PDB Short entry for 2K7X HEADER HYDROLASE 28-AUG-08 2K7X TITLE SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF SARS-COV MAIN PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SARS-COV MAIN PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 3 ORGANISM_TAXID: 255730; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ROSSETTA; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS SOLUTION STRUCTURE, C-TERMINAL DOMAIN, MAIN PROTEASE, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR B.XIA,N.ZHONG REVDAT 2 16-MAR-22 2K7X 1 REMARK REVDAT 1 12-MAY-09 2K7X 0 JRNL AUTH N.ZHONG,S.ZHANG,F.XUE,X.KANG,P.ZOU,J.CHEN,C.LIANG,Z.RAO, JRNL AUTH 2 C.JIN,Z.LOU,B.XIA JRNL TITL C-TERMINAL DOMAIN OF SARS-COV MAIN PROTEASE CAN FORM A 3D JRNL TITL 2 DOMAIN-SWAPPED DIMER. JRNL REF PROTEIN SCI. V. 18 839 2009 JRNL REFN ISSN 0961-8368 JRNL PMID 19319935 JRNL DOI 10.1002/PRO.76 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, D. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K7X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000100788. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-95% 13C; U-95% 15N] REMARK 210 MPROC, 50 MM POTASSIUM PHOSPHATE, REMARK 210 10 MM DTT, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, XWINNMR, NMRPIPE, NMRVIEW REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 TYR A 209 CG TYR A 209 CD2 -0.078 REMARK 500 1 TYR A 209 CG TYR A 209 CD1 -0.080 REMARK 500 1 ARG A 217 CD ARG A 217 NE -0.184 REMARK 500 1 ARG A 217 NE ARG A 217 CZ -0.126 REMARK 500 1 LYS A 236 CD LYS A 236 CE -0.159 REMARK 500 1 TYR A 237 CG TYR A 237 CD2 -0.091 REMARK 500 1 TYR A 237 CZ TYR A 237 CE2 -0.088 REMARK 500 1 TYR A 239 CG TYR A 239 CD2 -0.096 REMARK 500 1 TYR A 239 CG TYR A 239 CD1 -0.079 REMARK 500 1 TYR A 239 CZ TYR A 239 CE2 -0.082 REMARK 500 1 GLU A 240 CD GLU A 240 OE2 -0.066 REMARK 500 1 GLU A 270 CG GLU A 270 CD -0.146 REMARK 500 1 GLU A 270 CD GLU A 270 OE1 -0.070 REMARK 500 1 GLU A 270 CD GLU A 270 OE2 -0.095 REMARK 500 1 ARG A 279 CD ARG A 279 NE -0.213 REMARK 500 1 ARG A 279 NE ARG A 279 CZ -0.143 REMARK 500 1 GLU A 288 CG GLU A 288 CD -0.093 REMARK 500 1 GLU A 288 CD GLU A 288 OE1 -0.076 REMARK 500 1 GLU A 288 CD GLU A 288 OE2 -0.078 REMARK 500 1 GLU A 290 CD GLU A 290 OE2 -0.077 REMARK 500 1 PHE A 294 CB PHE A 294 CG -0.206 REMARK 500 1 PHE A 294 CG PHE A 294 CD2 -0.125 REMARK 500 1 PHE A 294 CG PHE A 294 CD1 -0.119 REMARK 500 1 ARG A 298 CG ARG A 298 CD -0.208 REMARK 500 1 ARG A 298 CD ARG A 298 NE -0.214 REMARK 500 1 ARG A 298 NE ARG A 298 CZ -0.124 REMARK 500 1 ARG A 298 CZ ARG A 298 NH2 -0.087 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 1 TRP A 207 NE1 - CE2 - CZ2 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 TYR A 209 CB - CG - CD2 ANGL. DEV. = 8.4 DEGREES REMARK 500 1 TYR A 209 CD1 - CG - CD2 ANGL. DEV. = -17.0 DEGREES REMARK 500 1 TYR A 209 CB - CG - CD1 ANGL. DEV. = 8.6 DEGREES REMARK 500 1 TYR A 209 CG - CD1 - CE1 ANGL. DEV. = 7.4 DEGREES REMARK 500 1 TYR A 209 CG - CD2 - CE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 TYR A 209 CD1 - CE1 - CZ ANGL. DEV. = 