HEADER VIRAL PROTEIN 10-JUN-20 7CB7
TITLE 1.7A RESOLUTION STRUCTURE OF SARS-COV-2 MAIN PROTEASE (MPRO) IN
TITLE 2 COMPLEX WITH BROAD-SPECTRUM CORONAVIRUS PROTEASE INHIBITOR GC376
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 3C-LIKE PROTEINASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: 3CL-PRO,3CLP;
COMPND 5 EC: 3.4.22.69;
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_STRAIN: BL21(DE3)
KEYWDS MAIN PROTEASE, 3C-LIKE PROTEINASE, PROTEIN-INHIBITOR COMPLEX, GC376,
KEYWDS 2 VIRAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.C.WANG,C.S.YANG,M.H.HOU,C.L.TSAI,Y.Z.CHOU,Y.CHEN,M.C.HUNG
REVDAT 3 30-OCT-24 7CB7 1 REMARK
REVDAT 2 29-NOV-23 7CB7 1 REMARK
REVDAT 1 05-MAY-21 7CB7 0
JRNL AUTH Y.C.WANG,W.H.YANG,C.S.YANG,M.H.HOU,C.L.TSAI,Y.Z.CHOU,
JRNL AUTH 2 M.C.HUNG,Y.CHEN
JRNL TITL STRUCTURAL BASIS OF SARS-COV-2 MAIN PROTEASE INHIBITION BY A
JRNL TITL 2 BROAD-SPECTRUM ANTI-CORONAVIRAL DRUG.
JRNL REF AM J CANCER RES V. 10 2535 2020
JRNL REFN ISSN 2156-6976
JRNL PMID 32905393
REMARK 2
REMARK 2 RESOLUTION. 1.69 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) : 1.69
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.78
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380
REMARK 3 COMPLETENESS FOR RANGE (%) : 80.8
REMARK 3 NUMBER OF REFLECTIONS : 106790
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.158
REMARK 3 R VALUE (WORKING SET) : 0.157
REMARK 3 FREE R VALUE : 0.192
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.090
REMARK 3 FREE R VALUE TEST SET COUNT : 3300
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 27.7800 - 4.8800 0.94 5000 158 0.1615 0.2119
REMARK 3 2 4.8800 - 3.8800 0.95 5089 155 0.1365 0.1526
REMARK 3 3 3.8700 - 3.3900 0.95 5084 158 0.1442 0.1877
REMARK 3 4 3.3900 - 3.0800 0.95 5043 166 0.1561 0.1988
REMARK 3 5 3.0800 - 2.8600 0.95 5100 170 0.1610 0.2109
REMARK 3 6 2.8600 - 2.6900 0.96 5092 168 0.1666 0.2054
REMARK 3 7 2.6900 - 2.5500 0.96 5189 161 0.1685 0.1970
REMARK 3 8 2.5500 - 2.4400 0.96 5154 168 0.1632 0.1917
REMARK 3 9 2.4400 - 2.3500 0.97 5157 162 0.1598 0.2060
REMARK 3 10 2.3500 - 2.2700 0.96 5123 173 0.1552 0.1971
REMARK 3 11 2.2700 - 2.2000 0.95 5106 138 0.1615 0.2014
REMARK 3 12 2.2000 - 2.1300 0.93 4921 176 0.1540 0.2058
REMARK 3 13 2.1300 - 2.0800 0.90 4844 172 0.1519 0.1843
REMARK 3 14 2.0800 - 2.0300 0.86 4533 145 0.1513 0.2104
REMARK 3 15 2.0300 - 1.9800 0.81 4385 104 0.1606 0.1719
REMARK 3 16 1.9800 - 1.9400 0.76 4104 138 0.1557 0.1672
REMARK 3 17 1.9400 - 1.9000 0.70 3703 119 0.1563 0.1550
REMARK 3 18 1.9000 - 1.8600 0.65 3462 118 0.1559 0.1804
REMARK 3 19 1.8600 - 1.8300 0.61 3276 101 0.1528 0.2037
REMARK 3 20 1.8300 - 1.8000 0.58 3060 92 0.1544 0.1519
REMARK 3 21 1.8000 - 1.7700 0.55 2992 103 0.1670 0.1769
REMARK 3 22 1.7700 - 1.7400 0.53 2833 84 0.1849 0.2025
REMARK 3 23 1.7400 - 1.7200 0.51 2669 82 0.1966 0.2227
REMARK 3 24 1.7200 - 1.6900 0.48 2571 89 0.2097 0.2346
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) : 0.149
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.194
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 11.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.50
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 : 0.009 4966
REMARK 3 ANGLE : 1.042 6745
REMARK 3 CHIRALITY : 0.066 752
REMARK 3 PLANARITY : 0.008 876
REMARK 3 DIHEDRAL : 18.310 688
