HEADER VIRAL PROTEIN/IMMUNE SYSTEM 29-SEP-21 7SD5 TITLE CRYSTALLOGRAPHIC STRUCTURE OF NEUTRALIZING ANTIBODY 10-40 IN COMPLEX TITLE 2 WITH SARS-COV-2 SPIKE RECEPTOR BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN (UNP RESIDUES 319-537); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 10-40 HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 10-40 LIGHT CHAIN; COMPND 12 CHAIN: L; 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; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 22 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS COVID-19, SARS-COV-2, VIRAL PROTEIN, SPIKE GLYCOPROTEIN, RECEPTOR KEYWDS 2 BINDING PROTEIN, RBD, NEUTRALIZING ANTIBODY, 10-40, FAB, VIRAL KEYWDS 3 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.R.REDDEM,R.G.CASNER,L.SHAPIRO REVDAT 5 23-OCT-24 7SD5 1 REMARK REVDAT 4 18-OCT-23 7SD5 1 REMARK REVDAT 3 08-JUN-22 7SD5 1 JRNL REVDAT 2 04-MAY-22 7SD5 1 JRNL REVDAT 1 27-APR-22 7SD5 0 JRNL AUTH L.LIU,S.IKETANI,Y.GUO,E.R.REDDEM,R.G.CASNER,M.S.NAIR,J.YU, JRNL AUTH 2 J.F.CHAN,M.WANG,G.CERUTTI,Z.LI,N.C.MORANO,C.D.CASTAGNA, JRNL AUTH 3 L.CORREDOR,H.CHU,S.YUAN,V.K.POON,C.C.CHAN,Z.CHEN,Y.LUO, JRNL AUTH 4 M.CUNNINGHAM,A.CHAVEZ,M.T.YIN,D.S.PERLIN,M.TSUJI,K.Y.YUEN, JRNL AUTH 5 P.D.KWONG,Z.SHENG,Y.HUANG,L.SHAPIRO,D.D.HO JRNL TITL AN ANTIBODY CLASS WITH A COMMON CDRH3 MOTIF BROADLY JRNL TITL 2 NEUTRALIZES SARBECOVIRUSES. JRNL REF SCI TRANSL MED V. 14 N6859 2022 JRNL REFN ESSN 1946-6242 JRNL PMID 35438546 JRNL DOI 10.1126/SCITRANSLMED.ABN6859 REMARK 2 REMARK 2 RESOLUTION. 1.53 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 106248 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 5520 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6137 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE SET COUNT : 329 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4851 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 678 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : 0.44000 REMARK 3 B12 (A**2) : 0.00000 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): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.655 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5102 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4573 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6978 ; 1.783 ; 1.656 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10600 ; 1.477 ; 1.581 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 7.416 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;33.779 ;22.807 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 770 ;11.765 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;20.777 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 675 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5852 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1191 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2563 ; 2.515 ; 2.817 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2562 ; 2.515 ; 2.816 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3208 ; 3.414 ; 4.221 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3209 ; 3.414 ; 4.221 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2539 ; 3.799 ; 3.162 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2540 ; 3.798 ; 3.162 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3766 ; 5.532 ; 4.595 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5687 ; 7.061 ;34.401 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5517 ; 6.936 ;33.541 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7SD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 111889 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 59.