PDB Short entry for 6VYO HEADER VIRAL PROTEIN 27-FEB-20 6VYO TITLE CRYSTAL STRUCTURE OF RNA BINDING DOMAIN OF NUCLEOCAPSID PHOSPHOPROTEIN TITLE 2 FROM SARS CORONAVIRUS 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RNA BINDING DOMAIN; COMPND 5 SYNONYM: NUCLEOCAPSID PROTEIN,PROTEIN N; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS CSGID, COVID-19, RNA BINDING DOMAIN, NUCLEOCAPSID PROTEIN, KEYWDS 2 NUCLEOPROTEIN, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS KEYWDS 3 OF INFECTIOUS DISEASES, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,K.MICHALSKA,R.JEDRZEJCZAK,N.MALTSEVA,M.ENDRES,A.GODZIK,Y.KIM, AUTHOR 2 A.JOACHIMIAK,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 3 (CSGID) REVDAT 6 28-FEB-24 6VYO 1 JRNL REVDAT 5 11-OCT-23 6VYO 1 COMPND LINK REVDAT 4 06-MAY-20 6VYO 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQADV LINK SITE ATOM REVDAT 3 08-APR-20 6VYO 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK SITE REVDAT 3 3 1 ATOM REVDAT 2 25-MAR-20 6VYO 1 KEYWDS REVDAT 1 11-MAR-20 6VYO 0 JRNL AUTH Y.KIM,N.MALTSEVA,C.TESAR,R.JEDRZEJCZAK,M.ENDRES,H.MA, JRNL AUTH 2 H.L.DUGAN,C.T.STAMPER,C.CHANG,L.LI,S.CHANGROB,N.Y.ZHENG, JRNL AUTH 3 M.HUANG,A.RAMANATHAN,P.WILSON,K.MICHALSKA,A.JOACHIMIAK JRNL TITL EPITOPES RECOGNITION OF SARS-COV-2 NUCLEOCAPSID RNA BINDING JRNL TITL 2 DOMAIN BY HUMAN MONOCLONAL ANTIBODIES. JRNL REF ISCIENCE V. 27 08976 2024 JRNL REFN ESSN 2589-0042 JRNL PMID 38327783 JRNL DOI 10.1016/J.ISCI.2024.108976 REMARK 2 REMARK 2 RESOLUTION. 1.70 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.3 REMARK 3 NUMBER OF REFLECTIONS : 56873 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2800 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 46.0500 - 4.6100 0.99 3297 179 0.1563 0.1740 REMARK 3 2 4.6100 - 3.6600 1.00 3181 155 0.1354 0.1655 REMARK 3 3 3.6600 - 3.2000 1.00 3166 148 0.1558 0.1923 REMARK 3 4 3.2000 - 2.9100 1.00 3114 164 0.1670 0.2203 REMARK 3 5 2.9100 - 2.7000 1.00 3109 166 0.1726 0.2174 REMARK 3 6 2.7000 - 2.5400 1.00 3086 154 0.1727 0.2239 REMARK 3 7 2.5400 - 2.4100 1.00 3115 165 0.1708 0.2219 REMARK 3 8 2.4100 - 2.3100 0.99 3045 151 0.1643 0.2368 REMARK 3 9 2.3100 - 2.2200 1.00 3077 152 0.1583 0.2429 REMARK 3 10 2.2200 - 2.1400 0.99 3046 174 0.1577 0.2020 REMARK 3 11 2.1400 - 2.0800 0.96 2954 153 0.1542 0.1996 REMARK 3 12 2.0800 - 2.0200 0.91 2785 149 0.1547 0.2011 REMARK 3 13 2.0200 - 1.9600 0.86 2614 141 0.1571 0.1864 REMARK 3 14 