HEADER VIRAL PROTEIN 28-APR-23 8OWW TITLE B5-5 NANOBODY BOUND TO SARS-COV-2 SPIKE RBD (WUHAN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S2'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: B5-5 NANOBODY; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 10 ORGANISM_TAXID: 9844; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOBODY, SARS-COV-2, RECEPTOR BINDING DOMAIN, COMPLEX, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.A.S.CORNISH,J.H.NAISMITH,R.J.OWENS REVDAT 2 19-JUN-24 8OWW 1 JRNL REVDAT 1 08-MAY-24 8OWW 0 JRNL AUTH K.CORNISH,J.HUO,L.JONES,P.SHARMA,J.W.THRUSH,S.ABDELKARIM, JRNL AUTH 2 A.KIPAR,S.RAMADURAI,M.WECKENER,H.MIKOLAJEK,S.LIU,I.BUCKLE, JRNL AUTH 3 E.BENTLEY,A.KIRBY,X.HAN,S.M.LAIDLAW,M.HILL,L.EYSSEN, JRNL AUTH 4 C.NORMAN,A.LE BAS,J.CLARKE,W.JAMES,J.P.STEWART,M.CARROLL, JRNL AUTH 5 J.H.NAISMITH,R.J.OWENS JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF NANOBODIES JRNL TITL 2 THAT NEUTRALIZE OMICRON VARIANTS OF SARS-COV-2. JRNL REF OPEN BIOLOGY V. 14 30252 2024 JRNL REFN ESSN 2046-2441 JRNL PMID 38835241 JRNL DOI 10.1098/RSOB.230252 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0403 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25113 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.033 REMARK 3 FREE R VALUE TEST SET COUNT : 1264 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1708 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.3340 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2496 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.96600 REMARK 3 B22 (A**2) : -1.46500 REMARK 3 B33 (A**2) : -0.50100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.161 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.128 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2605 ; 0.016 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 2327 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3537 ; 2.182 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5335 ; 0.684 ; 1.563 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 319 ; 7.695 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 18 ; 9.156 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 371 ;15.112 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3126 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 667 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 428 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 89 ; 0.204 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1289 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 98 ; 0.223 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1282 ; 4.283 ; 3.345 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1282 ; 4.282 ; 3.344 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1599 ; 5.823 ; 5.988 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1600 ; 5.822 ; 5.988 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1323 ; 5.513 ; 3.868 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1324 ; 5.511 ; 3.871 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1938 ; 7.684 ; 6.828 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1939 ; 7.682 ; 6.830 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 331 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1693 4.2858 21.6207 REMARK 3 T TENSOR REMARK 3 T11: 0.0522 T22: 0.1774 REMARK 3 T33: 0.0142 T12: -0.0457 REMARK 3 T13: -0.0156 T23: 0.0389 REMARK 3 L TENSOR REMARK 3 L11: 3.5201 L22: 2.0857 REMARK 3 L33: 2.5099 L12: -0.5935 REMARK 3 L13: -1.1220 L23: 0.5136 REMARK 3 S TENSOR REMARK 3 S11: 0.0031 S12: -0.5576 S13: -0.1812 REMARK 3 S21: 0.1882 S22: 0.0179 S23: -0.0198 REMARK 3 S31: 0.1947 S32: 0.2225 S33: -0.0210 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 9.4984 24.1469 7.1654 REMARK 3 T TENSOR REMARK 3 T11: 0.1086 T22: 0.1377 REMARK 3 T33: 0.0890 T12: -0.0126 REMARK 3 T13: 0.0281 T23: 0.0160 REMARK 3 L TENSOR REMARK 3 L11: 1.4788 L22: 5.4489 REMARK 3 L33: 1.8017 L12: -0.3617 REMARK 3 L13: -0.0502 L23: -1.0082 REMARK 3 S TENSOR REMARK 3 S11: 0.1166 S12: 0.0633 S13: 0.2587 REMARK 3 S21: -0.0342 S22: -0.1269 S23: -0.0192 REMARK 3 S31: -0.2933 S32: -0.1040 S33: 0.0103 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8OWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292129658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2.MULTIPLEX REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.969 REMARK 200 RESOLUTION RANGE LOW (A) : 45.079 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 53.60 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 9.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 45.04 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 45.90 REMARK 200 R MERGE FOR SHELL (I) : 0.06900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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, PARROT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS PH 8.5, PEG SMEAR LOW SEEDED FROM REMARK 280 CRYSTALS GROWN IN AMMONIUM NITRATE, PEG 3350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.01450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.50250 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.01450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.50250 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: 3730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 14.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 326 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 333 LIES ON A SPECIAL POSITION. 