HEADER PROTEIN BINDING 17-SEP-20 7D30 TITLE STRUCTURE OF SYBODY MR17-SR31 FUSION IN COMPLEX WITH THE SARS-COV-2 S TITLE 2 RECEPTOR BINDING DOMAIN (RBD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYBODY FUSION OF MR17-SR31 WITH A GS LINKER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE PROTEIN S1; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: RECEPTOR BINDING DOMAIN (RBD); COMPND 9 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 8 2; SOURCE 9 ORGANISM_COMMON: 2019-NCOV; SOURCE 10 ORGANISM_TAXID: 2697049; SOURCE 11 GENE: S, 2; SOURCE 12 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 14 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE KEYWDS CORONAVIRUS, COVID-19, NANOBODY, NEUTRALIZING ANTIBODY, RECEPTOR KEYWDS 2 BINDING PROTEIN, SARS-COV-2, S PROTEIN, SYNTHETIC ANTIBODY, VHH., KEYWDS 3 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.LI,H.YAO,H.CAI,W.QIN,D.LI REVDAT 3 29-NOV-23 7D30 1 REMARK REVDAT 2 01-SEP-21 7D30 1 JRNL REVDAT 1 17-FEB-21 7D30 0 JRNL AUTH H.YAO,H.CAI,T.LI,B.ZHOU,W.QIN,D.LAVILLETTE,D.LI JRNL TITL A HIGH-AFFINITY RBD-TARGETING NANOBODY IMPROVES FUSION JRNL TITL 2 PARTNER'S POTENCY AGAINST SARS-COV-2. JRNL REF PLOS PATHOG. V. 17 09328 2021 JRNL REFN ESSN 1553-7374 JRNL PMID 33657135 JRNL DOI 10.1371/JOURNAL.PPAT.1009328 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 46077 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4611 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 49.7000 - 6.5200 1.00 1637 186 0.2287 0.2494 REMARK 3 2 6.5200 - 5.1800 1.00 1494 169 0.2026 0.2213 REMARK 3 3 5.1800 - 4.5200 1.00 1431 184 0.1554 0.1847 REMARK 3 4 4.5200 - 4.1100 1.00 1440 152 0.1502 0.1782 REMARK 3 5 4.1100 - 3.8200 1.00 1437 150 0.1638 0.1957 REMARK 3 6 3.8200 - 3.5900 1.00 1437 144 0.1774 0.2282 REMARK 3 7 3.5900 - 3.4100 1.00 1421 139 0.1859 0.2163 REMARK 3 8 3.4100 - 3.2600 1.00 1393 165 0.1893 0.2587 REMARK 3 9 3.2600 - 3.1400 1.00 1372 178 0.2017 0.2435 REMARK 3 10 3.1400 - 3.0300 1.00 1374 140 0.2082 0.2782 REMARK 3 11 3.0300 - 2.9300 1.00 1393 143 0.2056 0.2539 REMARK 3 12 2.9300 - 2.8500 1.00 1397 157 0.2144 0.2678 REMARK 3 13 2.8500 - 2.7800 1.00 1379 147 0.2140 0.2700 REMARK 3 14 2.7800 - 2.7100 1.00 1367 144 0.2055 0.2506 REMARK 3 15 2.7100 - 2.6500 1.00 1373 146 0.1980 0.2316 REMARK 3 16 2.6500 - 2.5900 1.00 1379 153 0.2063 0.2743 REMARK 3 17 2.5900 - 2.5400 1.00 1366 151 0.2039 0.2660 REMARK 3 18 2.5400 - 2.4900 1.00 1369 145 0.1986 0.3168 REMARK 3 19 2.4900 - 2.4500 1.00 1344 139 0.2071 0.2543 REMARK 3 20 2.4500 - 2.4000 1.00 1405 156 0.2205 0.2518 REMARK 3 21 2.4000 - 2.3700 1.00 1313 157 0.2012 0.2632 REMARK 3 22 2.3700 - 2.3300 1.00 1388 161 0.2182 0.2887 REMARK 3 23 2.3300 - 2.2900 1.00 1318 142 0.2179 0.2995 REMARK 3 24 2.2900 - 2.2600 1.00 1390 154 0.2296 0.2764 REMARK 3 25 2.2600 - 2.2300 1.00 1297 154 0.2261 0.2719 REMARK 3 26 2.2300 - 2.2000 0.99 1346 173 0.2340 0.3155 REMARK 3 27 2.2000 - 2.1800 0.98 1335 146 0.2475 0.2954 REMARK 3 28 2.1800 - 2.1500 0.98 1327 142 0.2622 0.3384 REMARK 3 29 2.1500 - 2.1200 0.97 1302 162 0.2927 0.3675 REMARK 3 30 2.1200 - 2.1000 0.93 1242 132 0.2961 0.3256 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) : 0.242 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.464 