1.9600 - 1.9100 0.82 2511 123 0.1559 0.2174 REMARK 3 15 1.9100 - 1.8700 0.76 2352 121 0.1725 0.2086 REMARK 3 16 1.8700 - 1.8300 0.71 2165 116 0.1792 0.3046 REMARK 3 17 1.8300 - 1.7900 0.68 2075 100 0.1818 0.2476 REMARK 3 18 1.7900 - 1.7600 0.63 1926 104 0.1685 0.2115 REMARK 3 19 1.7600 - 1.7300 0.60 1848 100 0.1649 0.2585 REMARK 3 20 1.7300 - 1.7000 0.53 1607 85 0.1505 0.2094 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.09 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 6VYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000247334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64592 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 1.13400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: HKL-3000 REMARK 200 STARTING MODEL: 2OFZ.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.0% PEG6000, 0.1M MES, 10.0 MM ZINC REMARK 280 CHLORIDE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 33.11900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.01950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.71500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.01950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.11900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.71500 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -179.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 46 REMARK 465 ASN A 47 REMARK 465 ASN A 48 REMARK 465 THR A 49 REMARK 465 GLY B 46 REMARK 465 ASN B 47 REMARK 465 ASN B 48 REMARK 465 GLY C 46 REMARK 465 ASN C 47 REMARK 465 ASN C 48 REMARK 465 GLY D 46 REMARK 465 ASN D 47 REMARK 465 ASN D 48 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 OE1 GLU A 62 O HOH A 301 2.16 REMARK 500 O HOH D 312 O HOH D 460 2.17 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 ASN A 77 54.44 -91.44 REMARK 500 LYS A 143 52.63 -100.40 REMARK 500 LYS B 143 56.32 -99.02 REMARK 500 ASN C 77 54.26 -91.23 REMARK 500 LYS C 143 52.84 -100.25 REMARK 500 LYS D 143 58.71 -98.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 468 DISTANCE = 6.43 ANGSTROMS 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 ZN A 206 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 59 NE2 REMARK 620 2 ASP B 82 OD2 106.6 REMARK 620 3 HIS B 145 NE2 110.1 115.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 82 OD2 REMARK 620 2 HIS A 145 NE2 113.9 REMARK 620 3 HIS D 59 ND1 105.7 110.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 59 ND1 REMARK 620 2 ASP C 82 OD2 102.9 REMARK 620 3 HIS C 145 NE2 113.4 112.