HEADER VIRAL PROTEIN/IMMUNE SYSTEM 01-AUG-22 8DWA TITLE CRYSTAL STRUCTURE OF NEUTRALIZING ANTIBODY P1D9 FAB IN COMPLEX WITH TITLE 2 SARS-COV-2 SPIKE RECEPTOR BINDING DOMAIN (RBD) CAVEAT 8DWA SER A 366 HAS WRONG CHIRALITY AT ATOM CA VAL A 367 HAS WRONG CAVEAT 2 8DWA CHIRALITY AT ATOM CA VAL H 18 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 8DWA CA THR L 53 HAS WRONG CHIRALITY AT ATOM CA ENTRY CONTAINS CAVEAT 4 8DWA IMPROPER PEPTIDE LINKAGES. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN (UNP RESIDUES 335-515); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: P1D9 HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: P1D9 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, SARS-COV-2; 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, 10-28, FAB, VIRAL KEYWDS 3 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.R.REDDEM,L.SHAPIRO REVDAT 3 25-OCT-23 8DWA 1 REMARK REVDAT 2 18-JAN-23 8DWA 1 JRNL REVDAT 1 07-DEC-22 8DWA 0 JRNL AUTH M.LUO,B.ZHOU,E.R.REDDEM,B.TANG,B.CHEN,R.ZHOU,H.LIU,L.LIU, JRNL AUTH 2 P.S.KATSAMBA,K.K.AU,H.O.MAN,K.K.TO,K.Y.YUEN,L.SHAPIRO, JRNL AUTH 3 S.DANG,D.D.HO,Z.CHEN JRNL TITL STRUCTURAL INSIGHTS INTO BROADLY NEUTRALIZING ANTIBODIES JRNL TITL 2 ELICITED BY HYBRID IMMUNITY AGAINST SARS-COV-2. JRNL REF EMERG MICROBES INFECT V. 12 46538 2023 JRNL REFN ESSN 2222-1751 JRNL PMID 36354024 JRNL DOI 10.1080/22221751.2022.2146538 REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 14187 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 747 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1024 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4584 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 94.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.24000 REMARK 3 B22 (A**2) : 1.24000 REMARK 3 B33 (A**2) : -2.48000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.554 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.479 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 62.546 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4737 ; 0.009 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 4311 ; 0.001 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6448 ; 1.539 ; 1.851 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9945 ; 1.187 ; 2.693 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 595 ; 8.465 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 221 ;34.803 ;22.760 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 738 ;19.287 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.276 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 714 ; 0.236 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5428 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1133 ; 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): 2388 ; 2.621 ; 6.256 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2387 ; 2.622 ; 6.257 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2980 ; 4.436 ; 9.382 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2981 ; 4.435 ; 9.382 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2349 ; 2.896 ; 6.536 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2350 ; 2.896 ; 6.539 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3469 ; 4.923 ; 9.696 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 18810 ;10.726 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 18811 ;10.726 ; 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 335 A 515 REMARK 3 ORIGIN FOR THE GROUP (A): 25.6790 15.7340 25.3300 REMARK 3 T TENSOR REMARK 3 T11: 0.1035 T22: 0.0793 REMARK 3 T33: 0.1671 T12: 0.0702 REMARK 3 T13: 0.0239 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 3.5811 L22: 5.0015 REMARK 3 L33: 7.0339 L12: -1.6055 REMARK 3 L13: 1.1208 L23: -0.7980 REMARK 3 S TENSOR REMARK 3 S11: -0.3654 S12: -0.2276 S13: 0.0054 REMARK 3 S21: 0.1956 S22: 0.2734 S23: 0.1504 REMARK 3 S31: -0.1207 S32: -0.4733 S33: 0.0920 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 2 H 214 REMARK 3 ORIGIN FOR THE GROUP (A): 57.9570 -11.0040 37.0230 REMARK 3 T TENSOR REMARK 3 T11: 0.2601 T22: 