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 PRO A 330 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ALA B 0 REMARK 465 SER B 125 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 LYS A 444 CG CD CE NZ REMARK 470 LYS A 528 CG CD CE NZ REMARK 470 GLN B 1 CG CD OE1 NE2 REMARK 470 LYS B 77 CG CD CE NZ 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 HG SER A 359 HD21 ASN A 360 1.26 REMARK 500 HH TYR B 61 H ILE B 71 1.31 REMARK 500 O LYS A 444 H GLY A 447 1.45 REMARK 500 O HOH A 747 O HOH A 751 1.97 REMARK 500 O HOH A 763 O HOH A 764 2.07 REMARK 500 O HOH B 332 O HOH B 334 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 302 O HOH B 319 2565 1.75 REMARK 500 O HOH A 762 O HOH A 762 2555 1.99 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 GLU A 484 CD GLU A 484 OE1 0.152 REMARK 500 GLU A 516 CD GLU A 516 OE1 0.071 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 ARG A 357 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 357 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 466 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES 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 THR A 333 -23.38 -141.52 REMARK 500 ALA A 352 41.34 -109.11 REMARK 500 ASN A 487 19.02 56.66 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 ARG B 39 0.11 SIDE CHAIN REMARK 500 ARG B 73 0.07 SIDE CHAIN 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 763 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 764 DISTANCE = 6.43 ANGSTROMS DBREF 8OWW A 330 531 UNP P0DTC2 SPIKE_SARS2 330 531 DBREF 8OWW B 0 125 PDB 8OWW 8OWW 0 125 SEQRES 1 A 202 PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE SEQRES 2 A 202 ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG SEQRES 3 A 202 LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU SEQRES 4 A 202 TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY SEQRES 5 A 202 VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN SEQRES 6 A 202 VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL SEQRES 7 A 202 ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP SEQRES 8 A 202 TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL SEQRES 9 A 202 ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY SEQRES 10 A 202 GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER SEQRES 11 A 202 ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE SEQRES 12 A 202 TYR GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY SEQRES 13 A 202 PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN SEQRES 14 A 202 PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL SEQRES 15 A 202 VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL SEQRES 16 A 202 CYS GLY PRO LYS LYS SER THR SEQRES 1 B 125 ALA GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL SEQRES 2 B 125 GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA VAL PHE SEQRES 3 B 125 GLY SER THR LEU ASP ASN TYR SER VAL GLY TRP PHE ARG SEQRES 4 B 125 GLN LEU PRO GLY LYS GLU ARG GLU GLY LEU ALA CYS PHE SEQRES 5 B 125 SER ARG ARG TYR GLY ALA PRO TYR TYR ALA ASP SER ALA SEQRES 6 B 125 LYS ASP ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 B 125 THR VAL ASP LEU GLN LEU ASN GLY LEU LYS PRO GLU ASP SEQRES 8 B 125 THR ALA VAL TYR TYR CYS ALA THR ARG SER GLY PRO TYR SEQRES 9 B 125 CYS THR THR SER VAL SER ASP PHE ASP ASP TRP GLY ARG SEQRES 10 B 125 GLY THR GLN VAL THR VAL SER SER HET NAG A 601 28 HET EDO A 602 10 HET EDO A 603 10 HET EDO A 604 10 HET EDO A 605 10 HET GOL A 606 14 HET GOL B 201 14 HET NO3 B 202 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM NO3 NITRATE 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 EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG C8 H15 N O6 FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 10 NO3 N O3 1- FORMUL 11 HOH *100(H2 O) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 ASP A 364 ASN A 370 1 7 HELIX 4 AA4 SER A 383 ASP A 389 5 7 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 SER A 438 SER A 443 1 6 HELIX 8 AA8 GLY A 502 TYR A 505 5 4 HELIX 9 AA9 ASP B 63 LYS B 66 5 4 HELIX 10 AB1 LYS B 88 THR B 92 5 5 HELIX 11 AB2 SER B 108 PHE B 112 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N LYS A 378 O VAL A 433 SHEET 1 AA2 3 CYS A 361 VAL A 362 0 SHEET 2 AA2 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA2 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 GLN B 4 SER B 8 0 SHEET 2 AA5 4 LEU B 19 PHE B 26 -1 O PHE B 26 N GLN B 4 SHEET 3 AA5 4 THR B 79 LEU B 84 -1 O LEU B 84 N LEU B 19 SHEET 4 AA5 4 PHE B 69 ASP B 74 -1 N THR B 70 O GLN B 83 SHEET 1 AA6 6 GLY B 11 VAL B 13 0 SHEET 2 AA6 6 THR B 119 VAL B 123 1 O GLN B 120 N GLY B 11 SHEET 3 AA6 6 ALA B 93 SER B 101 -1 N TYR B 95 O THR B 119 SHEET 4 AA6 6 TYR B 33 GLN B 40 -1 N PHE B 38 O TYR B 96 SHEET 5 AA6 6 ARG B 46 SER B 53 -1 O GLU B 47 N ARG B 39 SHEET 6 AA6 6 ALA B 58 TYR B 61 -1 O TYR B 60 N CYS B 51 SHEET 1 AA7 4 GLY B 11 VAL B 13 0 SHEET 2 AA7 4 THR B 119 VAL B 123 1 O GLN B 120 N GLY B 11 SHEET 3 AA7 4 ALA B 93 SER B 101 -1 N TYR B 95 O THR B 119 SHEET 4 AA7 4 ASP B 114 TRP B 115 -1 O ASP B 114 N THR B 99 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.04 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.22 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.19 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.17 SSBOND 5 CYS B 23 CYS B 97 1555 1555 2.25 SSBOND 6 CYS B 51 CYS B 105 1555 1555 2.25 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.39 CRYST1 45.038 70.029 109.005 90.00 90.00 90.00 P 2 21 21 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 0.022203 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009174 0.00000