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.52 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 : 0.008 3723 REMARK 3 ANGLE : 0.824 5025 REMARK 3 CHIRALITY : 0.050 545 REMARK 3 PLANARITY : 0.005 643 REMARK 3 DIHEDRAL : 22.292 604 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 7D30 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300017460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97854 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46317 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 49.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 18.60 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 14.50 REMARK 200 R MERGE FOR SHELL (I) : 1.40900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 6M0J, 5M13 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CADMIUM CHLORIDE, 30% (V/V) PEG REMARK 280 400, 4%(V/V) 1,3-BUTANEDIOL, 0.1M SODIUM ACETATE PH 4.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 318.90867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 159.45433 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 239.18150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.72717 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 398.63583 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 318.90867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 159.45433 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 79.72717 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 239.18150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 398.63583 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 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 SER A 0 REMARK 465 TYR A 110 REMARK 465 TRP A 111 REMARK 465 GLY A 112 REMARK 465 GLY A 967 REMARK 465 GLY A 968 REMARK 465 GLY A 969 REMARK 465 GLY A 970 REMARK 465 SER A 971 REMARK 465 GLY A 972 REMARK 465 GLY A 973 REMARK 465 GLY A 974 REMARK 465 GLY A 975 REMARK 465 SER A 976 REMARK 465 GLY A 977 REMARK 465 GLY A 978 REMARK 465 GLY A 979 REMARK 465 GLY A 980 REMARK 465 SER A 981 REMARK 465 GLY A 982 REMARK 465 GLY A 983 REMARK 465 GLY A 984 REMARK 465 GLY A 985 REMARK 465 SER A 986 REMARK 465 GLY A 987 REMARK 465 GLY A 988 REMARK 465 GLY A 989 REMARK 465 GLY A 990 REMARK 465 SER A 991 REMARK 465 GLY A 992 REMARK 465 GLY A 993 REMARK 465 GLY A 994 REMARK 465 GLY A 995 REMARK 465 SER A 996 REMARK 465 GLY A 997 REMARK 465 SER A 998 REMARK 465 GLY A 1116 REMARK 465 ARG A 1117 REMARK 465 ALA A 1118 REMARK 465 GLY A 1119 REMARK 465 GLU A 1120 REMARK 465 GLN A 1121 REMARK 465 LYS A 1122 REMARK 465 LEU A 1123 REMARK 465 ILE A 1124 REMARK 465 SER A 1125 REMARK 465 GLU A 1126 REMARK 465 GLU A 1127 REMARK 465 ASP A 1128 REMARK 465 LEU A 1129 REMARK 465 ASN A 1130 REMARK 465 SER A 1131 REMARK 465 ALA A 1132 REMARK 465 VAL A 1133 REMARK 465 ASP A 1134 REMARK 465 HIS A 1135 REMARK 465 HIS A 1136 REMARK 465 HIS A 1137 REMARK 465 HIS A 1138 REMARK 465 HIS A 1139 REMARK 465 HIS A 1140 REMARK 465 ALA B 327 REMARK 465 GLY B 328 REMARK 465 SER B 329 REMARK 465 PRO B 330 REMARK 465 ASN B 331 REMARK 465 ILE B 332 REMARK 465 THR B 333 REMARK 465 PRO B 527 REMARK 465 LYS B 528 REMARK 465 LYS B 529 REMARK 465 SER B 530 REMARK 465 THR B 531 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 GLN A 13 CG CD OE1 NE2 REMARK 470 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 113 CG CD OE1 NE2 REMARK 470 LYS A1057 CG CD CE NZ REMARK 470 ALA A1115 CB REMARK 470 GLU B 484 CG CD OE1 OE2 REMARK 470 GLU B 535 CG CD OE1 OE2 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 TYR A 54 -129.63 52.64 REMARK 500 ALA A1092 168.60 175.81 REMARK 500 PRO B 337 46.01 -82.22 REMARK 500 ALA B 352 48.77 -108.29 REMARK 500 ASN B 422 -54.10 -129.85 REMARK 500 ASN B 487 32.64 -86.