0.1105 REMARK 3 T33: 0.4950 T12: -0.0886 REMARK 3 T13: -0.1270 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 2.4499 L22: 4.7767 REMARK 3 L33: 0.7218 L12: -3.1292 REMARK 3 L13: 0.7142 L23: -1.4701 REMARK 3 S TENSOR REMARK 3 S11: -0.1734 S12: -0.1060 S13: 0.2933 REMARK 3 S21: 0.2156 S22: 0.0084 S23: -0.5439 REMARK 3 S31: -0.0696 S32: 0.0155 S33: 0.1650 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 211 REMARK 3 ORIGIN FOR THE GROUP (A): 48.4790 -26.7120 33.3190 REMARK 3 T TENSOR REMARK 3 T11: 0.1415 T22: 0.0557 REMARK 3 T33: 0.3579 T12: -0.0708 REMARK 3 T13: -0.0607 T23: 0.0222 REMARK 3 L TENSOR REMARK 3 L11: 2.0325 L22: 4.5835 REMARK 3 L33: 1.3640 L12: -2.9530 REMARK 3 L13: 1.5384 L23: -2.3609 REMARK 3 S TENSOR REMARK 3 S11: -0.0049 S12: 0.0121 S13: -0.1036 REMARK 3 S21: -0.1976 S22: 0.0841 S23: 0.2423 REMARK 3 S31: 0.0942 S32: -0.0116 S33: -0.0792 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.30 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 8DWA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-22 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15333 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.120 REMARK 200 RESOLUTION RANGE LOW (A) : 144.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.60 REMARK 200 R MERGE (I) : 0.51600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 26.70 REMARK 200 R MERGE FOR SHELL (I) : 4.52000 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 7SD5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M MES, PH REMARK 280 6.5, 18% W/V PEG5000 MME, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 73.56800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 73.56800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.05400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 73.56800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 73.56800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.05400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 73.56800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 73.56800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.05400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 73.56800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 73.56800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.05400 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 VAL A 382 REMARK 465 SER A 383 REMARK 465 PRO A 384 REMARK 465 THR A 385 REMARK 465 LYS A 386 REMARK 465 LEU A 387 REMARK 465 ASN A 388 REMARK 465 ASP A 389 REMARK 465 LEU A 390 REMARK 465 CYS A 391 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 ASP L 1 N CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 HIS H 58 OH TYR L 92 2.08 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 SER A 366 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 VAL H 18 CB - CA - C ANGL. DEV. = 12.0 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 PRO A 337 -80.73 -69.57 REMARK 500 PHE A 338 -59.56 58.44 REMARK 500 ALA A 344 121.22 -31.60 REMARK 500 ASN A 360 84.53 53.42 REMARK 500 CYS A 361 171.11 161.31 REMARK 500 TYR A 365 -112.79 78.33 REMARK 500 SER A 366 -81.07 42.03 REMARK 500 TYR A 369 -65.66 71.29 REMARK 500 ALA A 372 -132.19 -85.37 REMARK 500 ASN A 422 -43.39 -136.25 REMARK 500 ASP A 428 -35.96 -37.02 REMARK 500 PHE A 429 113.28 -28.16 REMARK 500 ASN A 448 107.17 -19.97 REMARK 500 GLN A 474 82.42 78.23 REMARK 500 ASN A 487 -153.90 45.24 REMARK 500 ASN A 501 142.76 -36.93 REMARK 500 PRO H 14 163.13 -44.81 REMARK 500 SER H 16 -146.53 53.33 REMARK 500 SER H 17 136.69 172.99 REMARK 500 SER H 25 -73.45 -124.09 REMARK 500 THR H 28 -107.17 69.70 REMARK 500 PHE H 29 -84.16 37.54 REMARK 500 GLN H 43 -102.17 -164.93 REMARK 500 SER H 84 -42.77 58.41 REMARK 500 ASP H 95 -119.68 -97.35 REMARK 500 THR H 96 93.26 -162.26 REMARK 500 TRP H 98 -85.19 -127.53 REMARK 500 THR H 99 -144.11 -61.11 REMARK 500 THR H 100A -155.23 -117.82 REMARK 500 THR H 116 150.24 -48.85 REMARK 500 ASP H 144 77.30 52.88 REMARK 500 PHE H 146 140.58 -177.62 REMARK 500 ALA H 158 -89.50 54.50 REMARK 500 THR H 160 -44.87 