HEADER VIRAL PROTEIN/IMMUNE SYSTEM 25-FEB-22 7X2M TITLE CRYSTAL STRUCTURE OF NANOBODY 1-2C7 WITH SARS-COV-2 RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: RBD; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 1-2C7; COMPND 8 CHAIN: B; COMPND 9 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: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 11 ORGANISM_TAXID: 30538; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, NANOBODY, SPIKE, RECEPTOR BINDING DOMAIN, VIRAL PROTEIN- KEYWDS 2 IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.Q.WANG,L.Q.ZHANG,Y.F.REN,M.X.LI REVDAT 3 29-NOV-23 7X2M 1 REMARK REVDAT 2 28-JUN-23 7X2M 1 JRNL REVDAT 1 14-DEC-22 7X2M 0 JRNL AUTH M.LI,Y.REN,Z.Q.AW,B.CHEN,Z.YANG,Y.LEI,L.CHENG,Q.LIANG, JRNL AUTH 2 J.HONG,Y.YANG,J.CHEN,Y.H.WONG,J.WEI,S.SHAN,S.ZHANG,J.GE, JRNL AUTH 3 R.WANG,J.Z.DONG,Y.CHEN,X.SHI,Q.ZHANG,Z.ZHANG,J.J.H.CHU, JRNL AUTH 4 X.WANG,L.ZHANG JRNL TITL BROADLY NEUTRALIZING AND PROTECTIVE NANOBODIES AGAINST JRNL TITL 2 SARS-COV-2 OMICRON SUBVARIANTS BA.1, BA.2, AND BA.4/5 AND JRNL TITL 3 DIVERSE SARBECOVIRUSES. JRNL REF NAT COMMUN V. 13 7957 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36575191 JRNL DOI 10.1038/S41467-022-35642-2 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 2199 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 25.3900 - 4.5300 1.00 2815 154 0.1605 0.1746 REMARK 3 2 4.5200 - 3.6000 1.00 2770 122 0.1475 0.1833 REMARK 3 3 3.5900 - 3.1400 1.00 2746 142 0.1749 0.1855 REMARK 3 4 3.1400 - 2.8500 1.00 2736 120 0.1870 0.2318 REMARK 3 5 2.8500 - 2.6500 1.00 2713 142 0.1995 0.2246 REMARK 3 6 2.6500 - 2.4900 1.00 2729 133 0.1930 0.2688 REMARK 3 7 2.4900 - 2.3700 1.00 2681 175 0.1911 0.2413 REMARK 3 8 2.3700 - 2.2700 1.00 2685 140 0.2019 0.2326 REMARK 3 9 2.2700 - 2.1800 1.00 2705 111 0.1863 0.1840 REMARK 3 10 2.1800 - 2.1000 1.00 2692 159 0.1967 0.2327 REMARK 3 11 2.1000 - 2.0400 1.00 2719 131 0.1995 0.2164 REMARK 3 12 2.0400 - 1.9800 1.00 2699 136 0.1962 0.2552 REMARK 3 13 1.9800 - 1.9300 1.00 2721 135 0.2178 0.2144 REMARK 3 14 1.9300 - 1.8800 1.00 2648 134 0.2312 0.2651 REMARK 3 15 1.8800 - 1.8400 1.00 2735 126 0.2577 0.2611 REMARK 3 16 1.8400 - 1.8000 1.00 2694 139 0.3120 0.3309 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.69 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): -0.9167 -35.0990 -46.8231 REMARK 3 T TENSOR REMARK 3 T11: 0.2640 T22: 0.2429 REMARK 3 T33: 0.1939 T12: 0.0119 REMARK 3 T13: -0.0010 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 2.9422 L22: 1.5289 REMARK 3 L33: 1.2387 L12: 0.3278 REMARK 3 L13: -0.3395 L23: -0.2574 REMARK 3 S TENSOR REMARK 3 S11: 0.1305 S12: -0.0164 S13: 0.3693 REMARK 3 S21: 0.1098 S22: -0.0067 S23: 0.0390 REMARK 3 S31: -0.2596 S32: 0.0441 S33: -0.1123 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 7X2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300027521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 7.21 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 7.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45687 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 38.