HEADER VIRAL PROTEIN 06-MAY-20 6YZ5 TITLE H11-D4 COMPLEX WITH SARS-COV-2 RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: E; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: TRUNCATED VERSION EXPRESSED; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NANOBODY H11-D4; COMPND 9 CHAIN: F; COMPND 10 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 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 11 ORGANISM_COMMON: LLAMA; SOURCE 12 ORGANISM_TAXID: 9844; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOBODY, COMPLEX, SARS-COV-2, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.H.NAISMITH,J.HUO,H.MIKOLAJEK,P.WARD,M.DUMOUX,R.J.OWENS,A.LE BAS REVDAT 4 13-NOV-24 6YZ5 1 REMARK REVDAT 3 24-JAN-24 6YZ5 1 HETSYN REVDAT 2 29-JUL-20 6YZ5 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 03-JUN-20 6YZ5 0 JRNL AUTH J.H.NAISMITH JRNL TITL H11-D4 COMPLEX WITH SARS-COV-2 RBD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 40120 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2158 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2895 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2533 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 241 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : -1.89000 REMARK 3 B12 (A**2) : 0.29000 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): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.394 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2748 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2438 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3727 ; 1.441 ; 1.664 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5647 ; 1.353 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 344 ; 7.059 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;29.923 ;21.486 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 413 ;12.848 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;19.050 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 340 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3128 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 647 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : E 334 E 528 REMARK 3 ORIGIN FOR THE GROUP (A): 60.1560 19.0990 31.8930 REMARK 3 T TENSOR REMARK 3 T11: 0.0068 T22: 0.0551 REMARK 3 T33: 0.0898 T12: 0.0028 REMARK 3 T13: 0.0025 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.1723 L22: 1.6077 REMARK 3 L33: 1.4279 L12: 0.5204 REMARK 3 L13: 0.1883 L23: 0.6814 REMARK 3 S TENSOR REMARK 3 S11: 0.0479 S12: -0.1707 S13: 0.0090 REMARK 3 S21: -0.0042 S22: -0.0154 S23: -0.0636 REMARK 3 S31: 0.0094 S32: 0.0622 S33: -0.0325 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 1 F 127 REMARK 3 ORIGIN FOR THE GROUP (A): 32.3100 0.6600 17.0500 REMARK 3 T TENSOR REMARK 3 T11: 0.0802 T22: 0.0921 REMARK 3 T33: 0.1330 T12: -0.0600 REMARK 3 T13: 0.0069 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 3.1527 L22: 1.6551 REMARK 3 L33: 2.9928 L12: 0.8860 REMARK 3 L13: 1.8606 L23: 0.3431 REMARK 3 S TENSOR REMARK 3 S11: 0.0527 S12: -0.3901 S13: 0.0678 REMARK 3 S21: 0.0058 S22: -0.1203 S23: 0.1809 REMARK 3 S31: 0.2024 S32: -0.4344 S33: 0.0676 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6YZ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-20 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) : 0.97623 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40120 