HEADER VIRAL PROTEIN 30-OCT-25 9YZ8 TITLE CRYSTAL STRUCTURE OF VHH MOD203 IN COMPLEX WITH SARS-COV-2 KP.3 RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SARS-COV-2 KP.3 RBD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VHH MOD203; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 8 ORGANISM_TAXID: 9844; SOURCE 9 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS COVID, SARS-COV-2, SPIKE PROTEIN, RBD, NEUTRALIZING ANTIBODY, MRNA, KEYWDS 2 VHH, NANOBODY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.R.LACIAK,M.F.BENDER,A.SHARMA REVDAT 1 12-AUG-26 9YZ8 0 JRNL AUTH A.Z.WEC,A.CHO,S.PECETTA,J.HU,M.F.BENDER,A.R.LACIAK,J.HOU, JRNL AUTH 2 A.SHARMA,N.BOPP,S.SAZINSKY,D.MONTES-BERRUETA,T.SPEIDEL, JRNL AUTH 3 D.LEE,P.B.J.REDDY,Y.CAO,A.CARFI,W.R.SCHIEF,L.M.WALKER JRNL TITL MULTIPLEXED DELIVERY OF MRNA-ENCODED BISPECIFIC ANTIBODIES JRNL TITL 2 CONSTRAINS VIRAL ESCAPE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 36387 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1950 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2665 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 141 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2484 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : 0.49000 REMARK 3 B12 (A**2) : -0.08000 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.963 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2692 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2444 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3630 ; 1.546 ; 1.812 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5633 ; 0.595 ; 1.737 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 7.393 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ;13.000 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 392 ;12.931 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.190 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3158 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 672 ; 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): 1271 ; 2.050 ; 2.697 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1271 ; 2.050 ; 2.697 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1587 ; 3.046 ; 4.822 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1588 ; 3.046 ; 4.823 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1421 ; 3.285 ; 3.280 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1422 ; 3.284 ; 3.281 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2037 ; 4.864 ; 5.757 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 11207 ; 6.934 ;34.120 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 11208 ; 6.934 ;34.120 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 335 A 527 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8952 45.2841 5.0919 REMARK 3 T TENSOR REMARK 3 T11: 0.0899 T22: 0.1621 REMARK 3 T33: 0.1731 T12: -0.0210 REMARK 3 T13: 0.0100 T23: 0.0429 REMARK 3 L TENSOR REMARK 3 L11: 3.5517 L22: 1.2763 REMARK 3 L33: 3.0026 L12: -0.2573 REMARK 3 L13: -0.8401 L23: 0.2415 REMARK 3 S TENSOR REMARK 3 S11: -0.0156 S12: -0.2021 S13: -0.5653 REMARK 3 S21: 0.1129 S22: -0.0263 S23: 0.3508 REMARK 3 S31: 0.3808 S32: -0.4486 S33: 0.0420 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 : B 1 B 113 REMARK 3 ORIGIN FOR