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 59 NE2 REMARK 620 2 ASP D 82 OD2 105.3 REMARK 620 3 HIS D 145 NE2 110.8 116.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES C 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CSGID-IDP51003 RELATED DB: TARGETTRACK DBREF 6VYO A 47 173 UNP P0DTC9 NCAP_SARS2 47 173 DBREF 6VYO B 47 173 UNP P0DTC9 NCAP_SARS2 47 173 DBREF 6VYO C 47 173 UNP P0DTC9 NCAP_SARS2 47 173 DBREF 6VYO D 47 173 UNP P0DTC9 NCAP_SARS2 47 173 SEQADV 6VYO GLY A 46 UNP P0DTC9 EXPRESSION TAG SEQADV 6VYO GLY B 46 UNP P0DTC9 EXPRESSION TAG SEQADV 6VYO GLY C 46 UNP P0DTC9 EXPRESSION TAG SEQADV 6VYO GLY D 46 UNP P0DTC9 EXPRESSION TAG SEQRES 1 A 128 GLY ASN ASN THR ALA SER TRP PHE THR ALA LEU THR GLN SEQRES 2 A 128 HIS GLY LYS GLU ASP LEU LYS PHE PRO ARG GLY GLN GLY SEQRES 3 A 128 VAL PRO ILE ASN THR ASN SER SER PRO ASP ASP GLN ILE SEQRES 4 A 128 GLY TYR TYR ARG ARG ALA THR ARG ARG ILE ARG GLY GLY SEQRES 5 A 128 ASP GLY LYS MET LYS ASP LEU SER PRO ARG TRP TYR PHE SEQRES 6 A 128 TYR TYR LEU GLY THR GLY PRO GLU ALA GLY LEU PRO TYR SEQRES 7 A 128 GLY ALA ASN LYS ASP GLY ILE ILE TRP VAL ALA THR GLU SEQRES 8 A 128 GLY ALA LEU ASN THR PRO LYS ASP HIS ILE GLY THR ARG SEQRES 9 A 128 ASN PRO ALA ASN ASN ALA ALA ILE VAL LEU GLN LEU PRO SEQRES 10 A 128 GLN GLY THR THR LEU PRO LYS GLY PHE TYR ALA SEQRES 1 B 128 GLY ASN ASN THR ALA SER TRP PHE THR ALA LEU THR GLN SEQRES 2 B 128 HIS GLY LYS GLU ASP LEU LYS PHE PRO ARG GLY GLN GLY SEQRES 3 B 128 VAL PRO ILE ASN THR ASN SER SER PRO ASP ASP GLN ILE SEQRES 4 B 128 GLY TYR TYR ARG ARG ALA THR ARG ARG ILE ARG GLY GLY SEQRES 5 B 128 ASP GLY LYS MET LYS ASP LEU SER PRO ARG TRP TYR PHE SEQRES 6 B 128 TYR TYR LEU GLY THR GLY PRO GLU ALA GLY LEU PRO TYR SEQRES 7 B 128 GLY ALA ASN LYS ASP GLY ILE ILE TRP VAL ALA THR GLU SEQRES 8 B 128 GLY ALA LEU ASN THR PRO LYS ASP HIS ILE GLY THR ARG SEQRES 9 B 128 ASN PRO ALA ASN ASN ALA ALA ILE VAL LEU GLN LEU PRO SEQRES 10 B 128 GLN GLY THR THR LEU PRO LYS GLY PHE TYR ALA SEQRES 1 C 128 GLY ASN ASN THR ALA SER TRP PHE THR ALA LEU THR GLN SEQRES 2 C 128 HIS GLY LYS GLU ASP LEU LYS PHE PRO ARG GLY GLN GLY SEQRES 3 C 128 VAL PRO ILE ASN THR ASN SER SER PRO ASP ASP GLN ILE SEQRES 4 C 128 GLY TYR TYR ARG ARG ALA THR ARG ARG ILE ARG GLY GLY SEQRES 5 C 128 ASP GLY LYS MET LYS ASP LEU SER PRO ARG TRP TYR PHE SEQRES 6 C 128 TYR TYR LEU GLY THR GLY PRO GLU ALA GLY LEU PRO