HEADER VIRAL PROTEIN/IMMUNE SYSTEM 24-JAN-22 7TP4 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX TITLE 2 WITH NEUTRALIZING ANTIBODY K398.22 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: Z; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN, UNP RESIDUES 333-530; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: K398.22 HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: K398.22 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_TAXID: 2697049; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 10 ORGANISM_COMMON: RHESUS MONKEY; SOURCE 11 ORGANISM_TAXID: 9544; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 17 ORGANISM_COMMON: RHESUS MONKEY; SOURCE 18 ORGANISM_TAXID: 9544; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, ANTIBODY, NEUTRALIZING ANTIBODY, FAB, COVID-19, KEYWDS 2 CORONAVIRUS, RECEPTOR-BINDING DOMAIN, RBD, IMMUNE SYSTEM, VIRAL KEYWDS 3 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.YUAN,X.ZHU,I.A.WILSON REVDAT 4 13-NOV-24 7TP4 1 REMARK REVDAT 3 18-OCT-23 7TP4 1 REMARK REVDAT 2 24-AUG-22 7TP4 1 JRNL REVDAT 1 23-FEB-22 7TP4 0 JRNL AUTH W.T.HE,M.YUAN,S.CALLAGHAN,R.MUSHARRAFIEH,G.SONG,M.SILVA, JRNL AUTH 2 N.BEUTLER,W.H.LEE,P.YONG,J.L.TORRES,M.MELO,P.ZHOU,F.ZHAO, JRNL AUTH 3 X.ZHU,L.PENG,D.HUANG,F.ANZANELLO,J.RICKETTS,M.PARREN, JRNL AUTH 4 E.GARCIA,M.FERGUSON,W.RINALDI,S.A.RAWLINGS,D.NEMAZEE, JRNL AUTH 5 D.M.SMITH,B.BRINEY,Y.SAFONOVA,T.F.ROGERS,J.M.DAN,Z.ZHANG, JRNL AUTH 6 D.WEISKOPF,A.SETTE,S.CROTTY,D.J.IRVINE,A.B.WARD,I.A.WILSON, JRNL AUTH 7 D.R.BURTON,R.ANDRABI JRNL TITL BROADLY NEUTRALIZING ANTIBODIES TO SARS-RELATED VIRUSES CAN JRNL TITL 2 BE READILY INDUCED IN RHESUS MACAQUES. JRNL REF SCI TRANSL MED V. 14 L9605 2022 JRNL REFN ESSN 1946-6242 JRNL PMID 35947674 JRNL DOI 10.1126/SCITRANSLMED.ABL9605 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 63808 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 3294 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 46.2120 - 5.6216 1.00 2711 164 0.1704 0.1815 REMARK 3 2 5.6216 - 4.4632 1.00 2598 144 0.1514 0.1493 REMARK 3 3 4.4632 - 3.8993 1.00 2580 147 0.1573 0.1727 REMARK 3 4 3.8993 - 3.5430 1.00 2559 131 0.1990 0.2434 REMARK 3 5 3.5430 - 3.2891 1.00 2529 144 0.2235 0.2627 REMARK 3 6 3.2891 - 3.0952 1.00 2550 123 0.2333 0.2373 REMARK 3 7 3.0952 - 2.9402 1.00 2567 117 0.2342 0.2432 REMARK 3 8 2.9402 - 2.8123 1.00 2518 153 0.2327 0.2778 REMARK 3 9 2.8123 - 2.7040 1.00 2509 129 0.2479 0.2838 REMARK 3 10 2.7040 - 2.6107 1.00 2510 142 0.2362 0.2991 REMARK 3 11 2.6107 - 2.5291 1.00 2514 125 0.2419 0.3330 REMARK 3 12 2.5291 - 2.4568 1.00 2494 142 0.2382 0.2899 REMARK 3 13 2.4568 - 2.3921 1.00 2494 146 0.2436 0.2556 REMARK 3 14 2.3921 - 2.3338 1.00 2528 122 0.2448 0.3359 REMARK 3 15 2.3338 - 2.2807 0.99 2501 131 0.2456 0.3112 REMARK 3 16 2.2807 - 2.2322 0.99 2481 138 0.2564 0.3077 REMARK 3 17 2.2322 - 2.1875 0.99 2496 134 0.2593 0.3196 REMARK 3 18 2.1875 - 2.1462 0.99 2463 134 0.2591 0.3250 REMARK 3 19 2.1462 - 2.1079 1.00 2514 149 0.2620 0.3049 REMARK 3 20 2.1079 - 2.0722 0.99 2476 125 0.2678 0.3211 REMARK 3 21 2.0722 - 2.0388 0.99 2459 149 0.2748 0.3171 REMARK 3 22 2.0388 - 2.0074 1.00 2515 130 0.2918 0.3465 REMARK 3 23 2.0074 - 1.9779 0.99 2481 138 0.3114 0.3914 REMARK 3 24 1.9779 - 1.9500 0.99 2467 137 0.3249 0.3754 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.28 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 7TP4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000258373. