN GLU GLY PRO GLU TYR TRP ASP GLY GLU THR SEQRES 6 D 276 ARG LYS VAL LYS ALA HIS SER GLN THR HIS ARG VAL ASP SEQRES 7 D 276 LEU GLY THR LEU ARG GLY TYR TYR ASN GLN SER GLU ALA SEQRES 8 D 276 GLY SER HIS THR VAL GLN ARG MET TYR GLY CYS ASP VAL SEQRES 9 D 276 GLY SER ASP TRP ARG PHE LEU ARG GLY TYR HIS GLN TYR SEQRES 10 D 276 ALA TYR ASP GLY LYS ASP TYR ILE ALA LEU LYS GLU ASP SEQRES 11 D 276 LEU ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN THR SEQRES 12 D 276 THR LYS HIS LYS TRP GLU ALA ALA HIS VAL ALA GLU GLN SEQRES 13 D 276 LEU ARG ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU SEQRES 14 D 276 ARG ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG SEQRES 15 D 276 THR ASP ALA PRO LYS THR HIS MET THR HIS HIS ALA VAL SEQRES 16 D 276 SER ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU SER SEQRES 17 D 276 PHE TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP SEQRES 18 D 276 GLY GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR SEQRES 19 D 276 ARG PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA SEQRES 20 D 276 VAL VAL VAL PRO SER GLY GLN GLU GLN ARG TYR THR CYS SEQRES 21 D 276 HIS VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU SEQRES 22 D 276 ARG TRP GLU SEQRES 1 E 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 E 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 E 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 E 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 E 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 E 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 E 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 E 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 F 9 TYR LEU GLN PRO ARG THR PHE LEU LEU HET PG4 A 301 13 HET PG4 D 301 13 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 7 PG4 2(C8 H18 O5) FORMUL 9 HOH *482(H2 O) HELIX 1 AA1 ASP A 39 ALA A 41 5 3 HELIX 2 AA2 ALA A 49 GLN A 54 1 6 HELIX 3 AA3 GLY A 56 TYR A 85 1 30 HELIX 4 AA4 ASP A 137 ALA A 150 1 14 HELIX 5 AA5 HIS A 151 GLY A 162 1 12 HELIX 6 AA6 GLY A 162 GLY A 175 1 14 HELIX 7 AA7 GLY A 175 GLN A 180 1 6 HELIX 8 AA8 GLN A 253 GLN A 255 5 3 HELIX 9 AA9 ALA D 49 GLN D 54 1 6 HELIX 10 AB1 GLY D 56 TYR D 85 1 30 HELIX 11 AB2 ASP D 137 ALA D 150 1 14 HELIX 12 AB3 HIS D 151 GLY D 162 1 12 HELIX 13 AB4 GLY D 162 GLY D 175 1 14 HELIX 14 AB5 GLY D 175 GLN D 180 1 6 HELIX 15 AB6 GLN D 253 GLN D 255 5 3 SHEET 1 AA1 8 GLU A 46 PRO A 47 0 SHEET 2 AA1 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 AA1 8 ARG A 21 VAL A 28 -1 N VAL A 28 O THR A 31 SHEET 4 AA1 8 HIS A 3 VAL A 12 -1 N PHE A 8 O VAL A 25 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O ARG A 97 N PHE A 9 SHEET 6 AA1 8 PHE A 109 TYR A 118 -1 O LEU A 110 N ASP A 102 SHEET 7 AA1 8 LYS A 121 LEU A 126 -1 O ILE A 124 N TYR A 116 SHEET 8 AA1 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 AA2 4 LYS A 186 ALA A 193 0 SHEET 2 AA2 4 GLU A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA2 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203 SHEET 4 AA2 4 THR A 228 LEU A 230 -1 N GLU A 229 O ALA A 246 SHEET 1 AA3 4 LYS A 186 ALA A 193 0 SHEET 2 AA3 4 GLU A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA3 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203 