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 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 : 1.570 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.0 REMARK 200 STARTING MODEL: 6M0J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M BIS TRIS REMARK 280 PH 5.5, 25% W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+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 -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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 71.80950 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 71.80950 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 71.80950 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 71.80950 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 71.80950 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 71.80950 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 71.80950 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 71.80950 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 71.80950 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 71.80950 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 71.80950 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 71.80950 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 71.80950 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 71.80950 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 71.80950 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 71.80950 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 71.80950 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 71.80950 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 71.80950 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 71.80950 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 71.80950 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 71.80950 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 71.80950 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 71.80950 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 71.80950 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 71.80950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, B, A 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 LYS E 529 REMARK 465 HIS E 530 REMARK 465 HIS E 531 REMARK 465 HIS E 532 REMARK 465 HIS E 533 REMARK 465 HIS E 534 REMARK 465 HIS E 535 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 E 734 O HOH E 776 1.81 REMARK 500 O HOH E 731 O HOH E 754 1.88 REMARK 500 O HOH E 757 O HOH E 760 1.91 REMARK 500 O HOH E 611 O HOH E 754 2.04 REMARK 500 O HOH E 738 O HOH E 768 2.05 REMARK 500 O THR E 430 O HOH E 601 2.09 REMARK 500 O HOH E 722 O HOH E 759 2.11 REMARK 500 O HOH E 731 O HOH E 749 2.12 REMARK 500 O HOH B 234 O HOH B 244 2.13 REMARK 500 O HOH E 722 O HOH E 768 2.14 REMARK 500 O HOH E 611 O HOH E 731 2.15 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 E 377 71.59 -152.93 REMARK 500 ASN E 422 -53.57 -126.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 7X2M E 333 529 UNP P0DTC2 SPIKE_SARS2 333 529 DBREF 7X2M B 1 124 PDB 7X2M 7X2M 1 124 SEQADV 7X2M ASN E 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7X2M LYS E 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7X2M TYR E 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7X2M HIS E 530 UNP P0DTC2 EXPRESSION TAG SEQADV 7X2M HIS E 531 UNP P0DTC2 EXPRESSION TAG SEQADV 7X2M HIS E 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7X2M HIS E 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7X2M HIS E 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7X2M HIS E 535 UNP P0DTC2 EXPRESSION TAG SEQRES 1 E 203 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 E 203 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 E 203 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 E 203 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 E 203 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 E 203 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 E 203 ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR SEQRES 8 E 203 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 E 203 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 