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-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 : 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) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 47.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 5.24000 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: 6W41 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM FORMATE AND 20% (W/V) REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.69300 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 45.69300 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 1.000000 0.000000 0.000000 34.31900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 138.63650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.31900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 138.63650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.69300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.31900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 138.63650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.69300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.31900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 138.63650 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: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z, H, L, 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 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 L 532 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 THR Z 333 REMARK 465 LYS Z 528 REMARK 465 LYS Z 529 REMARK 465 SER Z 530 REMARK 465 GLY Z 531 REMARK 465 HIS Z 532 REMARK 465 HIS Z 533 REMARK 465 HIS Z 534 REMARK 465 HIS Z 535 REMARK 465 HIS Z 536 REMARK 465 HIS Z 537 REMARK 465 SER H 139 REMARK 465 LYS H 140 REMARK 465 SER H 141 REMARK 465 THR H 142 REMARK 465 SER H 143 REMARK 465 GLY H 144 REMARK 465 SER H 226 REMARK 465 CYS H 227 REMARK 465 GLU L 212 REMARK 465 CYS L 213 REMARK 465 SER L 214 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 ALA L 113 CB 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 L 480 O HOH L 511 1.93 REMARK 500 O HOH L 417 O HOH L 512 1.94 REMARK 500 O SER H 214 N THR H 216 2.00 REMARK 500 O GLY H 168 O HOH H 301 2.06 REMARK 500 O HOH L 484 O HOH L 524 2.06 REMARK 500 OG SER Z 375 O HOH Z 601 2.10 REMARK 500 OG SER Z 514 O HOH Z 602 2.11 REMARK 500 O HOH L 485 O HOH L 502 2.14 REMARK 500 NZ LYS L 168 O HOH L 401 2.16 REMARK 500 O GLU L 200 O HOH L 402 2.18 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 405 O HOH H 405 3555 1.82 REMARK 500 O HOH L 527 O HOH L 527 3455 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS H 151 CA - CB - SG ANGL. DEV. = 10.5 DEGREES REMARK 500 CYS H 207 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG H 221 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE Z 377 89.21 -150.46 REMARK 500 PHE Z 400 179.53 176.34 REMARK 