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1324 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 44 OE1 REMARK 620 2 ASP A 100 OD1 91.7 REMARK 620 3 ASP A 109 OD1 97.8 6.1 REMARK 620 4 ASP A 109 OD2 97.5 8.1 6.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1315 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 89 OE2 REMARK 620 2 HOH A1487 O 95.3 REMARK 620 3 HOH A1505 O 122.2 134.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1323 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 98 O REMARK 620 2 ASP A 100 OD1 95.1 REMARK 620 3 ASP A 109 OD1 150.1 100.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1325 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 100 OD2 REMARK 620 2 HIS A 107 O 141.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1314 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1062 OD1 REMARK 620 2 ASP A1062 OD2 57.0 REMARK 620 3 ACT A1302 O 95.2 101.6 REMARK 620 4 ACT A1302 OXT 76.8 130.6 63.4 REMARK 620 5 GLN B 539 O 88.1 114.6 138.3 77.1 REMARK 620 6 GLN B 539 OXT 143.6 129.0 115.0 98.1 56.0 REMARK 620 7 ACT B2104 OXT 120.9 70.6 122.0 158.4 90.3 60.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1318 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A1089 OE1 REMARK 620 2 GLU A1089 OE2 59.2 REMARK 620 3 ACT A1303 O 110.2 123.7 REMARK 620 4 ACT A1303 OXT 113.2 72.7 61.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1319 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ACT A1306 O REMARK 620 2 ACT A1306 OXT 61.7 REMARK 620 3 ACT A1307 O 75.9 119.0 REMARK 620 4 ACT A1307 OXT 122.7 174.6 61.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1317 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1468 O REMARK 620 2 HOH A1471 O 122.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B2116 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 340 OE1 REMARK 620 2 GLU B 340 OE2 59.0 REMARK 620 3 HOH B2221 O 73.3 127.3 REMARK 620 4 HOH B2292 O 137.7 118.1 82.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B2115 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 427 OD1 REMARK 620 2 ASP B 427 OD2 56.6 REMARK 620 3 HOH B2270 O 139.4 82.8 REMARK 620 4 HOH B2276 O 90.0 85.6 88.5 REMARK 620 5 HOH B2287 O 89.5 100.3 96.9 172.5 REMARK 620 6 HOH B2296 O 98.3 154.1 121.7 101.9 70.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B2114 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 428 OD1 REMARK 620 2 ASP B 428 OD2 57.4 REMARK 620 3 ACT B2108 O 100.2 108.6 REMARK 620 4 HOH B2218 O 107.6 165.1 71.8 REMARK 620 5 HOH B2293 O 162.7 111.4 96.0 83.2 REMARK 620 N 1 2 3 4 DBREF 7D30 A -3 1140 PDB 7D30 7D30 -3 1140 DBREF 7D30 B 330 531 UNP P0DTC2 SPIKE_SARS2 330 531 SEQADV 7D30 ALA B 327 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 GLY B 328 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 