E 203 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 E 203 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 E 203 GLY SER THR PRO CYS ASN GLY VAL LYS GLY PHE ASN CYS SEQRES 13 E 203 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR TYR SEQRES 14 E 203 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 E 203 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 16 E 203 LYS LYS HIS HIS HIS HIS HIS HIS SEQRES 1 B 124 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 124 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 124 ASP THR LEU ASP LEU TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 B 124 THR PRO GLY GLU GLU ARG GLU GLY VAL SER CYS ILE SER SEQRES 5 B 124 PRO SER GLY SER ARG THR ASN TYR ALA ASP SER VAL LYS SEQRES 6 B 124 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 124 VAL TYR LEU GLN MET ASN GLY LEU ARG PRO GLU ASP THR SEQRES 8 B 124 ALA VAL TYR PHE CYS ALA GLY SER ARG PRO SER ALA HIS SEQRES 9 B 124 TYR CYS SER HIS TYR PRO THR GLU TYR ASP ASP TRP GLY SEQRES 10 B 124 GLN GLY THR GLN VAL THR VAL HET NAG A 1 14 HET NAG A 2 14 HET MAN A 3 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 3 MAN C6 H12 O6 FORMUL 4 HOH *225(H2 O) HELIX 1 AA1 PRO E 337 ASN E 343 1 7 HELIX 2 AA2 SER E 349 TRP E 353 5 5 HELIX 3 AA3 ASP E 364 ASN E 370 1 7 HELIX 4 AA4 SER E 383 ASP E 389 5 7 HELIX 5 AA5 ASP E 405 ILE E 410 5 6 HELIX 6 AA6 GLY E 416 ASN E 422 1 7 HELIX 7 AA7 SER E 438 SER E 443 1 6 HELIX 8 AA8 GLY E 502 TYR E 505 5 4 HELIX 9 AA9 ASP B 62 LYS B 65 5 4 HELIX 10 AB1 ARG B 87 THR B 91 5 5 HELIX 11 AB2 TYR B 109 TYR B 113 5 5 SHEET 1 AA1 5 ASN E 354 ILE E 358 0 SHEET 2 AA1 5 ASN E 394 ARG E 403 -1 O VAL E 395 N ILE E 358 SHEET 3 AA1 5 PRO E 507 GLU E 516 -1 O VAL E 512 N ASP E 398 SHEET 4 AA1 5 GLY E 431 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA1 5 THR E 376 TYR E 380 -1 N TYR E 380 O GLY E 431 SHEET 1 AA2 3 CYS E 361 VAL E 362 0 SHEET 2 AA2 3 VAL E 524 CYS E 525 1 O CYS E 525 N CYS E 361 SHEET 3 AA2 3 CYS E 391 PHE E 392 -1 N PHE E 392 O VAL E 524 SHEET 1 AA3 2 LEU E 452 ARG E 454 0 SHEET 2 AA3 2 LEU E 492 SER E 494 -1 O GLN E 493 N TYR E 453 SHEET 1 AA4 2 TYR E 473 GLN E 474 0 SHEET 2 AA4 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 SHEET 1 AA5 4 VAL B 2 SER B 7 0 SHEET 2 AA5 4 LEU B 18 GLY B 26 -1 O ALA B 23 N GLN B 5 SHEET 3 AA5 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA5 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA6 6 GLY B 10 LEU B 11 0 SHEET 2 AA6 6 THR B 120 THR B 123 1 O THR B 123 N GLY B 10 SHEET 3 AA6 6 ALA B 92 SER B 99 -1 N TYR B 94 O THR B 120 SHEET 4 AA6 6 ALA B 33 GLN B 39 -1 N PHE B 37 O PHE B 95 SHEET 5 AA6 6 GLU B 46 ILE B 51 -1 O SER B 49 N TRP B 36 SHEET 6 AA6 6 THR B 58 TYR B 60 -1 O ASN B 59 N CYS B 50 SHEET 1 AA7 4 GLY B 10 LEU B 11 0 SHEET 2 AA7 4 THR B 120 THR B 123 1 O THR B 123 N GLY B 10 SHEET 3 AA7 4 ALA B 92 SER B 99 -1 N TYR B 94 O THR B 120 SHEET 4 AA7 4 ASP B 115 TRP B 116 -1 O ASP B 115 N GLY B 98 SSBOND 1 CYS E 336 CYS E 361 1555 1555 2.04 SSBOND 2 CYS E 379 CYS E 432 1555 1555 2.07 SSBOND 3 CYS E 391 CYS E 525 1555 1555 2.05 SSBOND 4 CYS E 480 CYS E 488 1555 1555 2.04 SSBOND 5 CYS B 22 CYS B 96 1555 1555 2.04 SSBOND 6 CYS B 50 CYS B 106 1555 1555 2.07 LINK ND2 ASN E 343 C1 NAG A 1 1555 1555 1.43 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.44 LINK O6 NAG A 1 C1 MAN A 3 1555 1555 1.44 CRYST1 143.619 143.619 143.619 90.00 90.00 90.00 I 2 3 24 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006963 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006963 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006963 0.00000