58.05 REMARK 500 THR H 191 -100.18 94.51 REMARK 500 ASN H 204 48.51 30.53 REMARK 500 LYS H 209 115.39 -161.80 REMARK 500 CYS L 23 79.09 -153.38 REMARK 500 ASN L 30 -104.73 -133.52 REMARK 500 THR L 31 40.42 -80.09 REMARK 500 ALA L 50 42.33 38.51 REMARK 500 ALA L 51 -63.38 84.26 REMARK 500 GLN L 55 -151.43 66.51 REMARK 500 SER L 56 110.58 -165.53 REMARK 500 ALA L 84 -168.88 -174.54 REMARK 500 TYR L 92 -159.99 87.37 REMARK 500 SER L 93 61.78 62.69 REMARK 500 ASN L 94 134.85 54.50 REMARK 500 LEU L 95 132.24 84.70 REMARK 500 PHE L 98 -167.28 -118.04 REMARK 500 REMARK 500 THIS ENTRY HAS 56 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 367 LEU A 368 143.13 REMARK 500 HIS H 58 TYR H 59 -148.87 REMARK 500 SER L 91 TYR L 92 147.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 8DWA A 335 515 UNP P0DTC2 SPIKE_SARS2 335 515 DBREF 8DWA H 2 214 PDB 8DWA 8DWA 2 214 DBREF 8DWA L 1 211 PDB 8DWA 8DWA 1 211 SEQRES 1 A 181 LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG PHE SEQRES 2 A 181 ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER ASN SEQRES 3 A 181 CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SER SEQRES 4 A 181 PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR LYS SEQRES 5 A 181 LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SER SEQRES 6 A 181 PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA PRO SEQRES 7 A 181 GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS LEU SEQRES 8 A 181 PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SER SEQRES 9 A 181 ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN TYR SEQRES 10 A 181 LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO PHE SEQRES 11 A 181 GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SER SEQRES 12 A 181 THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR PHE SEQRES 13 A 181 PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY VAL SEQRES 14 A 181 GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 1 H 214 VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS PRO SEQRES 2 H 214 GLY SER SER VAL ARG VAL SER CYS LYS ALA SER GLY GLY SEQRES 3 H 214 THR PHE GLY ASP ASP SER ILE THR TRP VAL ARG GLN ALA SEQRES 4 H 214 PRO GLY GLN GLY LEU GLU TRP MET GLY GLY ILE PHE PRO SEQRES 5 H 214 LEU ILE GLY LYS THR HIS TYR ALA GLN ARG PHE GLN GLY SEQRES 6 H 214 ARG LEU THR VAL THR ALA ASP LYS SER THR SER THR ALA SEQRES 7 H 214 TYR MET GLU LEU SER GLY LEU ARG SER GLU ASP THR ALA SEQRES 8 H 214 ILE TYR TYR CYS ALA ARG ASP THR GLY TRP THR LEU THR SEQRES 9 H 214 ALA PHE ASP ILE TRP GLY GLN GLY THR MET VAL THR VAL SEQRES 10 H 214 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 214 ALA PRO SER GLY THR ALA ALA LEU GLY CYS LEU VAL LYS SEQRES 12 H 214 ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER SEQRES 13 H 214 GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL SEQRES 14 H 214 LEU GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL SEQRES 15 H 214 THR VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE SEQRES 16 H 214 CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP SEQRES 17 H 214 LYS LYS VAL GLU PRO LYS SEQRES 1 L 211 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 211 SER VAL GLY ASP THR VAL THR ILE THR CYS ARG ALA GLY SEQRES 3 L 211 GLN THR ILE ASN THR PHE LEU ASN TRP TYR GLN GLN LYS SEQRES 4 L 211 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 L 211 THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 211 GLY SER GLY THR ASP PHE THR LEU THR ILE ASN SER LEU SEQRES 7 L 211 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 L 211 TYR SER ASN LEU TYR THR PHE SER GLN GLY THR LYS VAL SEQRES 9 L 211 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 211 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 211 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 211 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 211 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 211 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 211 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 211 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 