SER B 329 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 GLY B 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 THR B 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 LEU B 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 GLU B 535 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 VAL B 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 LEU B 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 PHE B 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7D30 GLN B 539 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 298 GLY SER SER SER GLN VAL GLN LEU VAL GLU SER GLY GLY SEQRES 2 A 298 GLY LEU VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS SEQRES 3 A 298 ALA ALA SER GLY PHE PRO VAL GLU VAL TRP ARG MET GLU SEQRES 4 A 298 TRP TYR ARG GLN ALA PRO GLY LYS GLU ARG GLU GLY VAL SEQRES 5 A 298 ALA ALA ILE GLU SER TYR GLY HIS GLY THR ARG TYR ALA SEQRES 6 A 298 ASP SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN SEQRES 7 A 298 ALA LYS ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS SEQRES 8 A 298 PRO GLU ASP THR ALA VAL TYR TYR CYS ASN VAL LYS ASP SEQRES 9 A 298 ASP GLY GLN LEU ALA TYR HIS TYR ASP TYR TRP GLY GLN SEQRES 10 A 298 GLY THR GLN VAL THR VAL SER GLY GLY GLY GLY SER GLY SEQRES 11 A 298 GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY GLY GLY SEQRES 12 A 298 SER GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY SER SEQRES 13 A 298 SER SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 14 A 298 VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 15 A 298 SER GLY PHE PRO VAL TRP GLN GLY GLU MET ALA TRP TYR SEQRES 16 A 298 ARG GLN ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA ALA SEQRES 17 A 298 ILE SER SER MET GLY TYR LYS THR TYR TYR ALA ASP SER SEQRES 18 A 298 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS SEQRES 19 A 298 ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU SEQRES 20 A 298 ASP THR ALA VAL TYR TYR CYS ALA VAL MET VAL GLY PHE SEQRES 21 A 298 TRP TYR ALA GLY GLN GLY THR GLN VAL THR VAL SER ALA SEQRES 22 A 298 GLY ARG ALA GLY GLU GLN LYS LEU ILE SER GLU GLU ASP SEQRES 23 A 298 LEU ASN SER ALA VAL ASP HIS HIS HIS HIS HIS HIS SEQRES 1 B 213 ALA GLY SER PRO ASN ILE THR ASN LEU CYS PRO PHE GLY SEQRES 2 B 213 GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA SEQRES 3 B 213 TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SEQRES 4 B 213 SER VAL LEU TYR ASN SER ALA SER PHE SER THR PHE LYS SEQRES 5 B 213 CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS SEQRES 6 B 213 PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY SEQRES 7 B 213 ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS SEQRES 8 B 213 ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR SEQRES 9 B 213 GLY CYS VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER SEQRES 10 B 213 LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE SEQRES 11 B 213 ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER SEQRES 12 B 213 THR GLU ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY SEQRES 13 B 213 VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR SEQRES 14 B 213 GLY PHE GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR SEQRES 15 B 213 ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO SEQRES 16 B 213 ALA THR