13.9 DEGREES REMARK 500 1 TYR A 209 OH - CZ - CE2 ANGL. DEV. = 23.1 DEGREES REMARK 500 1 TYR A 209 CE1 - CZ - CE2 ANGL. DEV. = -23.3 DEGREES REMARK 500 1 TYR A 209 CZ - CE2 - CD2 ANGL. DEV. = 11.2 DEGREES REMARK 500 1 ASP A 216 OD1 - CG - OD2 ANGL. DEV. = -35.4 DEGREES REMARK 500 1 ASP A 216 CB - CG - OD1 ANGL. DEV. = 12.1 DEGREES REMARK 500 1 ASP A 216 CB - CG - OD2 ANGL. DEV. = 10.0 DEGREES REMARK 500 1 ARG A 217 NH1 - CZ - NH2 ANGL. DEV. = 9.1 DEGREES REMARK 500 1 ARG A 217 NE - CZ - NH2 ANGL. DEV. = -12.0 DEGREES REMARK 500 1 ARG A 217 O - C - N ANGL. DEV. = -11.0 DEGREES REMARK 500 1 PHE A 219 CB - CG - CD2 ANGL. DEV. = 11.6 DEGREES REMARK 500 1 PHE A 219 CD1 - CG - CD2 ANGL. DEV. = -17.7 DEGREES REMARK 500 1 PHE A 219 CB - CG - CD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 PHE A 219 CG - CD1 - CE1 ANGL. DEV. = 8.7 DEGREES REMARK 500 1 PHE A 219 CG - CD2 - CE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 1 PHE A 219 CD1 - CE1 - CZ ANGL. DEV. = 11.5 DEGREES REMARK 500 1 PHE A 219 CE1 - CZ - CE2 ANGL. DEV. = -22.4 DEGREES REMARK 500 1 PHE A 219 CZ - CE2 - CD2 ANGL. DEV. = 10.9 DEGREES REMARK 500 1 ASN A 221 N - CA - CB ANGL. DEV. = -11.5 DEGREES REMARK 500 1 ASN A 221 CA - CB - CG ANGL. DEV. = 24.3 DEGREES REMARK 500 1 ARG A 222 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 PHE A 223 CB - CG - CD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 PHE A 223 CD1 - CG - CD2 ANGL. DEV. = -14.6 DEGREES REMARK 500 1 PHE A 223 CB - CG - CD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 PHE A 223 CG - CD1 - CE1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 PHE A 223 CG - CD2 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 PHE A 223 CD1 - CE1 - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 1 PHE A 223 CE1 - CZ - CE2 ANGL. DEV. = -18.8 DEGREES REMARK 500 1 PHE A 223 CZ - CE2 - CD2 ANGL. DEV. = 9.6 DEGREES REMARK 500 1 ASP A 229 OD1 - CG - OD2 ANGL. DEV. = -23.6 DEGREES REMARK 500 1 ASP A 229 CB - CG - OD1 ANGL. DEV. = 11.3 DEGREES REMARK 500 1 ASP A 229 CB - CG - OD2 ANGL. DEV. = 12.4 DEGREES REMARK 500 1 PHE A 230 CB - CG - CD2 ANGL. DEV. = 10.0 DEGREES REMARK 500 1 PHE A 230 CD1 - CG - CD2 ANGL. DEV. = -20.8 DEGREES REMARK 500 1 PHE A 230 CB - CG - CD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 PHE A 230 CG - CD1 - CE1 ANGL. DEV. = 9.8 DEGREES REMARK 500 1 PHE A 230 CG - CD2 - CE2 ANGL. DEV. = 9.3 DEGREES REMARK 500 1 PHE A 230 CD1 - CE1 - CZ ANGL. DEV. = 12.3 DEGREES REMARK 500 1 PHE A 230 CE1 - CZ - CE2 ANGL. DEV. = -25.1 DEGREES REMARK 500 1 PHE A 230 CZ - CE2 - CD2 ANGL. DEV. = 12.2 DEGREES REMARK 500 1 TYR A 237 CB - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 TYR A 237 CD1 - CG - CD2 ANGL. DEV. = -21.1 DEGREES REMARK 500 1 TYR A 237 CB - CG - CD1 ANGL. DEV. = 11.2 DEGREES REMARK 500 1 TYR A 237 CG - CD1 - CE1 ANGL. DEV. = 8.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 109 ANGLE DEVIATIONS. 