THE GROUP (A): 23.7403 74.9828 -5.7753 REMARK 3 T TENSOR REMARK 3 T11: 0.1621 T22: 0.0453 REMARK 3 T33: 0.0295 T12: 0.0531 REMARK 3 T13: 0.0419 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 2.0877 L22: 6.6134 REMARK 3 L33: 1.7392 L12: -0.2429 REMARK 3 L13: -0.2962 L23: 0.4670 REMARK 3 S TENSOR REMARK 3 S11: 0.0862 S12: -0.0048 S13: 0.2158 REMARK 3 S21: 0.2556 S22: -0.0029 S23: 0.0656 REMARK 3 S31: -0.3467 S32: 0.0201 S33: -0.0833 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 REMARK 4 REMARK 4 9YZ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000300619. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-24 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 : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000034 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38354 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 2.74300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE TRIBASIC, PH 5.0; REMARK 280 32% W/V PEG MME 550, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 30.18933 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 15.09467 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 15.09467 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 30.18933 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 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 373 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 GLN A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 VAL A 332 REMARK 465 THR A 333 REMARK 465 ASN A 334 REMARK 465 LEU A 516 REMARK 465 LEU A 517 REMARK 465 HIS A 518 REMARK 465 GLY A 528 REMARK 465 GLY A 529 REMARK 465 LEU A 530 REMARK 465 GLU A 531 REMARK 465 VAL A 532 REMARK 465 LEU A 533 REMARK 465 PHE A 534 REMARK 465 GLN A 535 REMARK 465 GLY B 114 REMARK 465 SER B 115 REMARK 465 GLY B 116 REMARK 465 GLY B 117 REMARK 465 GLY B 118 REMARK 465 HIS B 119 REMARK 465 HIS B 120 REMARK 465 HIS B 121 REMARK 465 HIS B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 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 466 NE - CZ - NH2 ANGL. DEV. = 3.6 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 ASN A 370 113.99 -163.69 REMARK 500 ASN A 422 -55.14 -127.03 REMARK 500 LYS A 481 69.31 -113.30 REMARK 500 PRO A 526 30.84 -78.64 REMARK 500 ALA B 88 167.13 175.33 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 A 357 0.18 SIDE CHAIN REMARK 500 ARG A 466 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9YZ9 RELATED DB: PDB REMARK 900 RELATED ID: 9YZ7 RELATED DB: PDB DBREF 9YZ8 A 329 535 PDB 9YZ8 9YZ8 329 535 DBREF 9YZ8 B 1 124 PDB 9YZ8 9YZ8 1 124 SEQRES 1 A 207 GLN PRO ASN VAL THR ASN LEU CYS PRO PHE HIS GLU VAL SEQRES 2 A 207 PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN SEQRES 3 A 207 ARG THR ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL SEQRES 4 A 207 LEU TYR ASN PHE ALA PRO PHE PHE ALA PHE LYS CYS TYR SEQRES 5 A 207 GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR SEQRES 6 A 207 ASN VAL TYR ALA ASP SER PHE VAL ILE LYS GLY ASN GLU SEQRES 7 A 207 VAL SER GLN ILE ALA PRO GLY GLN THR GLY ASN ILE ALA SEQRES 8 A 207 ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS SEQRES 9 A 207 VAL ILE ALA TRP ASN SER ASN LYS LEU ASP SER LYS HIS SEQRES 10 A 207 SER GLY ASN TYR ASP TYR TRP TYR ARG