VAL CYS GLY PRO LYS LYS SER THR GLY THR LEU SEQRES 17 B 213 GLU VAL LEU PHE GLN HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET FUC C 5 10 HET FUC C 6 10 HET GOL A1301 6 HET ACT A1302 4 HET ACT A1303 4 HET ACT A1304 4 HET 1PE A1305 16 HET ACT A1306 4 HET ACT A1307 4 HET GOL A1308 6 HET BU2 A1309 6 HET BU2 A1310 6 HET BU2 A1311 6 HET ACT A1312 4 HET ACT A1313 4 HET CD A1314 1 HET CD A1315 1 HET CD A1316 1 HET CD A1317 1 HET CD A1318 1 HET CD A1319 1 HET CD A1320 1 HET CD A1321 1 HET CD A1322 1 HET CD A1323 1 HET CD A1324 1 HET CD A1325 1 HET ACT B2101 4 HET 1PE B2102 16 HET ACT B2103 4 HET ACT B2104 4 HET ACT B2105 4 HET GOL B2106 6 HET GOL B2107 6 HET ACT B2108 4 HET ACT B2109 4 HET BU2 B2110 6 HET BU2 B2111 6 HET GOL B2112 6 HET ACT B2113 4 HET CD B2114 1 HET CD B2115 1 HET CD B2116 1 HET CD B2117 1 HET CD B2118 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM BU2 1,3-BUTANEDIOL HETNAM CD CADMIUM ION 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 BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 1PE PEG400 FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 3 BMA C6 H12 O6 FORMUL 3 MAN C6 H12 O6 FORMUL 3 FUC 2(C6 H12 O5) FORMUL 4 GOL 5(C3 H8 O3) FORMUL 5 ACT 14(C2 H3 O2 1-) FORMUL 8 1PE 2(C10 H22 O6) FORMUL 12 BU2 5(C4 H10 O2) FORMUL 17 CD 17(CD 2+) FORMUL 47 HOH *219(H2 O) HELIX 1 AA1 ASP A 62 LYS A 65 5 4 HELIX 2 AA2 LYS A 87 THR A 91 5 5 HELIX 3 AA3 PRO A 1028 GLY A 1032 5 5 HELIX 4 AA4 ASP A 1062 LYS A 1065 5 4 HELIX 5 AA5 LYS A 1087 THR A 1091 5 5 HELIX 6 AA6 PRO B 337 ALA B 344 1 8 HELIX 7 AA7 SER B 383 ASP B 389 5 7 HELIX 8 AA8 ASP B 405 ILE B 410 5 6 HELIX 9 AA9 GLY B 416 ASN B 422 1 7 HELIX 10 AB1 SER B 438 SER B 443 1 6 HELIX 11 AB2 GLY B 502 TYR B 505 5 4 HELIX 12 AB3 THR B 533 PHE B 538 5 6 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 21 N SER A 7 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N SER A 71 O TYR A 80 SHEET 1 AA2 6 GLY A 10 GLN A 13 0 SHEET 2 AA2 6 THR A 115 SER A 120 1 O SER A 120 N VAL A 12 SHEET 3 AA2 6 ALA A 92 VAL A 98 -1 N ALA A 92 O VAL A 117 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N TYR A 37 O TYR A 95 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O ALA A 49 N TRP A 36 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O ARG A 59 N ALA A 50 SHEET 1 AA3 6 SER A1000 GLN A1001 0 SHEET 2 AA3 6 THR B 376 TYR B 380 -1 O CYS B 379 N SER A1000 SHEET 3 AA3 6 GLY B 431 ASN B 437 -1 O VAL B 433 N LYS B 378 SHEET 4 AA3 6 PRO B 507 LEU B 517 -1 O VAL B 511 N ILE B 434 SHEET 5 AA3 6 THR B 393 ARG B 403 -1 N ILE B 402 O TYR B 508 SHEET 6 AA3 6 ASN B 354 ILE B 358 -1 N ILE B 358 O VAL B 395 SHEET 1 AA4 4 GLN A1003 SER A1007 0 SHEET 2 AA4 4 LEU A1018 SER A1025 -1 O SER A1025 N GLN A1003 SHEET 3 AA4 4 THR A1078 MET A1083 -1 O MET A1083 N LEU A1018 SHEET 4 AA4 4 PHE A1068 ASP A1073 -1 N ASP A1073 O THR A1078 SHEET 1 AA5 6 GLY A1010 GLN A1013 0 SHEET 2 AA5 6 THR A1109 SER A1114 1 O THR A1112 N GLY A1010 SHEET 3 AA5 6 ALA A1092 MET A1099 -1 N TYR A1094 O THR A1109 SHEET 4 AA5 6 MET A1034 GLN A1039 -1 N TYR A1037 O TYR A1095 SHEET 5 AA5 6 GLU A1046 ILE A1051 -1 O VAL A1048 N TRP A1036 SHEET 6 AA5 6 THR A1058 TYR A1060 -1 O TYR A1059 N ALA A1050 SHEET 1 AA6 5 GLY A1010 GLN A1013 0 SHEET 2 AA6 5 THR A1109 SER A1114 1 O THR A1112 N GLY A1010 