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 19.70 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 6YLA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTALLIZATION BUFFER CONTAINING REMARK 280 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M MES PH 6.0, 20 % W/V PEG REMARK 280 8000. THE CRYSTALS GREW OVERNIGHT AND WERE FLASH COOLED IN A REMARK 280 SOLUTION CONTAINING THE MOTHER LIQUOR WITH 30 % (V/V) ETHYLENE REMARK 280 GLYCOL., VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.36333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 84.72667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 84.72667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.36333 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: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 PRO E 330 REMARK 465 ASN E 331 REMARK 465 ILE E 332 REMARK 465 THR E 333 REMARK 465 LYS E 529 REMARK 465 SER E 530 REMARK 465 THR E 531 REMARK 465 ASN E 532 REMARK 465 LYS E 533 REMARK 465 HIS E 534 REMARK 465 HIS E 535 REMARK 465 HIS E 536 REMARK 465 HIS E 537 REMARK 465 HIS E 538 REMARK 465 HIS E 539 REMARK 465 LYS F 128 REMARK 465 HIS F 129 REMARK 465 HIS F 130 REMARK 465 HIS F 131 REMARK 465 HIS F 132 REMARK 465 HIS F 133 REMARK 465 HIS F 134 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 E 729 O HOH E 729 6765 1.62 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 PHE E 377 89.19 -152.95 REMARK 500 VAL E 382 138.51 -174.75 REMARK 500 VAL E 382 138.70 -174.89 REMARK 500 ASN E 422 -56.00 -125.45 REMARK 500 THR F 28 -51.17 -120.46 REMARK 500 ARG F 67 -50.61 -122.43 REMARK 500 SER F 126 -105.65 -96.01 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 SER E 494 TYR E 495 148.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6YZ5 E 330 532 UNP P0DTC2 SPIKE_SARS2 330 532 DBREF 6YZ5 F 1 134 PDB 6YZ5 6YZ5 1 134 SEQADV 6YZ5 LYS E 533 UNP P0DTC2 EXPRESSION TAG SEQADV 6YZ5 HIS E 534 UNP P0DTC2 EXPRESSION TAG SEQADV 6YZ5 HIS E 535 UNP P0DTC2 EXPRESSION TAG SEQADV 6YZ5 HIS E 536 UNP P0DTC2 EXPRESSION TAG SEQADV 6YZ5 HIS E 537 UNP P0DTC2 EXPRESSION TAG SEQADV 6YZ5 HIS E 538 UNP P0DTC2 EXPRESSION TAG SEQADV 6YZ5 HIS E 539 UNP P0DTC2 EXPRESSION TAG SEQRES 1 E 210 PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE SEQRES 2 E 210 ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG SEQRES 3 E 210 LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU SEQRES 4 E 210 TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY SEQRES 5 E 210 VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN SEQRES 6 E 210 VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL SEQRES 7 E 210 ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP SEQRES 8 E 210 TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL SEQRES 9 E 210 ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY SEQRES 10 E 210 GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER SEQRES 11 E 210 ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE SEQRES 12 E 210 TYR GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY SEQRES 13 E 210 PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN SEQRES 14 E 210 PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL SEQRES 15 E 210 VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL SEQRES 16 E 210 CYS GLY PRO LYS LYS SER THR ASN LYS HIS HIS HIS HIS SEQRES 17 E 210 HIS HIS SEQRES 1 F 134 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU MET GLN