SER LEU ARG LYS SEQRES 11 A 207 SER LYS LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU SEQRES 12 A 207 ILE TYR GLN ALA GLY ASN LYS PRO CYS LYS GLY LYS GLY SEQRES 13 A 207 PRO ASN CYS TYR PHE PRO LEU GLU SER TYR GLY PHE ARG SEQRES 14 A 207 PRO THR TYR GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL SEQRES 15 A 207 VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL SEQRES 16 A 207 CYS GLY PRO LYS GLY GLY LEU GLU VAL LEU PHE GLN SEQRES 1 B 136 GLN VAL GLN LEU VAL GLN SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 136 PRO GLY GLY SER LEU ARG LEU SER CYS THR ALA SER GLY SEQRES 3 B 136 PHE ARG LEU ASP ASP TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 B 136 ALA PRO GLY LYS GLU ARG VAL GLY ILE SER CYS MET SER SEQRES 5 B 136 ALA SER ASN ASP ASP PHE THR TYR TYR SER ASP SER VAL SEQRES 6 B 136 LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 B 136 THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 B 136 THR ALA VAL TYR TYR CYS ALA THR ALA ALA CYS SER GLY SEQRES 9 B 136 THR TYR TYR HIS THR ASN GLU TYR ASP TYR TRP GLY GLN SEQRES 10 B 136 GLY THR GLN VAL THR VAL SER SER GLY SER GLY GLY GLY SEQRES 11 B 136 HIS HIS HIS HIS HIS HIS HET NAG A 601 14 HET NAG A 602 14 HET EDO A 603 4 HET EDO A 604 4 HET EDO A 605 4 HET EDO A 606 4 HET EDO A 607 4 HET EDO A 608 4 HET EDO A 609 4 HET EDO A 610 4 HET EDO A 611 4 HET PEG A 612 7 HET PEG A 613 7 HET PEG A 614 7 HET EDO B 201 4 HET EDO B 202 4 HET EDO B 203 4 HET EDO B 204 4 HET EDO B 205 4 HET EDO B 206 4 HET EDO B 207 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER 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 2(C8 H15 N O6) FORMUL 5 EDO 16(C2 H6 O2) FORMUL 14 PEG 3(C4 H10 O3) FORMUL 24 HOH *190(H2 O) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 ASP A 364 TYR A 369 5 6 HELIX 3 AA3 SER A 383 ASP A 389 5 7 HELIX 4 AA4 ASN A 405 ILE A 410 5 6 HELIX 5 AA5 GLY A 416 ASN A 422 1 7 HELIX 6 AA6 SER A 438 SER A 443 1 6 HELIX 7 AA7 GLY A 501 HIS A 504 5 4 HELIX 8 AA8 ARG B 28 TYR B 32 5 5 HELIX 9 AA9 LYS B 83 THR B 87 5 5 SHEET 1 AA1 4 ASN A 354 ILE A 358 0 SHEET 2 AA1 4 CYS A 391 LYS A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 4 PRO A 520 CYS A 524 -1 O VAL A 523 N PHE A 392 SHEET 4 AA1 4 CYS A 361 VAL A 362 1 N CYS A 361 O CYS A 524 SHEET 1 AA2 5 ASN A 354 ILE A 358 0 SHEET 2 AA2 5 CYS A 391 LYS A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA2 5 PRO A 506 GLU A 515 -1 O VAL A 511 N ASP A 398 SHEET 4 AA2 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 510 SHEET 5 AA2 5 PHE A 375 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA3 2 TRP A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 491 SER A 493 -1 O GLU A 492 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 487 TYR A 488 -1 O TYR A 488 N TYR A 473 SHEET 1 AA5 4 GLN B 3 SER B 7 0 SHEET 2 AA5 4 LEU B 18 SER B 25 -1 O THR B 23 N VAL B 5 SHEET 3 AA5 4 THR B 77 MET B 82 -1 O MET B 82 N LEU B 18 SHEET 4 AA5 4 PHE B 67 ASP B 72 -1 N THR B 68 O GLN B 81 SHEET 1 AA6 6 GLY B 10 VAL B 12 0 SHEET 2 AA6 6 THR B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 AA6 6 ALA B 88 THR B 94 -1 N TYR B 90 O THR B 107 SHEET 4 AA6 6 ILE B 34 GLN B 39 -1 N PHE B 37 O TYR B 91 SHEET 5 AA6 6 VAL B 46 MET B 51 -1 O SER B 49 N TRP B 36 