SHEET 3 AA6 5 ALA A1092 MET A1099 -1 N TYR A1094 O THR A1109 SHEET 4 AA6 5 TRP A1103 ALA A1105 -1 O TYR A1104 N VAL A1098 SHEET 5 AA6 5 LEU B 368 ASN B 370 1 O TYR B 369 N TRP A1103 SHEET 1 AA7 2 LEU B 452 ARG B 454 0 SHEET 2 AA7 2 LEU B 492 SER B 494 -1 O GLN B 493 N TYR B 453 SHEET 1 AA8 2 TYR B 473 GLN B 474 0 SHEET 2 AA8 2 CYS B 488 TYR B 489 -1 O TYR B 489 N TYR B 473 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.01 SSBOND 2 CYS A 1022 CYS A 1096 1555 1555 2.05 SSBOND 3 CYS B 336 CYS B 361 1555 1555 2.05 SSBOND 4 CYS B 379 CYS B 432 1555 1555 2.06 SSBOND 5 CYS B 391 CYS B 525 1555 1555 2.04 SSBOND 6 CYS B 480 CYS B 488 1555 1555 2.04 LINK ND2 ASN B 343 C1 NAG C 1 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46 LINK O3 NAG C 1 C1 FUC C 5 1555 1555 1.45 LINK O6 NAG C 1 C1 FUC C 6 1555 1555 1.45 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.45 LINK OE1 GLU A 44 CD CD A1324 1555 10555 2.42 LINK OD2 ASP A 62 CD CD A1320 1555 1555 2.19 LINK OE2 GLU A 89 CD CD A1315 1555 1555 2.27 LINK O VAL A 98 CD CD A1323 1555 1555 2.25 LINK OD1 ASP A 100 CD CD A1323 1555 1555 2.25 LINK OD1 ASP A 100 CD CD A1324 1555 1555 2.19 LINK OD2 ASP A 100 CD CD A1325 1555 1555 2.49 LINK O HIS A 107 CD CD A1325 1555 1555 2.50 LINK OD1 ASP A 109 CD CD A1323 1555 1555 2.26 LINK OD1 ASP A 109 CD CD A1324 1555 1555 2.21 LINK OD2 ASP A 109 CD CD A1324 1555 1555 2.22 LINK OD1 ASP A1062 CD CD A1314 1555 1555 2.34 LINK OD2 ASP A1062 CD CD A1314 1555 1555 2.23 LINK OE1 GLU A1089 CD CD A1318 1555 1555 2.22 LINK OE2 GLU A1089 CD CD A1318 1555 1555 2.23 LINK O ACT A1302 CD CD A1314 1555 1555 2.19 LINK OXT ACT A1302 CD CD A1314 1555 1555 2.18 LINK O ACT A1303 CD CD A1318 1555 1555 2.22 LINK OXT ACT A1303 CD CD A1318 1555 1555 2.19 LINK O ACT A1306 CD CD A1319 1555 1555 2.21 LINK OXT ACT A1306 CD CD A1319 1555 1555 2.21 LINK O ACT A1307 CD CD A1319 1555 1555 2.22 LINK OXT ACT A1307 CD CD A1319 1555 1555 2.23 LINK CD CD A1314 O GLN B 539 1555 1555 2.24 LINK CD CD A1314 OXT GLN B 539 1555 1555 2.23 LINK CD CD A1314 OXT ACT B2104 1555 1555 2.18 LINK CD CD A1315 O HOH A1487 1555 1555 2.21 LINK CD CD A1315 O HOH A1505 1555 1555 2.22 LINK CD CD A1317 O HOH A1468 1555 1555 2.24 LINK CD CD A1317 O HOH A1471 1555 1555 2.26 LINK CD CD A1322 O HOH A1443 1555 1555 2.28 LINK OE1 GLU B 340 CD CD B2116 1555 1555 2.23 LINK OE2 GLU B 340 CD CD B2116 1555 1555 2.22 LINK OD1 ASP B 427 CD CD B2115 1555 1555 2.31 LINK OD2 ASP B 427 CD CD B2115 1555 1555 2.28 LINK OD1 ASP B 428 CD CD B2114 1555 1555 2.28 LINK OD2 ASP B 428 CD CD B2114 1555 1555 2.24 LINK OG SER B 469 CD CD B2117 1555 1555 2.25 LINK O GLY B 482 CD CD B2118 1555 1555 2.22 LINK O ACT B2108 CD CD B2114 1555 1555 2.27 LINK CD CD B2114 O HOH B2218 1555 1555 2.22 LINK CD CD B2114 O HOH B2293 1555 1555 2.21 LINK CD CD B2115 O HOH B2270 1555 1555 2.22 LINK CD CD B2115 O HOH B2276 1555 1555 2.17 LINK CD CD B2115 O HOH B2287 1555 1555 2.19 LINK CD CD B2115 O HOH B2296 1555 1555 2.23 LINK CD CD B2116 O HOH B2221 1555 1555 2.22 LINK CD CD B2116 O HOH B2292 1555 1555 2.22 CRYST1 73.384 73.384 478.363 90.00 90.00 120.00 P 65 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013627 0.007868 0.000000 0.00000 SCALE2 0.000000 0.015735 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002090 0.00000