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 6
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID -4 THROUGH 110 )
REMARK 3 ORIGIN FOR THE GROUP (A): 12.2554 -4.9056 29.5354
REMARK 3 T TENSOR
REMARK 3 T11: 0.0894 T22: 0.1872
REMARK 3 T33: 0.0709 T12: -0.0135
REMARK 3 T13: 0.0048 T23: 0.0401
REMARK 3 L TENSOR
REMARK 3 L11: 3.0707 L22: 1.1275
REMARK 3 L33: 0.8222 L12: 0.8608
REMARK 3 L13: 0.3996 L23: 0.0038
REMARK 3 S TENSOR
REMARK 3 S11: 0.1198 S12: -0.5661 S13: -0.1574
REMARK 3 S21: 0.1424 S22: -0.1355 S23: -0.0803
REMARK 3 S31: 0.0267 S32: -0.0185 S33: 0.0099
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 155 )
REMARK 3 ORIGIN FOR THE GROUP (A): 4.4841 -1.7786 19.1200
REMARK 3 T TENSOR
REMARK 3 T11: 0.0687 T22: 0.0672
REMARK 3 T33: 0.0536 T12: -0.0191
REMARK 3 T13: -0.0089 T23: 0.0002
REMARK 3 L TENSOR
REMARK 3 L11: 3.5811 L22: 1.8624
REMARK 3 L33: 1.6183 L12: 1.1797
REMARK 3 L13: 0.0590 L23: -0.6778
REMARK 3 S TENSOR
REMARK 3 S11: -0.0581 S12: -0.0362 S13: 0.1125
REMARK 3 S21: -0.1017 S22: 0.0356 S23: 0.0703
REMARK 3 S31: 0.0269 S32: -0.0628 S33: 0.0055
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 213 )
REMARK 3 ORIGIN FOR THE GROUP (A): 9.7840 3.8441 13.7511
REMARK 3 T TENSOR
REMARK 3 T11: 0.0633 T22: 0.0706
REMARK 3 T33: 0.0851 T12: -0.0214
REMARK 3 T13: 0.0052 T23: 0.0293
REMARK 3 L TENSOR
REMARK 3 L11: 1.3779 L22: 0.2605
REMARK 3 L33: 1.5635 L12: 0.3209
REMARK 3 L13: 0.2845 L23: 0.1112
REMARK 3 S TENSOR
REMARK 3 S11: -0.1164 S12: 0.0508 S13: 0.1873
REMARK 3 S21: -0.0828 S22: 0.0620 S23: -0.0439
REMARK 3 S31: -0.0945 S32: 0.0192 S33: 0.0711
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 302 )
REMARK 3 ORIGIN FOR THE GROUP (A): 1.4212 2.4190 -6.2037
REMARK 3 T TENSOR
REMARK 3 T11: 0.1416 T22: 0.1541
REMARK 3 T33: 0.0582 T12: -0.0348
REMARK 3 T13: 0.0092 T23: 0.0275
REMARK 3 L TENSOR
REMARK 3 L11: 2.3698 L22: 2.0072
REMARK 3 L33: 2.3640 L12: 0.7067
REMARK 3 L13: -0.5238 L23: 0.1292
REMARK 3 S TENSOR
REMARK 3 S11: 0.0748 S12: 0.0287 S13: -0.0370
REMARK 3 S21: -0.1171 S22: -0.0576 S23: -0.0912
REMARK 3 S31: 0.1212 S32: -0.4069 S33: -0.0111
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 180 )
REMARK 3 ORIGIN FOR THE GROUP (A): -17.4002 -18.4255 15.8872
REMARK 3 T TENSOR
REMARK 3 T11: 0.0574 T22: 0.0464
REMARK 3 T33: 0.0321 T12: -0.0140
REMARK 3 T13: 0.0235 T23: -0.0156
REMARK 3 L TENSOR
REMARK 3 L11: 1.3477 L22: 3.3165
REMARK 3 L33: 0.9436 L12: -0.3369
REMARK 3 L13: 0.1706 L23: -0.7940
REMARK 3 S TENSOR
REMARK 3 S11: -0.0260 S12: 0.0699 S13: -0.0370
REMARK 3 S21: -0.1945 S22: 0.0546 S23: 0.0464
REMARK 3 S31: 0.0076 S32: -0.0006 S33: -0.0260
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 181 THROUGH 305 )
REMARK 3 ORIGIN FOR THE GROUP (A): -19.9796 10.8645 16.1567
REMARK 3 T TENSOR
REMARK 3 T11: 0.0861 T22: 0.0813
REMARK 3 T33: 0.0804 T12: -0.0126
REMARK 3 T13: 0.0058 T23: 0.0053
REMARK 3 L TENSOR
REMARK 3 L11: 1.5308 L22: 2.6259
REMARK 3 L33: 1.4119 L12: 0.8418
REMARK 3 L13: 0.6400 L23: 0.6329
REMARK 3 S TENSOR
REMARK 3 S11: -0.0484 S12: 0.0327 S13: 0.1365
REMARK 3 S21: -0.2517 S22: 0.0887 S23: 0.0272
REMARK 3 S31: -0.1436 S32: 0.1628 S33: -0.0314
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : 1
REMARK 3 NCS GROUP : 1
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND (RESID 23 OR RESID 26