500 ASN Z 422 -51.40 -125.50 REMARK 500 SER H 30 0.86 -68.57 REMARK 500 GLN H 104 -0.93 77.07 REMARK 500 THR H 109 38.36 -88.87 REMARK 500 THR H 127 122.22 -39.61 REMARK 500 ASN H 215 40.98 2.71 REMARK 500 ASP L 28 -89.09 -130.10 REMARK 500 TYR L 34 48.07 -85.21 REMARK 500 VAL L 53 -43.88 73.47 REMARK 500 SER L 54 -2.51 -140.26 REMARK 500 ALA L 86 173.86 178.90 REMARK 500 ALA L 94 58.07 -90.62 REMARK 500 ALA L 132 109.75 -162.10 REMARK 500 ASP L 153 -112.44 61.77 REMARK 500 LYS L 158 -74.36 -79.24 REMARK 500 ASN L 172 -3.87 76.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 7TP4 Z 333 530 UNP P0DTC2 SPIKE_SARS2 333 530 DBREF 7TP4 H 1 227 PDB 7TP4 7TP4 1 227 DBREF 7TP4 L 1 214 PDB 7TP4 7TP4 1 214 SEQADV 7TP4 GLY Z 531 UNP P0DTC2 EXPRESSION TAG SEQADV 7TP4 HIS Z 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7TP4 HIS Z 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7TP4 HIS Z 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7TP4 HIS Z 535 UNP P0DTC2 EXPRESSION TAG SEQADV 7TP4 HIS Z 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7TP4 HIS Z 537 UNP P0DTC2 EXPRESSION TAG SEQRES 1 Z 205 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 Z 205 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 Z 205 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 Z 205 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 Z 205 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 Z 205 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 Z 205 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 Z 205 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 Z 205 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 Z 205 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 Z 205 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 Z 205 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 Z 205 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 Z 205 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 Z 205 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 16 Z 205 LYS LYS SER GLY HIS HIS HIS HIS HIS HIS SEQRES 1 H 227 GLU VAL GLN LEU ALA GLU SER GLY GLY GLY LEU VAL LYS SEQRES 2 H 227 PRO GLY GLY SER LEU ARG LEU SER CYS VAL ALA SER GLY SEQRES 3 H 227 PHE THR PHE SER SER ASN GLU MET HIS TRP VAL ARG GLN SEQRES 4 H 227 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE SER SEQRES 5 H 227 GLU SER GLY PHE THR THR GLU TYR ALA ASP SER VAL LYS SEQRES 6 H 227 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 227 LEU PHE LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 227 ALA VAL TYR TYR CYS THR ARG VAL SER ILE PHE GLY GLN SEQRES 9 H 227 PHE ILE VAL ALA THR TYR PHE ASP TYR TRP GLY GLN GLY SEQRES 10 H 227 VAL LEU VAL THR VAL SER SER ALA SER THR LYS GLY PRO SEQRES 11 H 227 SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER SEQRES 12 H 227 GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR SEQRES 13 H 227 PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA SEQRES 14 H 227 LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SEQRES 15 H 227 SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL SEQRES 16 H 227 PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN SEQRES 17 H 227 VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS ARG SEQRES 18 H 227 VAL GLU PRO LYS SER CYS SEQRES 1 L 214 GLN ALA ALA LEU THR GLN PRO ARG SER VAL SER GLY SER SEQRES 2 L 214 PRO GLY GLN SER VAL THR ILE SER CYS THR GLY THR SER SEQRES 3 L 214 SER ASP ILE GLY GLY TYR ASN TYR VAL SER TRP TYR GLN SEQRES 4 L 214 GLN HIS PRO GLY THR ALA PRO LYS LEU MET ILE TYR ALA SEQRES 5 L 214 VAL SER GLU ARG PRO SER GLY VAL SER ASP ARG PHE SER SEQRES 6 L 214 GLY SER LYS SER GLY ASN THR ALA SER LEU THR ILE SER SEQRES 7 L 214 GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS CYS SEQRES 8 L 214 SER TYR ALA GLY THR VAL LEU PHE GLY GLY GLY THR ARG SEQRES 9 L 214 LEU THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SER VAL SEQRES 10 L 214 THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN ALA ASN SEQRES 11 L 214 LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE TYR PRO SEQRES 12 L 214 GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SER PRO SEQRES 13 L 214 VAL LYS ALA GLY VAL GLU THR THR THR PRO SER LYS GLN SEQRES 14 L 214 SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SER LEU SEQRES 15 L 214 THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SER CYS SEQRES 16 L 214 GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS THR VAL SEQRES 17 L 214 ALA PRO THR GLU CYS SER HET NAG A 1 14 HET NAG A 2 14 HET FUC A 3 10 HET EDO L 301 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL 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 FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 FUC C6 H12 O5 FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *305(H2 O) HELIX 1 AA1 PHE Z 338 ASN Z 343 1 6 HELIX 2 AA2 SER Z 349 TRP Z 353 5 5 HELIX 3 AA3 ASP Z 364 ASN Z 370 1 7 HELIX 4 AA4 SER Z 383 ASN Z 388 1 6 HELIX 5 AA5 ASP Z 405 ILE Z 410 5 6 HELIX 6 AA6 GLY Z 416 ASN Z 422 1 7 HELIX 7 AA7 SER Z 438 SER Z 443 1 6 HELIX 8 AA8 GLY Z 502 TYR Z 505 5 4 HELIX 9 AA9 THR H 28 SER H 30 5 3 HELIX 10 AB1 ASN H 74 LYS H 76 5 3 HELIX 11 AB2 ARG H 87 THR H 91 5 5 HELIX 12 AB3 SER H 167 ALA H 169 5 3 HELIX 13 AB4 SER H 198 LEU H 200 5 3 HELIX 14 AB5 GLN L 81 GLU L 85 5 5 HELIX 15 AB6 SER L 123 ALA L 129 1 7 HELIX 16 AB7 THR L 183 HIS L 190 1 8 SHEET 1 AA1 5 ASN Z 354 ILE Z 358 0 SHEET 2 AA1 5 ASN Z 394 ARG Z 403 -1 O VAL Z 395 N ILE Z 358 SHEET 3 AA1 5 PRO Z 507 GLU Z 516 -1 O GLU Z 516 N ASN Z 394 SHEET 4 AA1 5 CYS Z 432 ASN Z 437 -1 N CYS Z 432 O LEU Z 513 SHEET 5 AA1 5 THR Z 376 CYS Z 379 -1 N LYS Z 378 O VAL Z 433 SHEET 1 AA2 3 CYS Z 361 VAL Z 362 0 SHEET 2 AA2 3 VAL Z 524 CYS Z 525 1 O CYS Z 525 N CYS Z 361 SHEET 3 AA2 3 CYS Z 391 PHE Z 392 -1 N PHE Z 392 O VAL Z 524 SHEET 1 AA3 2 LEU Z 452 ARG Z 454 0 SHEET 2 AA3 2 LEU Z 492 SER Z 494 -1 O GLN Z 493 N TYR Z 453 SHEET 1 AA4 2 TYR Z 473 GLN Z 474 0 SHEET 2 AA4 2 CYS Z 488 TYR Z 489 -1 O TYR Z 489 N TYR Z 473 SHEET 1 AA5 4 GLN H 3 SER H 7 0 SHEET 2 AA5 4 LEU H 18 SER H 25 -1 O VAL H 23 N ALA H 5 SHEET 3 AA5 4 SER H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 AA5 4 PHE H 68 ASP H 73 -1 N SER H 71 O PHE H 80 SHEET 1 AA6 6 GLY H 10 VAL H 12 0 SHEET 2 AA6 6 VAL H 118 VAL H 122 1 O THR H 121 N GLY H 10 SHEET 