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 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: PDB ENTRY 7L5B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM THIOCYANATE, 0.1 M REMARK 280 SODIUM ACETATE, PH 5.5, 8% PEG550 MME, 8% PEG20000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 37.87800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.43200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.92250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.43200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.87800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.92250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L, 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 ALA A 316 REMARK 465 PRO A 317 REMARK 465 ARG A 318 REMARK 465 ARG A 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 GLU A 324 REMARK 465 SER A 325 REMARK 465 ILE A 326 REMARK 465 VAL A 327 REMARK 465 ARG A 328 REMARK 465 PHE A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 ASN A 334 REMARK 465 LYS A 528 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 REMARK 465 VAL A 534 REMARK 465 LYS A 535 REMARK 465 ASN A 536 REMARK 465 LYS A 537 REMARK 465 GLY A 538 REMARK 465 SER A 539 REMARK 465 LEU A 540 REMARK 465 GLU A 541 REMARK 465 VAL A 542 REMARK 465 LEU A 543 REMARK 465 PHE A 544 REMARK 465 GLN A 545 REMARK 465 GLY A 546 REMARK 465 PRO A 547 REMARK 465 GLY A 548 REMARK 465 HIS A 549 REMARK 465 HIS A 550 REMARK 465 HIS A 551 REMARK 465 HIS A 552 REMARK 465 HIS A 553 REMARK 465 HIS A 554 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 GLY H 133 REMARK 465 ASP H 217 REMARK 465 LYS H 218 REMARK 465 THR H 219 REMARK 465 GLU L 211 REMARK 465 CYS L 212 REMARK 465 SER L 213 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH H 551 O HOH H 557 2.01 REMARK 500 O HOH L 412 O HOH L 488 2.05 REMARK 500 O HOH H 331 O HOH H 536 2.06 REMARK 500 O HOH A 700 O HOH A 737 2.09 REMARK 500 N GLN H 1 O HOH H 301 2.11 REMARK 500 O HOH A 735 O HOH H 508 2.17 REMARK 500 OG SER L 95 O HOH L 301 2.18 REMARK 500 O HOH A 694 O HOH A 756 2.19 REMARK 500 O HOH H 460 O HOH L 497 2.19 REMARK 500 OD1 ASN A 440 O HOH A 601 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH H 350 O HOH H 502 3544 1.86 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 484 CD GLU A 484 OE1 0.101 REMARK 500 GLU H 16 CD GLU H 16 OE1 0.129 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 A 454 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG H 66 NE - CZ - NH1 ANGL. DEV. = 3.8 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 ASN A 422 -54.04 -123.38 REMARK 500 PHE A 486 109.55 -55.59 REMARK 500 SER H 15 -12.83 82.49 REMARK 500 ASP H 101 -60.85 -101.11 REMARK 500 ASP L 51 -40.42 77.47 REMARK 500 SER L 90 -156.53 -142.88 REMARK 500 ASP L 152 -121.37 55.12 REMARK 500 ASN L 171 -13.30 78.01 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 H 574 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH H 575 DISTANCE = 6.32 ANGSTROMS DBREF 7SD5 A 319 537 UNP P0DTC2 SPIKE_SARS2 319 537 DBREF 7SD5 H 1 219 PDB 7SD5 7SD5 1 219 DBREF 7SD5 L 1 213 PDB 7SD5 7SD5 1 213 SEQADV 7SD5 ALA A 316 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 PRO A 317 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 ARG A 318 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 GLY A 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 SER A 539 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 LEU A 540 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 GLU A 541 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 VAL A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 LEU A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 PHE A 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 GLN A 545 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 GLY A 546 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 PRO A 547 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 GLY A 548 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 HIS A 549 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 HIS A 550 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 HIS A 551 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 HIS A 552 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 HIS A 553 UNP P0DTC2 EXPRESSION TAG SEQADV 7SD5 HIS A 554 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 239 