REMARK 3 THROUGH 79 OR RESID 81 THROUGH 93 OR
REMARK 3 RESID 95 THROUGH 116 OR RESID 118 THROUGH
REMARK 3 147 OR RESID 149 THROUGH 207 OR RESID 209
REMARK 3 THROUGH 236 OR RESID 238 THROUGH 241 OR
REMARK 3 RESID 244 THROUGH 289 OR RESID 291
REMARK 3 THROUGH 298 OR RESID 300 THROUGH 313 OR
REMARK 3 RESID 315 THROUGH 317 OR RESID 319
REMARK 3 THROUGH 320))
REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 23 OR RESID 26
REMARK 3 THROUGH 79 OR RESID 81 THROUGH 93 OR
REMARK 3 RESID 95 THROUGH 116 OR RESID 118 THROUGH
REMARK 3 147 OR RESID 149 THROUGH 207 OR RESID 209
REMARK 3 THROUGH 236 OR RESID 238 THROUGH 241 OR
REMARK 3 RESID 244 THROUGH 289 OR RESID 291
REMARK 3 THROUGH 298 OR RESID 300 THROUGH 313 OR
REMARK 3 RESID 315 THROUGH 317 OR RESID 319
REMARK 3 THROUGH 320))
REMARK 3 ATOM PAIRS NUMBER : NULL
REMARK 3 RMSD : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7CB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-20.
REMARK 100 THE DEPOSITION ID IS D_1300017287.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-MAY-20
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSRRC
REMARK 200 BEAMLINE : BL15A1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000
REMARK 200 MONOCHROMATOR : M
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 106790
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690
REMARK 200 RESOLUTION RANGE LOW (A) : 27.780
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : 0.02300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.12800
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: PHASER
REMARK 200 STARTING MODEL: 7CAM
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE, 0.02 M
REMARK 280 SODIUM/POTASSIUM PHOSPHATE, 20% (W/V) PEG3350, PH 6.5, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 49.39600
REMARK 290 SMTRY3 2 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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2660 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25090 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 VAL A 303
REMARK 465 THR A 304
REMARK 465 PHE A 305
REMARK 465 GLN A 306
REMARK 465 GLY B -4
REMARK 465 SER B -3
REMARK 465 GLY B -2
REMARK 465 GLY B -1
REMARK 465 GLY B 0
REMARK 465 GLN B 306
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 ARG B 4 CG CD NE CZ NH1 NH2
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 OD1 ASP A 153 O HOH A 501 1.79
REMARK 500 NZ LYS B 97 O HOH B 501 1.85
REMARK 500 NZ LYS B 5 O HOH B 502 2.13
REMARK 500 OE1 GLU A 47 O HOH A 502 2.15
REMARK 500
REMARK 500 REMARK: NULL
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 ARG A 222 CG ARG A 222 CD -0.161
REMARK 500 CYS B 22 CB CYS B 22 SG -0.098
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 ASP A 33 -127.04 52.68
REMARK 500 ASN A 51 74.40 -163.98
REMARK 500 ASN A 84 -123.31 52.55
REMARK 500 TYR A 154 -112.41 62.45
REMARK 500 PRO A 184 35.79 -85.55
REMARK 500 ASP B 33 -129.85 52.35
REMARK 500 ASN B 51 73.41 -162.42
REMARK 500 ASN B 84 -124.15 50.67
REMARK 500 TYR B 154 -106.60 58.37
REMARK 500 PRO B 184 31.61 -90.24
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ARG A 222 PHE A 223 146.24
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 B 784 DISTANCE = 5.86 ANGSTROMS
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 K36 AND B1S HAVE ALTERNATE CONFORMATIONS.