3 AA6 6 ALA H 92 PHE H 102 -1 N TYR H 94 O VAL H 118 SHEET 4 AA6 6 ASN H 32 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA6 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA6 6 THR H 58 TYR H 60 -1 O GLU H 59 N VAL H 50 SHEET 1 AA7 4 GLY H 10 VAL H 12 0 SHEET 2 AA7 4 VAL H 118 VAL H 122 1 O THR H 121 N GLY H 10 SHEET 3 AA7 4 ALA H 92 PHE H 102 -1 N TYR H 94 O VAL H 118 SHEET 4 AA7 4 PHE H 105 ILE H 106 -1 O PHE H 105 N PHE H 102 SHEET 1 AA8 4 SER H 131 LEU H 135 0 SHEET 2 AA8 4 THR H 146 TYR H 156 -1 O LEU H 152 N PHE H 133 SHEET 3 AA8 4 TYR H 187 PRO H 196 -1 O LEU H 189 N VAL H 153 SHEET 4 AA8 4 VAL H 174 THR H 176 -1 N HIS H 175 O VAL H 192 SHEET 1 AA9 4 SER H 131 LEU H 135 0 SHEET 2 AA9 4 THR H 146 TYR H 156 -1 O LEU H 152 N PHE H 133 SHEET 3 AA9 4 TYR H 187 PRO H 196 -1 O LEU H 189 N VAL H 153 SHEET 4 AA9 4 VAL H 180 LEU H 181 -1 N VAL H 180 O SER H 188 SHEET 1 AB1 3 THR H 162 TRP H 165 0 SHEET 2 AB1 3 TYR H 205 HIS H 211 -1 O ASN H 210 N THR H 162 SHEET 3 AB1 3 THR H 216 VAL H 222 -1 O VAL H 218 N VAL H 209 SHEET 1 AB2 5 SER L 9 GLY L 12 0 SHEET 2 AB2 5 THR L 103 VAL L 107 1 O THR L 106 N VAL L 10 SHEET 3 AB2 5 ALA L 86 TYR L 93 -1 N ALA L 86 O LEU L 105 SHEET 4 AB2 5 VAL L 35 GLN L 40 -1 N TYR L 38 O TYR L 89 SHEET 5 AB2 5 LYS L 47 ILE L 50 -1 O MET L 49 N TRP L 37 SHEET 1 AB3 4 SER L 9 GLY L 12 0 SHEET 2 AB3 4 THR L 103 VAL L 107 1 O THR L 106 N VAL L 10 SHEET 3 AB3 4 ALA L 86 TYR L 93 -1 N ALA L 86 O LEU L 105 SHEET 4 AB3 4 VAL L 97 PHE L 99 -1 O LEU L 98 N SER L 92 SHEET 1 AB4 3 VAL L 18 THR L 23 0 SHEET 2 AB4 3 THR L 72 ILE L 77 -1 O ILE L 77 N VAL L 18 SHEET 3 AB4 3 PHE L 64 SER L 69 -1 N SER L 65 O THR L 76 SHEET 1 AB5 4 SER L 116 PHE L 120 0 SHEET 2 AB5 4 ALA L 132 PHE L 141 -1 O LEU L 137 N THR L 118 SHEET 3 AB5 4 TYR L 174 LEU L 182 -1 O SER L 178 N CYS L 136 SHEET 4 AB5 4 VAL L 161 THR L 163 -1 N GLU L 162 O TYR L 179 SHEET 1 AB6 4 SER L 116 PHE L 120 0 SHEET 2 AB6 4 ALA L 132 PHE L 141 -1 O LEU L 137 N THR L 118 SHEET 3 AB6 4 TYR L 174 LEU L 182 -1 O SER L 178 N CYS L 136 SHEET 4 AB6 4 SER L 167 LYS L 168 -1 N SER L 167 O ALA L 175 SHEET 1 AB7 4 SER L 155 PRO L 156 0 SHEET 2 AB7 4 THR L 147 ALA L 152 -1 N ALA L 152 O SER L 155 SHEET 3 AB7 4 TYR L 193 HIS L 199 -1 O THR L 198 N THR L 147 SHEET 4 AB7 4 SER L 202 VAL L 208 -1 O VAL L 204 N VAL L 197 SSBOND 1 CYS Z 336 CYS Z 361 1555 1555 2.05 SSBOND 2 CYS Z 379 CYS Z 432 1555 1555 2.09 SSBOND 3 CYS Z 391 CYS Z 525 1555 1555 2.01 SSBOND 4 CYS Z 480 CYS Z 488 1555 1555 2.03 SSBOND 5 CYS H 22 CYS H 96 1555 1555 2.09 SSBOND 6 CYS H 151 CYS H 207 1555 1555 2.09 SSBOND 7 CYS L 22 CYS L 90 1555 1555 2.05 SSBOND 8 CYS L 136 CYS L 195 1555 1555 2.04 LINK ND2 ASN Z 343 C1 NAG A 1 1555 1555 1.43 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 LINK O6 NAG A 1 C1 FUC A 3 1555 1555 1.44 CISPEP 1 PHE H 157 PRO H 158 0 -8.26 CISPEP 2 GLU H 159 PRO H 160 0 -1.49 CISPEP 3 TYR L 142 PRO L 143 0 -1.38 CRYST1 68.638 277.273 91.386 90.00 90.00 90.00 C 2 2 21 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 0.014569 0.000000 0.000000 0.00000 SCALE2 0.000000 0.003607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010943 0.00000