ALA PRO ARG ARG VAL GLN PRO THR GLU SER ILE VAL ARG SEQRES 2 A 239 PHE PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL SEQRES 3 A 239 PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN SEQRES 4 A 239 ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL SEQRES 5 A 239 LEU TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR SEQRES 6 A 239 GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR SEQRES 7 A 239 ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU SEQRES 8 A 239 VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA SEQRES 9 A 239 ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS SEQRES 10 A 239 VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL SEQRES 11 A 239 GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SEQRES 12 A 239 SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU SEQRES 13 A 239 ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU SEQRES 14 A 239 GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE SEQRES 15 A 239 GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL SEQRES 16 A 239 VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR SEQRES 17 A 239 VAL CYS GLY PRO LYS LYS SER THR ASN LEU VAL LYS ASN SEQRES 18 A 239 LYS GLY SER LEU GLU VAL LEU PHE GLN GLY PRO GLY HIS SEQRES 19 A 239 HIS HIS HIS HIS HIS SEQRES 1 H 236 GLN LEU GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 H 236 PRO SER GLU THR LEU SER LEU THR CYS THR VAL SER GLY SEQRES 3 H 236 GLY SER ILE SER SER SER ASN PHE TYR TRP GLY TRP ILE SEQRES 4 H 236 ARG GLN PRO PRO GLY LYS GLY LEU GLU TRP ILE ALA SER SEQRES 5 H 236 ILE THR TYR SER GLY ARG THR PHE TYR ASN PRO SER LEU SEQRES 6 H 236 LYS SER ARG VAL ALA ILE SER VAL ASP THR SER LYS ASN SEQRES 7 H 236 GLN PHE SER LEU LYS LEU SER SER VAL THR ALA ALA ASP SEQRES 8 H 236 THR ALA VAL TYR TYR CYS ALA ARG THR PHE PRO SER TYR SEQRES 9 H 236 TYR ASP ARG SER GLY TYR HIS TYR LEU ASN TYR GLY MET SEQRES 10 H 236 ASP VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SER SEQRES 11 H 236 ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SEQRES 12 H 236 SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY SEQRES 13 H 236 CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SEQRES 14 H 236 SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR SEQRES 15 H 236 PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SEQRES 16 H 236 SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR SEQRES 17 H 236 GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN SEQRES 18 H 236 THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS ASP SEQRES 19 H 236 LYS THR SEQRES 1 L 216 ASN PHE MET LEU THR GLN PRO HIS SER MET SER GLU SER SEQRES 2 L 216 PRO GLY LYS THR VAL THR ILE SER CYS THR ARG SER SER SEQRES 3 L 216 GLY SER ILE ALA SER ASN TYR VAL GLN TRP TYR GLN GLN SEQRES 4 L 216 ARG PRO GLY SER SER PRO THR THR VAL ILE TYR GLU ASP SEQRES 5 L 216 ASN GLN ARG PRO SER GLY VAL PRO ASP ARG PHE SER GLY SEQRES 6 L 216 SER ILE ASP SER SER SER ASN SER ALA SER LEU THR ILE SEQRES 7 L 216 SER GLY LEU LYS THR GLU ASP GLU ALA ASP TYR TYR CYS SEQRES 8 L 216 GLN SER TYR ASP SER SER SER TRP VAL PHE GLY GLY GLY SEQRES 9 L 216 THR LYS LEU THR VAL LEU GLY GLN PRO LYS ALA ASN PRO SEQRES 10 L 216 THR VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 L 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 L 216 TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP GLY SEQRES 13 L 216 SER PRO VAL LYS ALA GLY VAL GLU THR THR LYS PRO SER SEQRES 14 L 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 L 216 SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SEQRES 16 L 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 L 216 THR VAL ALA PRO THR GLU CYS SER HET NAG B 1 14 HET NAG B 2 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 HOH *678(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 1 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 LEU H 63 SER H 65 5 3 HELIX 10 AB1 THR H 73 LYS H 75 5 3 HELIX 11 AB2 THR H 83 THR H 87 5 5 HELIX 12 AB3 SER H 156 ALA H 158 5 3 HELIX 13 