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 NA A 401 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLY A -2 O
REMARK 620 2 SER A 1 OG 124.4
REMARK 620 3 HOH A 745 O 126.0 89.9
REMARK 620 N 1 2
REMARK 630
REMARK 630 MOLECULE TYPE: NULL
REMARK 630 MOLECULE NAME: (1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-
REMARK 630 1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 K36 A 402
REMARK 630 K36 B 402
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: PHQ LEU 04F
REMARK 630 DETAILS: NULL
REMARK 630 MOLECULE TYPE: NULL
REMARK 630 MOLECULE NAME: (1R,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-
REMARK 630 1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 B1S A 403
REMARK 630 B1S B 401
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: PHQ LEU B1Y
REMARK 630 DETAILS: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue K36 A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue B1S A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide B1S B 401 and CYS B
REMARK 800 165
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide K36 B 402 and CYS B
REMARK 800 165
DBREF 7CB7 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569
DBREF 7CB7 B 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569
SEQADV 7CB7 GLY A -4 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 SER A -3 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 GLY A -2 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 GLY A -1 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 GLY A 0 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 GLY B -4 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 SER B -3 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 GLY B -2 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 GLY B -1 UNP P0DTD1 EXPRESSION TAG
SEQADV 7CB7 GLY B 0 UNP P0DTD1 EXPRESSION TAG
SEQRES 1 A 311 GLY SER GLY GLY GLY SER GLY PHE ARG LYS MET ALA PHE
SEQRES 2 A 311 PRO SER GLY LYS VAL GLU GLY CYS MET VAL GLN VAL THR
SEQRES 3 A 311 CYS GLY THR THR THR LEU ASN GLY LEU TRP LEU ASP ASP
SEQRES 4 A 311 VAL VAL TYR CYS PRO ARG HIS VAL ILE CYS THR SER GLU
SEQRES 5 A 311 ASP MET LEU ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG
SEQRES 6 A 311 LYS SER ASN HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL
SEQRES 7 A 311 GLN LEU ARG VAL ILE GLY HIS SER MET GLN ASN CYS VAL
SEQRES 8 A 311 LEU LYS LEU LYS VAL ASP THR ALA ASN PRO LYS THR PRO
SEQRES 9 A 311 LYS TYR LYS PHE VAL ARG ILE GLN PRO GLY GLN THR PHE
SEQRES 10 A 311 SER VAL LEU ALA CYS TYR ASN GLY SER PRO SER GLY VAL
SEQRES 11 A 311 TYR GLN CYS ALA MET ARG PRO ASN PHE THR ILE LYS GLY
SEQRES 12 A 311 SER PHE LEU ASN GLY SER CYS GLY SER VAL GLY PHE ASN
SEQRES 13 A 311 ILE ASP TYR ASP CYS VAL SER PHE CYS TYR MET HIS HIS
SEQRES 14 A 311 MET GLU LEU PRO THR GLY VAL HIS ALA GLY THR ASP LEU
SEQRES 15 A 311 GLU GLY ASN PHE TYR GLY PRO PHE VAL ASP ARG GLN THR
SEQRES 16 A 311 ALA GLN ALA ALA GLY THR ASP THR THR ILE THR VAL ASN
SEQRES 17 A 311 VAL LEU ALA TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP
SEQRES 18 A 311 ARG TRP PHE LEU ASN ARG PHE THR THR THR LEU ASN ASP
SEQRES 19 A 311 PHE ASN LEU VAL ALA MET LYS TYR ASN TYR GLU PRO LEU
SEQRES 20 A 311 THR GLN ASP HIS VAL ASP ILE LEU GLY PRO LEU SER ALA
