HEADER PROTEIN BINDING 07-NOV-24 9KFW TITLE NMR STRUCTURE OF AN AGONISTIC OX40 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_TAXID: 30538; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ANTIBODY, NANOBODY, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.NAGATA,N.KOBAYASHI,T.IEMURA,T.KITAWAKI,R.MAEDA,K.NAGATA,K.YAMAZAKI, AUTHOR 2 K.SHIRAKAWA,A.IMURA,A.TAKAORI-KONDO REVDAT 1 12-NOV-25 9KFW 0 JRNL AUTH T.IEMURA,T.KITAWAKI,R.MAEDA,K.NAGATA,K.YAMAZAKI,K.SHIRAKAWA, JRNL AUTH 2 N.KOBAYASHI,T.NAGATA,A.IMURA,A.TAKAORI-KONDO JRNL TITL EPITOPE-DIRECTED CLONE DISCOVERY AND ENGINEERING OF AN JRNL TITL 2 AGONISTIC OX40 NANOBODY FOR ENHANCED IN VIVO EFFICACY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING, IMPLICIT WATER REMARK 4 REMARK 4 9KFW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300050523. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 470 UM [U-13C; U-15N] NANOBODY, REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HNCA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D C(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MAGRO, CYANA, NMRPIPE REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 1 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 9 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 13 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 17 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 17 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 19 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 20 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 4.2 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 1 THR A 105 -179.55 -69.41 REMARK 500 1 MET A 109 38.75 -75.57 REMARK 500 1 TYR A 117 -76.19 -81.51 REMARK 500 2 VAL A 48 -63.26 -109.01 REMARK 500 2 VAL A 111 45.03 -76.22 REMARK 500 3 ASP A 100 53.10 -69.22 REMARK 500 4 HIS A 112 33.64 -88.33 REMARK 500 4 GLU A 113 76.04 54.37 REMARK 500 4 TYR A 115 -1.47 -140.06 REMARK 500 5 GLU A 46 26.62 -141.20 REMARK 500 5 ASP A 100 35.79 -69.40 REMARK 500 5 ASP A 101 47.98 -79.18 REMARK 500 5 GLN A 107 46.88 -81.19 REMARK 500 5 HIS A 112 -22.64 -145.36 REMARK 500 5 GLU A 116 -38.12 -136.93 REMARK 500 6 VAL A 48 -65.77 -108.83 REMARK 500 6 SER A 54 13.51 54.46 REMARK 500 6 ASP A 100 57.20 -67.79 REMARK 500 6 THR A 105 21.30 -67.99 REMARK 500 7 ASP A 100 39.44 -69.72 REMARK 500 8 VAL A 48 -65.16 -123.99 REMARK 500 8 SER A 54 14.42 51.11 REMARK 500 8 GLU A 116 38.50 -142.94 REMARK 500 9 GLN A 107 32.74 -75.34 REMARK 500 10 VAL A 48 -65.27 -121.48 REMARK 500 10 SER A 54 5.11 56.69 REMARK 500 10 HIS A 112 40.27 -75.87 REMARK 500 10 TYR A 117 74.23 41.22 REMARK 500 11 VAL A 48 -65.78 -121.57 REMARK 500 11 GLN A 107 41.21 -84.86 REMARK 500 11 PRO A 114 43.63 -78.51 REMARK 500 11 TYR A 115 84.26 52.75 REMARK 500 12 VAL A 48 -60.68 -100.71 REMARK 500 12 SER A 53 -16.02 59.86 REMARK 500 12 ASP A 100 50.30 -69.83 REMARK 500 12 THR A 105 -28.13 -158.57 REMARK 500 12 VAL A 111 10.93 -66.18 REMARK 500 12 HIS A 112 72.75 55.49 REMARK 500 13 VAL A 48 -62.12 -103.45 REMARK 500 13 ASP A 100 61.77 -68.23 REMARK 500 13 GLU A 113 166.16 67.26 REMARK 500 14 GLN A 107 84.71 -69.23 REMARK 500 14 TRP A 120 -3.40 -148.60 REMARK 500 14 GLN A 122 -28.97 -148.02 REMARK 500 15 VAL A 48 -79.28 -129.75 REMARK 500 15 SER A 54 6.74 58.07 REMARK 500 15 THR A 105 -10.79 -143.17 REMARK 500 15 VAL A 111 45.95 -74.98 REMARK 500 15 HIS A 112 26.67 -75.57 REMARK 500 16 SER A 54 7.76 55.35 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. 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 ARG A 72 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36708 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF AN AGONISTIC OX40 NANOBODY DBREF 9KFW A 1 130 PDB 9KFW 9KFW 1 130 SEQRES 1 A 130 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 130 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 130 PHE THR LEU ASP TYR TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 A 130 ALA PRO GLY LYS GLU ARG GLU GLY VAL SER ALA ILE SER SEQRES 5 A 130 SER SER GLY GLY SER THR ASN TYR ALA ASP SER VAL LYS SEQRES 6 A 130 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 A 130 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 130 ALA VAL TYR TYR CYS ALA ALA VAL ASP ASP VAL GLY THR SEQRES 9 A 130 THR VAL GLN ALA MET ALA VAL HIS GLU PRO TYR GLU TYR SEQRES 10 A 130 ASP TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HELIX 1 AA1 THR A 28 TYR A 32 5 5 HELIX 2 AA2 LYS A 87 THR A 91 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O VAL A 79 N CYS A 22 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N THR A 69 O GLN A 82 SHEET 1 AA2 6 LEU A 11 VAL A 12 0 SHEET 2 AA2 6 THR A 124 VAL A 128 1 O THR A 127 N VAL A 12 SHEET 3 AA2 6 ALA A 92 VAL A 99 -1 N TYR A 94 O THR A 124 SHEET 4 AA2 6 ALA A 33 GLN A 39 -1 N PHE A 37 O TYR A 95 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O SER A 49 N TRP A 36 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O ASN A 59 N ALA A 50 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.03 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