211 PHE ASN ARG HET NAG A 601 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 C8 H15 N O6 HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 ARG A 403 ILE A 410 5 8 HELIX 4 AA4 GLY A 416 ASN A 422 1 7 HELIX 5 AA5 SER A 438 SER A 443 1 6 HELIX 6 AA6 GLY A 502 GLN A 506 5 5 HELIX 7 AA7 GLN H 61 GLN H 64 5 4 HELIX 8 AA8 LYS H 201 ASN H 204 5 4 HELIX 9 AA9 GLN L 79 PHE L 83 5 5 HELIX 10 AB1 SER L 121 SER L 127 1 7 HELIX 11 AB2 LYS L 183 GLU L 187 1 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 VAL A 395 ILE A 402 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 5 TYR A 508 SER A 514 -1 O TYR A 508 N ILE A 402 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 LYS A 378 O VAL A 433 SHEET 1 AA2 2 LEU A 452 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA3 4 LEU H 4 GLN H 6 0 SHEET 2 AA3 4 GLY H 15 ALA H 24 -1 O LYS H 23 N VAL H 5 SHEET 3 AA3 4 THR H 77 LEU H 82C-1 O LEU H 82C N GLY H 15 SHEET 4 AA3 4 LEU H 67 ASP H 72 -1 N THR H 68 O GLU H 81 SHEET 1 AA4 6 GLU H 10 LYS H 12 0 SHEET 2 AA4 6 MET H 108 VAL H 111 1 O THR H 110 N GLU H 10 SHEET 3 AA4 6 ALA H 88 ARG H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 AA4 6 THR H 35 GLN H 39 -1 N GLN H 39 O ILE H 89 SHEET 5 AA4 6 LEU H 45 PHE H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 AA4 6 LYS H 56 TYR H 59 -1 O HIS H 58 N GLY H 50 SHEET 1 AA5 4 GLU H 10 LYS H 12 0 SHEET 2 AA5 4 MET H 108 VAL H 111 1 O THR H 110 N GLU H 10 SHEET 3 AA5 4 ALA H 88 ARG H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 AA5 4 ILE H 102 TRP H 103 -1 O ILE H 102 N ARG H 94 SHEET 1 AA6 4 SER H 120 LEU H 124 0 SHEET 2 AA6 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA6 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AA6 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AA7 4 SER H 120 LEU H 124 0 SHEET 2 AA7 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA7 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AA7 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AA8 3 THR H 151 TRP H 154 0 SHEET 2 AA8 3 TYR H 194 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AA8 3 THR H 205 VAL H 211 -1 O VAL H 207 N VAL H 198 SHEET 1 AA9 4 MET L 4 SER L 7 0 SHEET 2 AA9 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA9 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 AA9 4 PHE L 62 SER L 63 -1 N SER L 63 O THR L 74 SHEET 1 AB1 4 MET L 4 SER L 7 0 SHEET 2 AB1 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AB1 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 AB1 4 GLY L 66 SER L 67 -1 N SER L 67 O ASP L 70 SHEET 1 AB2 5 SER L 10 ALA L 13 0 SHEET 2 AB2 5 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 AB2 5 THR L 85 TYR L 87 -1 N TYR L 86 O THR L 102 SHEET 4 AB2 5 TRP L 35 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 AB2 5 PRO L 44 ILE L 48 -1 O LYS L 45 N GLN L 37 SHEET 1 AB3 2 GLN L 89 SER L 91 0 SHEET 2 AB3 2 TYR L 96 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB4 4 SER L 114 PHE L 118 0 SHEET 2 AB4 4 THR L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 AB4 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AB4 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AB5 4 ALA L 153 GLN L 155 0 SHEET 2 AB5 4 VAL L 146 VAL L 150 -1 N TRP L 148 O GLN L 155 SHEET 3 AB5 4 VAL L 191 VAL L 196 -1 O ALA L 193 N LYS L 149 SHEET 4 AB5 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.04 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.07 SSBOND 3 CYS A 480 CYS A 488 1555 1555 2.02 SSBOND 4 CYS H 22 CYS H 92 1555 1555 2.05 SSBOND 5 CYS H 140 CYS H 196 1555 1555 2.06 SSBOND 6 CYS L 23 CYS L 88 1555 1555 2.07 SSBOND 7 CYS L 134 CYS L 194 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.45 CISPEP 1 PHE H 146 PRO H 147 0 -6.72 CISPEP 2 SER L 7 PRO L 8 0 -6.33 CISPEP 3 TYR L 140 PRO L 141 0 1.34 CRYST1 147.136 147.136 80.108 90.00 90.00 90.00 P 42 21 2 8 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 0.006796 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006796 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012483 0.00000