SEQRES 21 A 311 GLN THR GLY ILE ALA VAL LEU ASP MET CYS ALA SER LEU
SEQRES 22 A 311 LYS GLU LEU LEU GLN ASN GLY MET ASN GLY ARG THR ILE
SEQRES 23 A 311 LEU GLY SER ALA LEU LEU GLU ASP GLU PHE THR PRO PHE
SEQRES 24 A 311 ASP VAL VAL ARG GLN CYS SER GLY VAL THR PHE GLN
SEQRES 1 B 311 GLY SER GLY GLY GLY SER GLY PHE ARG LYS MET ALA PHE
SEQRES 2 B 311 PRO SER GLY LYS VAL GLU GLY CYS MET VAL GLN VAL THR
SEQRES 3 B 311 CYS GLY THR THR THR LEU ASN GLY LEU TRP LEU ASP ASP
SEQRES 4 B 311 VAL VAL TYR CYS PRO ARG HIS VAL ILE CYS THR SER GLU
SEQRES 5 B 311 ASP MET LEU ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG
SEQRES 6 B 311 LYS SER ASN HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL
SEQRES 7 B 311 GLN LEU ARG VAL ILE GLY HIS SER MET GLN ASN CYS VAL
SEQRES 8 B 311 LEU LYS LEU LYS VAL ASP THR ALA ASN PRO LYS THR PRO
SEQRES 9 B 311 LYS TYR LYS PHE VAL ARG ILE GLN PRO GLY GLN THR PHE
SEQRES 10 B 311 SER VAL LEU ALA CYS TYR ASN GLY SER PRO SER GLY VAL
SEQRES 11 B 311 TYR GLN CYS ALA MET ARG PRO ASN PHE THR ILE LYS GLY
SEQRES 12 B 311 SER PHE LEU ASN GLY SER CYS GLY SER VAL GLY PHE ASN
SEQRES 13 B 311 ILE ASP TYR ASP CYS VAL SER PHE CYS TYR MET HIS HIS
SEQRES 14 B 311 MET GLU LEU PRO THR GLY VAL HIS ALA GLY THR ASP LEU
SEQRES 15 B 311 GLU GLY ASN PHE TYR GLY PRO PHE VAL ASP ARG GLN THR
SEQRES 16 B 311 ALA GLN ALA ALA GLY THR ASP THR THR ILE THR VAL ASN
SEQRES 17 B 311 VAL LEU ALA TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP
SEQRES 18 B 311 ARG TRP PHE LEU ASN ARG PHE THR THR THR LEU ASN ASP
SEQRES 19 B 311 PHE ASN LEU VAL ALA MET LYS TYR ASN TYR GLU PRO LEU
SEQRES 20 B 311 THR GLN ASP HIS VAL ASP ILE LEU GLY PRO LEU SER ALA
SEQRES 21 B 311 GLN THR GLY ILE ALA VAL LEU ASP MET CYS ALA SER LEU
SEQRES 22 B 311 LYS GLU LEU LEU GLN ASN GLY MET ASN GLY ARG THR ILE
SEQRES 23 B 311 LEU GLY SER ALA LEU LEU GLU ASP GLU PHE THR PRO PHE
SEQRES 24 B 311 ASP VAL VAL ARG GLN CYS SER GLY VAL THR PHE GLN
HET NA A 401 1
HET K36 A 402 59
HET B1S A 403 59
HET B1S B 401 58
HET K36 B 402 58
HETNAM NA SODIUM ION
HETNAM K36 (1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-
HETNAM 2 K36 HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-
HETNAM 3 K36 SULFONIC ACID
HETNAM B1S (1R,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-
HETNAM 2 B1S HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-
HETNAM 3 B1S SULFONIC ACID
HETSYN K36 GC376
FORMUL 3 NA NA 1+
FORMUL 4 K36 2(C21 H31 N3 O8 S)
FORMUL 5 B1S 2(C21 H31 N3 O8 S)
FORMUL 8 HOH *565(H2 O)
HELIX 1 AA1 SER A 10 GLY A 15 1 6
HELIX 2 AA2 HIS A 41 CYS A 44 5 4
HELIX 3 AA3 GLU A 47 ASN A 51 5 5
HELIX 4 AA4 ASN A 53 ARG A 60 1 8
HELIX 5 AA5 SER A 62 PHE A 66 5 5
HELIX 6 AA6 ILE A 200 ASN A 214 1 15
HELIX 7 AA7 THR A 226 TYR A 237 1 12
HELIX 8 AA8 THR A 243 LEU A 250 1 8
HELIX 9 AA9 LEU A 250 GLY A 258 1 9
HELIX 10 AB1 ALA A 260 GLY A 275 1 16
HELIX 11 AB2 THR A 292 SER A 301 1 10
HELIX 12 AB3 SER B 10 GLY B 15 1 6
HELIX 13 AB4 HIS B 41 CYS B 44 5 4
HELIX 14 AB5 GLU B 47 ASN B 51 5 5
HELIX 15 AB6 ASN B 53 ARG B 60 1 8
HELIX 16 AB7 SER B 62 PHE B 66 5 5
HELIX 17 AB8 ILE B 200 ASN B 214 1 15
HELIX 18 AB9 THR B 226 TYR B 237 1 12
HELIX 19 AC1 THR B 243 LEU B 250 1 8
HELIX 20 AC2 LEU B 250 GLY B 258 1 9
HELIX 21 AC3 ALA B 260 GLY B 275 1 16