TYR SEQRES 7 C 128 GLY ALA ASN LYS ASP GLY ILE ILE TRP VAL ALA THR GLU SEQRES 8 C 128 GLY ALA LEU ASN THR PRO LYS ASP HIS ILE GLY THR ARG SEQRES 9 C 128 ASN PRO ALA ASN ASN ALA ALA ILE VAL LEU GLN LEU PRO SEQRES 10 C 128 GLN GLY THR THR LEU PRO LYS GLY PHE TYR ALA SEQRES 1 D 128 GLY ASN ASN THR ALA SER TRP PHE THR ALA LEU THR GLN SEQRES 2 D 128 HIS GLY LYS GLU ASP LEU LYS PHE PRO ARG GLY GLN GLY SEQRES 3 D 128 VAL PRO ILE ASN THR ASN SER SER PRO ASP ASP GLN ILE SEQRES 4 D 128 GLY TYR TYR ARG ARG ALA THR ARG ARG ILE ARG GLY GLY SEQRES 5 D 128 ASP GLY LYS MET LYS ASP LEU SER PRO ARG TRP TYR PHE SEQRES 6 D 128 TYR TYR LEU GLY THR GLY PRO GLU ALA GLY LEU PRO TYR SEQRES 7 D 128 GLY ALA ASN LYS ASP GLY ILE ILE TRP VAL ALA THR GLU SEQRES 8 D 128 GLY ALA LEU ASN THR PRO LYS ASP HIS ILE GLY THR ARG SEQRES 9 D 128 ASN PRO ALA ASN ASN ALA ALA ILE VAL LEU GLN LEU PRO SEQRES 10 D 128 GLN GLY THR THR LEU PRO LYS GLY PHE TYR ALA HET MES A 201 12 HET CL A 202 1 HET MES A 203 12 HET ZN A 204 1 HET CL A 205 1 HET ZN A 206 1 HET GOL B 201 6 HET MES B 202 12 HET ZN B 203 1 HET CL C 201 1 HET CL C 202 1 HET GOL C 203 6 HET MES C 204 12 HET ZN C 205 1 HET GOL D 201 6 HET GOL D 202 6 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM CL CHLORIDE ION HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MES 4(C6 H13 N O4 S) FORMUL 6 CL 4(CL 1-) FORMUL 8 ZN 4(ZN 2+) FORMUL 11 GOL 4(C3 H8 O3) FORMUL 21 HOH *664(H2 O) HELIX 1 AA1 SER A 79 ASP A 82 5 4 HELIX 2 AA2 SER B 79 ASP B 82 5 4 HELIX 3 AA3 SER C 79 ASP C 82 5 4 HELIX 4 AA4 SER D 79 ASP D 82 5 4 SHEET 1 AA1 4 LEU A 56 THR A 57 0 SHEET 2 AA1 4 ARG A 107 TYR A 112 -1 O TRP A 108 N LEU A 56 SHEET 3 AA1 4 ILE A 84 ALA A 90 -1 N ALA A 90 O ARG A 107 SHEET 4 AA1 4 ILE A 130 ALA A 134 -1 O VAL A 133 N GLY A 85 SHEET 1 AA2 2 ARG A 93 ARG A 95 0 SHEET 2 AA2 2 MET A 101 ASP A 103 -1 O LYS A 102 N ILE A 94 SHEET 1 AA3 5 ILE B 130 ALA B 134 0 SHEET 2 AA3 5 ILE B 84 ALA B 90 -1 N TYR B 87 O ILE B 131 SHEET 3 AA3 5 ARG B 107 TYR B 112 -1 O TYR B 111 N TYR B 86 SHEET 4 AA3 5 LEU B 56 GLN B 58 -1 N LEU B 56 O TRP B 108 SHEET 5 AA3 5 PHE B 171 TYR B 172 -1 O TYR B 172 N THR B 57 SHEET 1 AA4 2 ARG B 93 ARG B 95 0 SHEET 2 AA4 2 MET B 101 ASP B 103 -1 O LYS B 102 N ILE B 94 SHEET 1 AA5 4 LEU C 56 THR C 57 0 SHEET 2 AA5 4 ARG C 107 TYR C 112 -1 O TRP C 108 N LEU C 56 SHEET 3 AA5 4 ILE C 84 ALA C 90 -1 N ALA C 90 O ARG C 107 SHEET 4 AA5 4 ILE C 130 ALA C 134 -1 O VAL C 133 N GLY C 85 SHEET 