SEQRES 2 F 134 ALA GLY GLY SER LEU ARG LEU SER CYS ALA VAL SER GLY SEQRES 3 F 134 ARG THR PHE SER THR ALA ALA MET GLY TRP PHE ARG GLN SEQRES 4 F 134 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE ARG SEQRES 5 F 134 TRP SER GLY GLY SER ALA TYR TYR ALA ASP SER VAL LYS SEQRES 6 F 134 GLY ARG PHE THR ILE SER ARG ASP LYS ALA LYS ASN THR SEQRES 7 F 134 VAL TYR LEU GLN MET ASN SER LEU LYS TYR GLU ASP THR SEQRES 8 F 134 ALA VAL TYR TYR CYS ALA ARG THR GLU ASN VAL ARG SER SEQRES 9 F 134 LEU LEU SER ASP TYR ALA THR TRP PRO TYR ASP TYR TRP SEQRES 10 F 134 GLY GLN GLY THR GLN VAL THR VAL SER SER LYS HIS HIS SEQRES 11 F 134 HIS HIS HIS HIS HET NAG E 601 14 HET EDO E 602 4 HET EDO E 603 4 HET EDO E 604 4 HET EDO E 605 4 HET EDO E 606 4 HET EDO E 607 4 HET EDO E 608 4 HET ACT E 609 4 HET ACT E 610 4 HET EDO E 611 4 HET EDO E 612 4 HET EDO E 613 4 HET EDO E 614 4 HET EDO F 201 4 HET ACT F 202 4 HET ACT F 203 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE 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 FORMUL 3 NAG C8 H15 N O6 FORMUL 4 EDO 12(C2 H6 O2) FORMUL 11 ACT 4(C2 H3 O2 1-) FORMUL 20 HOH *241(H2 O) HELIX 1 AA1 PRO E 337 ASN E 343 1 7 HELIX 2 AA2 SER E 349 TRP E 353 5 5 HELIX 3 AA3 TYR E 365 ASN E 370 1 6 HELIX 4 AA4 SER E 383 ASN E 388 1 6 HELIX 5 AA5 ASP E 405 ILE E 410 5 6 HELIX 6 AA6 GLY E 416 ASN E 422 1 7 HELIX 7 AA7 SER E 438 SER E 443 1 6 HELIX 8 AA8 GLY E 502 TYR E 505 5 4 HELIX 9 AA9 ASP F 62 LYS F 65 5 4 HELIX 10 AB1 LYS F 87 THR F 91 5 5 HELIX 11 AB2 LEU F 105 THR F 111 5 7 SHEET 1 AA1 5 ASN E 354 ILE E 358 0 SHEET 2 AA1 5 ASN E 394 ARG E 403 -1 O VAL E 395 N ILE E 358 SHEET 3 AA1 5 PRO E 507 GLU E 516 -1 O TYR E 508 N ILE E 402 SHEET 4 AA1 5 GLY E 431 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA1 5 THR E 376 TYR E 380 -1 N LYS E 378 O VAL E 433 SHEET 1 AA2 3 CYS E 361 VAL E 362 0 SHEET 2 AA2 3 VAL E 524 CYS E 525 1 O CYS E 525 N CYS E 361 SHEET 3 AA2 3 CYS E 391 PHE E 392 -1 N PHE E 392 O VAL E 524 SHEET 1 AA3 2 LEU E 452 ARG E 454 0 SHEET 2 AA3 2 LEU E 492 SER E 494 -1 O GLN E 493 N TYR E 453 SHEET 1 AA4 2 TYR E 473 GLN E 474 0 SHEET 2 AA4 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 SHEET 1 AA5 4 GLN F 3 SER F 7 0 SHEET 2 AA5 4 LEU F 18 SER F 25 -1 O ALA F 23 N VAL F 5 SHEET 3 AA5 4 THR F 78 MET F 83 -1 O MET F 83 N LEU F 18 SHEET 4 AA5 4 PHE F 68 ASP F 73 -1 N THR F 69 O GLN F 82 SHEET 1 AA6 6 GLY F 10 MET F 12 0 SHEET 2 AA6 6 THR F 121 VAL F 125 1 O THR F 124 N MET F 12 SHEET 3 AA6 6 ALA F 92 THR F 99 -1 N TYR F 94 O THR F 121 SHEET 4 AA6 6 ALA F 33 GLN F 39 -1 N PHE F 37 O TYR F 95 SHEET 5 AA6 6 GLU F 46 ARG F 52 -1 O GLU F 46 N ARG F 38 SHEET 6 AA6 6 ALA F 58 TYR F 60 -1 O TYR F 59 N ALA F 50 SHEET 1 AA7 4 GLY F 10 MET F 12 0 SHEET 2 AA7 4 THR F 121 VAL F 125 1 O THR F 124 N MET F 12 SHEET 3 AA7 4 ALA F 92 THR F 99 -1 N TYR F 94 O THR F 121 SHEET 4 AA7 4 TYR F 116 TRP F 117 -1 O TYR F 116 N ARG F 98 SSBOND 1 CYS E 336 CYS E 361 1555 1555 2.06 SSBOND 2 CYS E 379 CYS E 432 1555 1555 2.22 SSBOND 3 CYS E 391 CYS E 525 1555 1555 2.16 SSBOND 4 CYS E 480 CYS E 488 1555 1555 2.17 SSBOND 5 CYS F 22 CYS F 96 1555 1555 2.11 LINK ND2 ASN E 343 C1 NAG E 601 1555 1555 1.44 CRYST1 78.280 78.280 127.090 90.00 90.00 120.00 P 31 2 1 6 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 0.012775 0.007375 0.000000 0.00000 SCALE2 0.000000 0.014751 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007868 0.00000