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 1 ARG A 188 -90.10 40.71 REMARK 500 1 GLN A 189 -84.04 47.73 REMARK 500 1 THR A 190 72.43 -65.88 REMARK 500 1 ALA A 191 -178.70 -63.02 REMARK 500 1 GLN A 192 -0.17 61.72 REMARK 500 1 THR A 196 -148.13 -158.89 REMARK 500 1 ASP A 197 -28.15 74.75 REMARK 500 1 ARG A 217 44.30 -103.52 REMARK 500 1 ASN A 238 63.52 64.33 REMARK 500 1 MET A 276 -17.12 68.71 REMARK 500 1 ASN A 277 -24.91 60.21 REMARK 500 1 SER A 301 21.65 -65.65 REMARK 500 1 VAL A 303 -24.08 105.22 REMARK 500 2 ARG A 217 20.97 -147.02 REMARK 500 2 ASN A 238 65.31 65.97 REMARK 500 2 ASN A 277 81.64 -67.75 REMARK 500 3 ALA A 191 12.30 59.17 REMARK 500 3 ALA A 193 39.83 -145.53 REMARK 500 3 ARG A 217 21.27 -67.89 REMARK 500 3 ARG A 222 20.16 -143.45 REMARK 500 3 ASN A 238 65.51 66.54 REMARK 500 3 MET A 276 -5.47 60.66 REMARK 500 3 ASN A 277 47.67 38.31 REMARK 500 3 SER A 301 175.58 61.12 REMARK 500 3 VAL A 303 33.57 -149.11 REMARK 500 3 PHE A 305 -177.78 59.84 REMARK 500 4 THR A 190 25.33 -69.22 REMARK 500 4 ARG A 217 23.59 -148.43 REMARK 500 4 ASN A 221 -169.90 -116.82 REMARK 500 4 ASN A 238 65.87 64.57 REMARK 500 4 ASN A 277 -33.05 63.26 REMARK 500 4 THR A 304 -173.40 56.61 REMARK 500 5 ASP A 197 57.73 -146.96 REMARK 500 5 TRP A 218 -42.23 -153.79 REMARK 500 5 ARG A 222 16.89 -144.81 REMARK 500 5 ASN A 238 65.25 67.92 REMARK 500 5 ASN A 277 -32.82 66.67 REMARK 500 5 SER A 301 27.58 46.78 REMARK 500 5 THR A 304 165.81 59.40 REMARK 500 6 GLN A 189 -142.30 29.70 REMARK 500 6 ASP A 197 49.27 -80.11 REMARK 500 6 THR A 304 -175.68 55.78 REMARK 500 6 PHE A 305 -179.04 59.94 REMARK 500 7 GLN A 192 149.81 -171.24 REMARK 500 7 TRP A 218 -39.72 -152.94 REMARK 500 7 ARG A 222 18.44 -141.76 REMARK 500 7 ASN A 238 61.23 71.70 REMARK 500 7 VAL A 303 21.29 -79.71 REMARK 500 8 ARG A 217 27.57 -72.03 REMARK 500 8 ASN A 238 66.30 65.77 REMARK 500 REMARK 500 THIS ENTRY HAS 116 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ASP A 216 0.12 SIDE CHAIN REMARK 500 1 GLU A 240 0.15 SIDE CHAIN REMARK 500 1 ASP A 248 0.10 SIDE CHAIN REMARK 500 1 GLU A 288 0.17 SIDE CHAIN REMARK 500 1 ASP A 289 0.17 SIDE CHAIN REMARK 500 1 GLU A 290 0.17 SIDE CHAIN REMARK 500 1 PHE A 294 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2K7X A 187 306 UNP Q6JH47 Q6JH47_CVHSA 3427 3546 SEQRES 1 A 120 ASP ARG GLN THR ALA GLN ALA ALA GLY THR ASP THR THR SEQRES 2 A 120 ILE THR LEU ASN VAL LEU ALA TRP LEU TYR ALA ALA VAL SEQRES 3 A 120 ILE ASN GLY ASP ARG TRP PHE LEU ASN ARG PHE THR THR SEQRES 4 A 120 THR LEU ASN ASP PHE ASN LEU VAL ALA MET LYS TYR ASN SEQRES 5 A 120 TYR GLU PRO LEU THR GLN ASP HIS VAL ASP ILE LEU GLY SEQRES 6 A 120 PRO LEU SER ALA GLN THR GLY ILE ALA VAL LEU ASP MET SEQRES 7 A 120 CYS ALA ALA LEU LYS GLU LEU LEU GLN ASN GLY MET ASN SEQRES 8 A 120 GLY ARG THR ILE LEU GLY SER THR ILE LEU GLU ASP GLU SEQRES 9 A 120 PHE THR PRO PHE ASP VAL VAL ARG GLN CYS SER GLY VAL SEQRES 10 A 120 THR PHE GLN HELIX 1 1 ILE A 200 GLY A 215 1 16 HELIX 2 2 THR A 226 MET A 235 1 10 HELIX 3 3 LYS A 236 ASN A 238 5 3 HELIX 4 4 THR A 243 GLY A 258 1 16 HELIX 5 5 ALA A 260 GLY A 275 1 16 HELIX 6 6 THR A 292 CYS A 300 1 9 CISPEP 1 PHE A 305 GLN A 306 1 -10.83 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