AB4 SER H 187 LEU H 189 5 3 HELIX 14 AB5 LYS H 201 ASN H 204 5 4 HELIX 15 AB6 SER L 27B ASN L 31 5 5 HELIX 16 AB7 LYS L 79 GLU L 83 5 5 HELIX 17 AB8 SER L 122 ALA L 128 1 7 HELIX 18 AB9 THR L 182 HIS L 189 1 8 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O VAL A 512 N ASP A 398 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 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 GLN H 3 SER H 7 0 SHEET 2 AA5 4 LEU H 18 SER H 25 -1 O SER H 25 N GLN H 3 SHEET 3 AA5 4 GLN H 77 LEU H 82 -1 O LEU H 82 N LEU H 18 SHEET 4 AA5 4 VAL H 67 ASP H 72 -1 N ASP H 72 O GLN H 77 SHEET 1 AA6 6 LEU H 11 VAL H 12 0 SHEET 2 AA6 6 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AA6 6 ALA H 88 THR H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA6 6 TRP H 35A GLN H 39 -1 N ILE H 37 O TYR H 91 SHEET 5 AA6 6 GLU H 46 ILE H 51 -1 O ILE H 48 N TRP H 36 SHEET 6 AA6 6 THR H 57 TYR H 59 -1 O PHE H 58 N SER H 50 SHEET 1 AA7 4 LEU H 11 VAL H 12 0 SHEET 2 AA7 4 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AA7 4 ALA H 88 THR H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA7 4 MET H 100L TRP H 103 -1 O ASP H 101 N ARG H 94 SHEET 1 AA8 2 TYR H 99 TYR H 100 0 SHEET 2 AA8 2 HIS H 100F TYR H 100G-1 O TYR H 100G N TYR H 99 SHEET 1 AA9 4 SER H 120 LEU H 124 0 SHEET 2 AA9 4 THR H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AA9 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AA9 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AB1 4 SER H 120 LEU H 124 0 SHEET 2 AB1 4 THR H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AB1 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AB1 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB2 3 THR H 151 TRP H 154 0 SHEET 2 AB2 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB2 3 THR H 205 LYS H 210 -1 O VAL H 207 N VAL H 198 SHEET 1 AB3 4 LEU L 4 THR L 5 0 SHEET 2 AB3 4 VAL L 18 ARG L 24 -1 O THR L 23 N THR L 5 SHEET 3 AB3 4 SER L 70 ILE L 75 -1 O LEU L 73 N ILE L 20 SHEET 4 AB3 4 PHE L 62 ASP L 66A-1 N ASP L 66A O SER L 70 SHEET 1 AB4 5 SER L 9 GLU L 12 0 SHEET 2 AB4 5 THR L 102 VAL L 106 1 O THR L 105 N MET L 10 SHEET 3 AB4 5 ALA L 84 ASP L 92 -1 N ALA L 84 O LEU L 104 SHEET 4 AB4 5 GLN L 34 GLN L 38 -1 N GLN L 38 O ASP L 85 SHEET 5 AB4 5 THR L 45 ILE L 48 -1 O THR L 45 N GLN L 37 SHEET 1 AB5 4 SER L 9 GLU L 12 0 SHEET 2 AB5 4 THR L 102 VAL L 106 1 O THR L 105 N MET L 10 SHEET 3 AB5 4 ALA L 84 ASP L 92 -1 N ALA L 84 O LEU L 104 SHEET 4 AB5 4 SER L 95 PHE L 98 -1 O VAL L 97 N SER L 90 SHEET 1 AB6 4 THR L 115 PHE L 119 0 SHEET 2 AB6 4 ALA L 131 PHE L 140 -1 O LEU L 136 N THR L 117 SHEET 3 AB6 4 TYR L 173 LEU L 181 -1 O SER L 177 N CYS L 135 SHEET 4 AB6 4 VAL L 160 THR L 162 -1 N GLU L 161 O TYR L 178 SHEET 1 AB7 4 THR L 115 PHE L 119 0 SHEET 2 AB7 4 ALA L 131 PHE L 140 -1 O LEU L 136 N THR L 117 SHEET 3 AB7 4 TYR L 173 LEU L 181 -1 O SER L 177 N CYS L 135 SHEET 4 AB7 4 SER L 166 LYS L 167 -1 N SER L 166 O ALA L 174 SHEET 1 AB8 4 SER L 154 PRO L 155 0 SHEET 2 AB8 4 THR L 146 ALA L 151 -1 N ALA L 151 O SER L 154 SHEET 3 AB8 4 TYR L 192 HIS L 198 -1 O GLN L 195 N ALA L 148 SHEET 4 AB8 4 SER L 201 VAL L 207 -1 O VAL L 203 N VAL L 196 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.06 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.07 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.11 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.08 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.24 SSBOND 6 CYS H 140 CYS H 196 1555 1555 2.05 SSBOND 7 CYS L 22 CYS L 88 1555 1555 2.10 SSBOND 8 CYS L 135 CYS L 194 1555 1555 2.07 LINK ND2 ASN A 343 C1 NAG B 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.35 CISPEP 1 PHE H 146 PRO H 147 0 -6.18 CISPEP 2 GLU H 148 PRO H 149 0 -5.91 CISPEP 3 TYR L 141 PRO L 142 0 1.67 CRYST1 75.756 79.845 118.864 90.00 90.00 90.00 P 21 21 21 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 0.013200 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012524 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008413 0.00000