HEADER IMMUNE SYSTEM 28-MAR-21 7EH3 TITLE STRUCTURE OF NANOBODY NB23 IN SOLUTION USING NMR SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NB23; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SINGLE-DOMAIN ANTIBODY, ANTIBODY FRAGMENT, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.PERCIPALLE,Y.HUNASHAL,G.ESPOSITO,F.FOGOLARI REVDAT 2 14-JUN-23 7EH3 1 REMARK REVDAT 1 14-JUL-21 7EH3 0 JRNL AUTH M.PERCIPALLE,Y.HUNASHAL,J.STEYAERT,F.FOGOLARI,G.ESPOSITO JRNL TITL STRUCTURE OF NANOBODY NB23. JRNL REF MOLECULES V. 26 2021 JRNL REFN ESSN 1420-3049 JRNL PMID 34207949 JRNL DOI 10.3390/MOLECULES26123567 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PONDEROSA, PONDEROSA-C/S, NAMD NAMD2 REMARK 3 AUTHORS : LEE W, KIM JH, WESTLER WM, MARKLEY JL (PONDEROSA), REMARK 3 LEE W, STARK JL, MARKLEY JL (PONDEROSA-C/S), KALE REMARK 3 L, SKEEL R, BHANDARKAR M, BRUNNER R, GURSOY A, REMARK 3 KRAWETZ N, PHILLIPS J, SHI- NOZAKI A, VARADARAJAN REMARK 3 K, SCHULTEN K (NAMD) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7EH3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021309. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298 REMARK 210 PH : 6.95; 6.95; 6.95; 6.95 REMARK 210 IONIC STRENGTH : 21 (SODIUM CHLORIDE); 0; 6.3; 20 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 250 UM [U-10% 13C; U-100% 15N] REMARK 210 NB23, 10 MM SODIUM PHOSPHATE, 5 % REMARK 210 D2O, 19.5 MM TRIS, 21 MM SODIUM REMARK 210 CHLORIDE, 95% H2O/5% D2O; 290 UM REMARK 210 [U-10% 13C; U-100% 15N] NB23, 10 REMARK 210 MM SODIUM PHOSPHATE, 5 % D2O, 95% REMARK 210 H2O/5% D2O; 190 UM NB23, 10 MM REMARK 210 SODIUM PHOSPHATE, 5 % D2O, 6.3 REMARK 210 MM SODIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 100 UM NB23, 10 MM SODIUM REMARK 210 PHOSPHATE, 100 % D2O, 20 MM REMARK 210 SODIUM CHLORIDE, 100% D2O; 190 REMARK 210 UM NB23, 10 MM SODIUM PHOSPHATE, REMARK 210 100 % D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N TROSY; REMARK 210 3D CBCANH; 3D CBCA(CO)NH; 3D REMARK 210 HNCA; 3D C(CO)NH; 3D H(CCO)NH; REMARK 210 3D HBHA(CO)NH; 3D HNCO; 3D HN(CA) REMARK 210 CO; 2D 1H-1H TOCSY; 3D 1H-15N REMARK 210 NOESY; 2D HBCBCGCDHD; 2D REMARK 210 HBCBCGCDCEHE; 2D 1H-1H NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D 1H-13C REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFAM-SPARKY, CS REMARK 210 -ROSETTA, MOLPROBITY, PONDEROSA, REMARK 210 PONDEROSA-C/S, PROCHECK / REMARK 210 PROCHECK-NMR, PYMOL, TALOS-N REMARK 210 METHOD USED : ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 MET A 0 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 VAL A 48 -50.59 -122.16 REMARK 500 2 SER A 85 70.99 52.13 REMARK 500 2 ASP A 106 53.05 -150.90 REMARK 500 3 ASP A 106 104.78 -162.65 REMARK 500 4 TYR A 103 146.79 61.00 REMARK 500 4 ASP A 106 60.30 -174.66 REMARK 500 5 VAL A 48 -54.05 -120.09 REMARK 500 5 ARG A 67 -51.67 -123.93 REMARK 500 5 TYR A 103 137.02 59.76 REMARK 500 5 ASP A 106 64.34 -154.83 REMARK 500 5 TYR A 110 40.44 -84.65 REMARK 500 6 SER A 85 71.02 54.22 REMARK 500 6 TYR A 104 45.56 -84.24 REMARK 500 6 ASP A 106 147.81 -173.79 REMARK 500 6 GLN A 121 15.18 56.79 REMARK 500 7 THR A 28 36.46 -92.58 REMARK 500 7 ASP A 106 87.28 -156.55 REMARK 500 8 ARG A 27 161.62 56.97 REMARK 500 8 ASN A 57 96.44 65.60 REMARK 500 8 ASP A 106 107.99 -160.12 REMARK 500 10 SER A 85 70.93 51.18 REMARK 500 10 LYS A 87 -167.85 -125.48 REMARK 500 10 PRO A 88 26.48 -62.02 REMARK 500 10 GLU A 89 49.26 -82.67 REMARK 500 10 ASP A 90 39.23 -73.84 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 8 TYR A 101 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 50808 RELATED DB: BMRB DBREF 7EH3 A 0 135 PDB 7EH3 7EH3 0 135 SEQRES 1 A 136 MET GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL SEQRES 2 A 136 GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SEQRES 3 A 136 GLY ARG THR PHE SER SER TYR ALA MET ALA TRP PHE ARG SEQRES 4 A 136 GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ARG ILE SEQRES 5 A 136 SER GLY VAL GLY THR ASN THR TYR TYR THR ASP SER VAL SEQRES 6 A 136 LYS GLY ARG VAL THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 A 136 THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 A 136 THR ALA VAL TYR TYR CYS ALA ALA SER ILE TYR GLY TYR SEQRES 9 A 136 TYR SER ASP THR SER TYR TYR THR ARG LEU ASN ASN TYR SEQRES 10 A 136 LEU TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 11 A 136 HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ARG A 27 SER A 30 5 4 HELIX 2 AA2 ASP A 62 LYS A 65 5 4 HELIX 3 AA3 LYS A 87 THR A 91 5 5 HELIX 4 AA4 ASP A 106 THR A 111 5 6 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 SER A 17 SER A 25 -1 O ALA A 23 N GLN A 5 SHEET 3 AA1 4 THR A 78 ASN A 84 -1 O LEU A 81 N LEU A 20 SHEET 4 AA1 4 VAL A 68 ASP A 73 -1 N SER A 71 O TYR A 80 SHEET 1 AA2 5 TYR A 59 TYR A 60 0 SHEET 2 AA2 5 GLU A 46 ILE A 51 -1 N ARG A 50 O TYR A 59 SHEET 3 AA2 5 TYR A 32 GLN A 39 -1 N MET A 34 O ILE A 51 SHEET 4 AA2 5 VAL A 93 ILE A 100 -1 O VAL A 93 N GLN A 39 SHEET 5 AA2 5 TYR A 116 TYR A 118 -1 O TYR A 118 N ALA A 98 SHEET 1 AA3 5 TYR A 59 TYR A 60 0 SHEET 2 AA3 5 GLU A 46 ILE A 51 -1 N ARG A 50 O TYR A 59 SHEET 3 AA3 5 TYR A 32 GLN A 39 -1 N MET A 34 O ILE A 51 SHEET 4 AA3 5 VAL A 93 ILE A 100 -1 O VAL A 93 N GLN A 39 SHEET 5 AA3 5 THR A 123 GLN A 124 -1 O THR A 123 N TYR A 94 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.05 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1