HEADER ANTIVIRAL PROTEIN 14-JUL-21 7P5S TITLE NMR STRUCTURE OF A PEPTIDE DERIVING FROM SARS-COV-2 LINEAGES P.1 AND TITLE 2 B.1.351 S RBD 482-506 FRAGMENT IN HFIP/H2O COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 4 2; SOURCE 5 ORGANISM_TAXID: 2697049 KEYWDS SARS-COV-2, MIMICKING PEPTIDES, SPIKE, RECEPTOR BINDING DOMAIN, KEYWDS 2 COVID-19, LINEAGE P.1, LINEAGE B.1.351, E484K, N501Y, ANTIVIRAL KEYWDS 3 PROTEIN EXPDTA SOLUTION NMR NUMMDL 35 AUTHOR A.SANTORO,M.BUONOCORE,M.GRIMALDI,A.M.D'URSI REVDAT 5 14-JUN-23 7P5S 1 REMARK REVDAT 4 07-DEC-22 7P5S 1 JRNL REVDAT 3 30-NOV-22 7P5S 1 JRNL REVDAT 2 05-OCT-22 7P5S 1 SOURCE REMARK HELIX ATOM REVDAT 1 27-JUL-22 7P5S 0 JRNL AUTH M.BUONOCORE,A.SANTORO,M.GRIMALDI,V.COVELLI,M.FIROZNEZHAD, JRNL AUTH 2 M.RODRIQUEZ,M.SANTIN,A.M.D'URSI JRNL TITL STRUCTURAL ANALYSIS OF A SIMPLIFIED MODEL REPRODUCING JRNL TITL 2 SARS-COV-2 S RBD/ACE2 BINDING SITE. JRNL REF HELIYON V. 8 11568 2022 JRNL REFN ESSN 2405-8440 JRNL PMID 36406731 JRNL DOI 10.1016/J.HELIYON.2022.E11568 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TALOS-N REMARK 3 AUTHORS : BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7P5S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292117057. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 2.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.5 MM SMIMIC-BG, 50 % V/V REMARK 210 HEXAFLUOROISOPROPANOL, 40 % V/V REMARK 210 H2O, 10 % V/V [U-100% 2H] D2O, REMARK 210 50% HEXAFLUOROISOPROPANOL/40% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, CYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 35 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 1 ASN A 487 27.20 -163.65 REMARK 500 1 SER A 494 31.35 -141.57 REMARK 500 1 TYR A 495 22.57 -159.05 REMARK 500 1 PHE A 497 -45.19 -179.32 REMARK 500 2 SER A 494 31.29 -141.67 REMARK 500 2 TYR A 495 22.54 -159.00 REMARK 500 2 PHE A 497 -44.98 -179.25 REMARK 500 3 TYR A 489 -73.96 -96.88 REMARK 500 3 SER A 494 31.32 -141.65 REMARK 500 3 TYR A 495 22.58 -159.03 REMARK 500 3 PHE A 497 -45.10 -179.24 REMARK 500 4 SER A 494 31.15 -141.52 REMARK 500 4 TYR A 495 22.48 -158.95 REMARK 500 4 PHE A 497 -44.90 -179.27 REMARK 500 5 SER A 494 31.35 -141.55 REMARK 500 5 TYR A 495 22.62 -159.04 REMARK 500 5 PHE A 497 -45.68 -177.97 REMARK 500 5 THR A 500 39.62 -140.60 REMARK 500 5 TYR A 505 81.22 52.19 REMARK 500 6 PHE A 486 76.14 -117.97 REMARK 500 6 ASN A 487 33.17 -144.68 REMARK 500 6 SER A 494 31.26 -141.59 REMARK 500 6 TYR A 495 22.58 -159.02 REMARK 500 6 PHE A 497 -44.93 -179.25 REMARK 500 7 TYR A 489 -73.83 -96.45 REMARK 500 7 SER A 494 31.29 -141.59 REMARK 500 7 TYR A 495 22.55 -159.03 REMARK 500 7 PHE A 497 -43.71 -177.23 REMARK 500 7 THR A 500 43.93 -148.63 REMARK 500 7 TYR A 501 26.49 -156.47 REMARK 500 8 TYR A 489 93.95 -63.39 REMARK 500 8 SER A 494 31.23 -141.57 REMARK 500 8 TYR A 495 22.51 -158.92 REMARK 500 8 PHE A 497 -44.95 -179.20 REMARK 500 9 SER A 494 31.30 -141.52 REMARK 500 9 TYR A 495 22.63 -159.13 REMARK 500 9 PHE A 497 -45.12 -179.26 REMARK 500 10 SER A 494 31.29 -141.56 REMARK 500 10 TYR A 495 22.53 -158.98 REMARK 500 10 PHE A 497 -44.84 -179.34 REMARK 500 11 SER A 494 31.19 -141.52 REMARK 500 11 TYR A 495 22.57 -158.92 REMARK 500 11 PHE A 497 -43.69 -177.17 REMARK 500 12 PHE A 486 75.05 -116.05 REMARK 500 12 ASN A 487 27.18 -161.75 REMARK 500 12 SER A 494 31.22 -141.59 REMARK 500 12 TYR A 495 22.55 -158.91 REMARK 500 12 PHE A 497 -35.01 -179.25 REMARK 500 12 PRO A 499 74.43 -69.78 REMARK 500 13 TYR A 489 -73.71 -90.74 REMARK 500 REMARK 500 THIS ENTRY HAS 183 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7P55 RELATED DB: PDB REMARK 900 RELATED ID: 7P5G RELATED DB: PDB REMARK 900 RELATED ID: 7P5Q RELATED DB: PDB REMARK 900 RELATED ID: 34653 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF A PEPTIDE DERIVING FROM SARS-COV-2 LINEAGES P.1 REMARK 900 AND B.1.351 S RBD 482-506 FRAGMENT IN HFIP/H2O DBREF 7P5S A 482 506 UNP P0DTC2 SPIKE_SARS2 482 506 SEQADV 7P5S LYS A 484 UNP P0DTC2 GLU 484 ENGINEERED MUTATION SEQADV 7P5S TYR A 501 UNP P0DTC2 ASN 501 ENGINEERED MUTATION SEQRES 1 A 25 GLY VAL LYS GLY PHE ASN CYS TYR PHE PRO LEU GLN SER SEQRES 2 A 25 TYR GLY PHE GLN PRO THR TYR GLY VAL GLY TYR GLN HELIX 1 AA1 PRO A 491 TYR A 495 5 5 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1