1 AA6 2 ARG C 93 ARG C 95 0 SHEET 2 AA6 2 MET C 101 ASP C 103 -1 O LYS C 102 N ILE C 94 SHEET 1 AA7 5 ILE D 130 ALA D 134 0 SHEET 2 AA7 5 ILE D 84 ALA D 90 -1 N TYR D 87 O ILE D 131 SHEET 3 AA7 5 ARG D 107 TYR D 112 -1 O ARG D 107 N ALA D 90 SHEET 4 AA7 5 LEU D 56 GLN D 58 -1 N LEU D 56 O TRP D 108 SHEET 5 AA7 5 PHE D 171 TYR D 172 -1 O TYR D 172 N THR D 57 SHEET 1 AA8 2 ARG D 93 ARG D 95 0 SHEET 2 AA8 2 MET D 101 ASP D 103 -1 O LYS D 102 N ILE D 94 LINK NE2 HIS A 59 ZN ZN A 206 1555 1555 2.07 LINK OD2 ASP A 82 ZN ZN A 204 1555 1555 1.99 LINK NE2 HIS A 145 ZN ZN A 204 1555 1555 2.12 LINK ZN ZN A 204 ND1 HIS D 59 1555 1555 2.00 LINK ZN ZN A 206 OD2 ASP B 82 1555 1555 1.95 LINK ZN ZN A 206 NE2 HIS B 145 1555 1555 2.09 LINK ND1 HIS B 59 ZN ZN B 203 1555 1555 2.04 LINK ZN ZN B 203 OD2 ASP C 82 1555 1555 1.97 LINK ZN ZN B 203 NE2 HIS C 145 1555 1555 2.06 LINK NE2 HIS C 59 ZN ZN C 205 1555 1555 2.07 LINK ZN ZN C 205 OD2 ASP D 82 1555 1555 1.98 LINK ZN ZN C 205 NE2 HIS D 145 1555 1555 2.05 SITE 1 AC1 8 TRP A 52 ASN A 75 ASN A 77 ASN A 154 SITE 2 AC1 8 HOH A 303 ARG D 107 HOH D 307 HOH D 426 SITE 1 AC2 5 HIS A 59 ZN A 206 ASN B 77 ASP B 82 SITE 2 AC2 5 HIS B 145 SITE 1 AC3 8 THR A 54 ALA A 55 ARG A 107 HOH A 392 SITE 2 AC3 8 TRP B 52 ASN B 75 ASN B 77 ASN B 154 SITE 1 AC4 4 ASP A 82 HIS A 145 CL A 205 HIS D 59 SITE 1 AC5 5 SER A 79 ASP A 82 HIS A 145 ZN A 204 SITE 2 AC5 5 HIS D 59 SITE 1 AC6 4 HIS A 59 CL A 202 ASP B 82 HIS B 145 SITE 1 AC7 5 ASN A 140 ARG B 68 TYR B 123 HOH B 344 SITE 2 AC7 5 HOH B 383 SITE 1 AC8 7 ARG B 92 ARG B 107 HOH B 402 TRP C 52 SITE 2 AC8 7 ASN C 75 ASN C 77 ASN C 154 SITE 1 AC9 4 HIS B 59 ASP C 82 HIS C 145 CL C 201 SITE 1 AD1 5 HIS B 59 ZN B 203 SER C 79 ASP C 82 SITE 2 AD1 5 HIS C 145 SITE 1 AD2 5 HIS C 59 ZN C 205 ASN D 77 ASP D 82 SITE 2 AD2 5 HIS D 145 SITE 1 AD3 9 ASN C 75 THR C 76 SER C 78 SER C 79 SITE 2 AD3 9 PRO C 80 GLN C 83 HOH C 335 HOH C 371 SITE 3 AD3 9 ARG D 95 SITE 1 AD4 10 THR C 54 ALA C 55 ARG C 107 HOH C 305 SITE 2 AD4 10 HOH C 307 HOH C 374 HOH C 411 TRP D 52 SITE 3 AD4 10 ASN D 75 ASN D 154 SITE 1 AD5 4 HIS C 59 CL C 202 ASP D 82 HIS D 145 SITE 1 AD6 6 ASN C 140 THR C 141 TYR D 123 TRP D 132 SITE 2 AD6 6 HOH D 368 HOH D 373 SITE 1 AD7 4 ASN D 75 SER D 78 PRO D 80 GLN D 83 CRYST1 66.238 77.430 114.039 90.00 90.00 90.00 P 21 21 21 16 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 0.015097 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008769 0.00000