SHEET 4 AA3 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 AA4 4 GLU A 222 ASP A 223 0 SHEET 2 AA4 4 THR A 214 ARG A 219 -1 N ARG A 219 O GLU A 222 SHEET 3 AA4 4 TYR A 257 GLN A 262 -1 O HIS A 260 N THR A 216 SHEET 4 AA4 4 LEU A 270 ARG A 273 -1 O LEU A 272 N CYS A 259 SHEET 1 AA5 4 LYS B 6 SER B 11 0 SHEET 2 AA5 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA5 4 PHE B 62 PHE B 70 -1 O THR B 68 N LEU B 23 SHEET 4 AA5 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 AA6 4 LYS B 6 SER B 11 0 SHEET 2 AA6 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA6 4 PHE B 62 PHE B 70 -1 O THR B 68 N LEU B 23 SHEET 4 AA6 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 AA7 4 GLU B 44 ARG B 45 0 SHEET 2 AA7 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 AA7 4 TYR B 78 ASN B 83 -1 O ARG B 81 N ASP B 38 SHEET 4 AA7 4 LYS B 91 LYS B 94 -1 O VAL B 93 N CYS B 80 SHEET 1 AA8 8 GLU D 46 PRO D 47 0 SHEET 2 AA8 8 THR D 31 ASP D 37 -1 N ARG D 35 O GLU D 46 SHEET 3 AA8 8 ARG D 21 VAL D 28 -1 N ALA D 24 O PHE D 36 SHEET 4 AA8 8 HIS D 3 VAL D 12 -1 N PHE D 8 O VAL D 25 SHEET 5 AA8 8 THR D 94 VAL D 103 -1 O VAL D 103 N HIS D 3 SHEET 6 AA8 8 PHE D 109 TYR D 118 -1 O ARG D 111 N ASP D 102 SHEET 7 AA8 8 LYS D 121 LEU D 126 -1 O LEU D 126 N HIS D 114 SHEET 8 AA8 8 TRP D 133 ALA D 135 -1 O THR D 134 N ALA D 125 SHEET 1 AA9 4 LYS D 186 HIS D 192 0 SHEET 2 AA9 4 GLU D 198 PHE D 208 -1 O TRP D 204 N HIS D 188 SHEET 3 AA9 4 PHE D 241 PRO D 250 -1 O ALA D 245 N CYS D 203 SHEET 4 AA9 4 THR D 228 LEU D 230 -1 N GLU D 229 O ALA D 246 SHEET 1 AB1 4 LYS D 186 HIS D 192 0 SHEET 2 AB1 4 GLU D 198 PHE D 208 -1 O TRP D 204 N HIS D 188 SHEET 3 AB1 4 PHE D 241 PRO D 250 -1 O ALA D 245 N CYS D 203 SHEET 4 AB1 4 ARG D 234 PRO D 235 -1 N ARG D 234 O GLN D 242 SHEET 1 AB2 4 GLU D 222 GLN D 224 0 SHEET 2 AB2 4 THR D 214 ARG D 219 -1 N ARG D 219 O GLU D 222 SHEET 3 AB2 4 TYR D 257 GLN D 262 -1 O HIS D 260 N THR D 216 SHEET 4 AB2 4 LEU D 270 LEU D 272 -1 O LEU D 272 N CYS D 259 SHEET 1 AB3 4 LYS E 6 SER E 11 0 SHEET 2 AB3 4 ASN E 21 PHE E 30 -1 O ASN E 24 N TYR E 10 SHEET 3 AB3 4 PHE E 62 PHE E 70 -1 O TYR E 66 N CYS E 25 SHEET 4 AB3 4 GLU E 50 HIS E 51 -1 N GLU E 50 O TYR E 67 SHEET 1 AB4 4 LYS E 6 SER E 11 0 SHEET 2 AB4 4 ASN E 21 PHE E 30 -1 O ASN E 24 N TYR E 10 SHEET 3 AB4 4 PHE E 62 PHE E 70 -1 O TYR E 66 N CYS E 25 SHEET 4 AB4 4 SER E 55 PHE E 56 -1 N SER E 55 O TYR E 63 SHEET 1 AB5 3 GLU E 36 LYS E 41 0 SHEET 2 AB5 3 TYR E 78 ASN E 83 -1 O ARG E 81 N ASP E 38 SHEET 3 AB5 3 LYS E 91 LYS E 94 -1 O LYS E 91 N VAL E 82 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.03 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.01 SSBOND 3 CYS B 25 CYS B 80 1555 1555 1.99 SSBOND 4 CYS D 101 CYS D 164 1555 1555 2.07 SSBOND 5 CYS D 203 CYS D 259 1555 1555 2.05 SSBOND 6 CYS E 25 CYS E 80 1555 1555 2.03 CISPEP 1 TYR A 209 PRO A 210 0 2.66 CISPEP 2 HIS B 31 PRO B 32 0 3.76 CISPEP 3 TYR D 209 PRO D 210 0 0.25 CISPEP 4 HIS E 31 PRO E 32 0 -2.20 CRYST1 85.069 85.069 214.213 90.00 90.00 120.00 P 32 1 2 12 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 0.011755 0.006787 0.000000 0.00000 SCALE2 0.000000 0.013574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004668 0.00000