SHEET 6 AA6 6 THR B 57 TYR B 59 -1 O TYR B 58 N CYS B 50 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.05 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.10 SSBOND 3 CYS A 391 CYS A 524 1555 1555 2.05 SSBOND 4 CYS A 480 CYS A 487 1555 1555 2.20 SSBOND 5 CYS B 22 CYS B 92 1555 1555 2.30 SSBOND 6 CYS B 50 CYS B 97 1555 1555 2.24 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.43 LINK ND2 ASN A 354 C1 NAG A 602 1555 1555 1.44 CRYST1 136.490 136.490 45.284 90.00 90.00 120.00 P 32 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 0.007327 0.004230 0.000000 0.00000 SCALE2 0.000000 0.008460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022083 0.00000 CONECT 14 225 CONECT 77 2518 CONECT 168 2532 CONECT 225 14 CONECT 374 779 CONECT 464 1526 CONECT 779 374 CONECT 1202 1249 CONECT 1249 1202 CONECT 1526 464 CONECT 1698 2301 CONECT 1923 2329 CONECT 2301 1698 CONECT 2329 1923 CONECT 2518 77 2519 2529 CONECT 2519 2518 2520 2526 CONECT 2520 2519 2521 2527 CONECT 2521 2520 2522 2528 CONECT 2522 2521 2523 2529 CONECT 2523 2522 2530 CONECT 2524 2525 2526 2531 CONECT 2525 2524 CONECT 2526 2519 2524 CONECT 2527 2520 CONECT 2528 2521 CONECT 2529 2518 2522 CONECT 2530 2523 CONECT 2531 2524 CONECT 2532 168 2533 2543 CONECT 2533 2532 2534 2540 CONECT 2534 2533 2535 2541 CONECT 2535 2534 2536 2542 CONECT 2536 2535 2537 2543 CONECT 2537 2536 2544 CONECT 2538 2539 2540 2545 CONECT 2539 2538 CONECT 2540 2533 2538 CONECT 2541 2534 CONECT 2542 2535 CONECT 2543 2532 2536 CONECT 2544 2537 CONECT 2545 2538 CONECT 2546 2547 2548 CONECT 2547 2546 CONECT 2548 2546 2549 CONECT 2549 2548 CONECT 2550 2551 2552 CONECT 2551 2550 CONECT 2552 2550 2553 CONECT 2553 2552 CONECT 2554 2555 2556 CONECT 2555 2554 CONECT 2556 2554 2557 CONECT 2557 2556 CONECT 2558 2559 2560 CONECT 2559 2558 CONECT 2560 2558 2561 CONECT 2561 2560 CONECT 2562 2563 2564 CONECT 2563 2562 CONECT 2564 2562 2565 CONECT 2565 2564 CONECT 2566 2567 2568 CONECT 2567 2566 CONECT 2568 2566 2569 CONECT 2569 2568 CONECT 2570 2571 2572 CONECT 2571 2570 CONECT 2572 2570 2573 CONECT 2573 2572 CONECT 2574 2575 2576 CONECT 2575 2574 CONECT 2576 2574 2577 CONECT 2577 2576 CONECT 2578 2579 2580 CONECT 2579 2578 CONECT 2580 2578 2581 CONECT 2581 2580 CONECT 2582 2583 2584 CONECT 2583 2582 CONECT 2584 2582 2585 CONECT 2585 2584 2586 CONECT 2586 2585 2587 CONECT 2587 2586 2588 CONECT 2588 2587 CONECT 2589 2590 2591 CONECT 2590 2589 CONECT 2591 2589 2592 CONECT 2592 2591 2593 CONECT 2593 2592 2594 CONECT 2594 2593 2595 CONECT 2595 2594 CONECT 2596 2597 2598 CONECT 2597 2596 CONECT 2598 2596 2599 CONECT 2599 2598 2600 CONECT 2600 2599 2601 CONECT 2601 2600 2602 CONECT 2602 2601 CONECT 2603 2604 2605 CONECT 2604 2603 CONECT 2605 2603 2606 CONECT 2606 2605 CONECT 2607 2608 2609 CONECT 2608 2607 CONECT 2609 2607 2610 CONECT 2610 2609 CONECT 2611 2612 2613 CONECT 2612 2611 CONECT 2613 2611 2614 CONECT 2614 2613 CONECT 2615 2616 2617 CONECT 2616 2615 CONECT 2617 2615 2618 CONECT 2618 2617 CONECT 2619 2620 2621 CONECT 2620 2619 CONECT 2621 2619 2622 CONECT 2622 2621 CONECT 2623 2624 2625 CONECT 2624 2623 CONECT 2625 2623 2626 CONECT 2626 2625 CONECT 2627 2628 2629 CONECT 2628 2627 CONECT 2629 2627 2630 CONECT 2630 2629 MASTER 384 0 21 9 23 0 0 6 2787 2 127 27 END