HELIX 22 AC4 THR B 292 GLY B 302 1 11
SHEET 1 AA1 7 VAL A 73 LEU A 75 0
SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N VAL A 68 O LEU A 75
SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69
SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O THR A 25 N CYS A 22
SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O VAL A 35 N LEU A 32
SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 87 N CYS A 38
SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88
SHEET 1 AA2 5 LYS A 100 PHE A 103 0
SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158
SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150
SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O TYR A 126 N VAL A 114
SHEET 1 AA3 3 LYS A 100 PHE A 103 0
SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100
SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165
SHEET 1 AA4 7 VAL B 73 LEU B 75 0
SHEET 2 AA4 7 LEU B 67 ALA B 70 -1 N VAL B 68 O LEU B 75
SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N GLN B 19 O GLN B 69
SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O LEU B 27 N VAL B 20
SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O VAL B 35 N LEU B 32
SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38
SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N ILE B 78 O LYS B 90
SHEET 1 AA5 5 LYS B 100 PHE B 103 0
SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 100
SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158
SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150
SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O TYR B 126 N VAL B 114
SHEET 1 AA6 3 LYS B 100 PHE B 103 0
SHEET 2 AA6 3 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 100
SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165
LINK SG CYS A 145 C21AK36 A 402 1555 1555 1.77
LINK SG CYS A 145 C21BB1S A 403 1555 1555 1.77
LINK SG CYS B 145 C21AB1S B 401 1555 1555 1.73
LINK SG CYS B 145 C21BK36 B 402 1555 1555 1.73
LINK O GLY A -2 NA NA A 401 1555 1555 2.71
LINK OG SER A 1 NA NA A 401 1555 1555 2.60
LINK NA NA A 401 O HOH A 745 1555 1555 2.99
SITE 1 AC1 5 GLY A -2 GLY A -1 GLY A 0 SER A 1
SITE 2 AC1 5 HOH A 745
SITE 1 AC2 14 PHE A 140 ASN A 142 GLY A 143 SER A 144
SITE 2 AC2 14 CYS A 145 HIS A 163 HIS A 164 MET A 165
SITE 3 AC2 14 GLU A 166 HIS A 172 GLN A 189 B1S A 403
SITE 4 AC2 14 HOH A 517 HOH A 588
SITE 1 AC3 13 HIS A 41 PHE A 140 ASN A 142 CYS A 145
SITE 2 AC3 13 HIS A 163 HIS A 164 MET A 165 GLU A 166
SITE 3 AC3 13 HIS A 172 GLN A 189 K36 A 402 HOH A 517
SITE 4 AC3 13 HOH A 588
SITE 1 AC4 18 LEU B 27 ASN B 28 HIS B 41 PHE B 140
SITE 2 AC4 18 ASN B 142 GLY B 143 SER B 144 GLY B 146
SITE 3 AC4 18 SER B 147 HIS B 163 HIS B 164 MET B 165
SITE 4 AC4 18 GLU B 166 HIS B 172 GLN B 189 K36 B 402
SITE 5 AC4 18 HOH B 554 HOH B 666
SITE 1 AC5 17 LEU B 27 ASN B 28 HIS B 41 PHE B 140
SITE 2 AC5 17 ASN B 142 GLY B 143 SER B 144 GLY B 146
SITE 3 AC5 17 SER B 147 HIS B 163 HIS B 164 MET B 165
SITE 4 AC5 17 GLU B 166 HIS B 172 GLN B 189 B1S B 401
SITE 5 AC5 17 HOH B 554
CRYST1 55.029 98.792 59.492 90.00 108.41 90.00 P 1 21 1 4
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 0.018172 0.000000 0.006049 0.00000
SCALE2 0.000000 0.010122 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017716 0.00000