1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Vranken, W. Tolkatchev, D. Xu, P. Tanha, J. Chen, Z. Narang, S. Ni, F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Biochemistry BICHAW 0033 0006-2960 41 8570 8579 10.1021/bi012169a 12093273 Solution structure of a llama single-domain antibody with hydrophobic residues typical of the VH/VL interface. 2002 10.2210/pdb1ieh/pdb pdb_00001ieh 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 14618.006 BRUC.D4.4 SINGLE DOMAIN ANTIBODY FROM A NAIVE LLAMA LIBRARY 1 man polymer no no DVQLQASGGGLVQPGGSLRVSCAASGFTFSSYHMAWVRQAPGKGLEWVSTINPGDGSTYYADSVKGRFTISRDNAKNTLY LQMNSLKSEDTAVYYCAKYSGGALDAWGQGTQVTVSSQSEQKLISEEDLNHHHHH DVQLQASGGGLVQPGGSLRVSCAASGFTFSSYHMAWVRQAPGKGLEWVSTINPGDGSTYYADSVKGRFTISRDNAKNTLY LQMNSLKSEDTAVYYCAKYSGGALDAWGQGTQVTVSSQSEQKLISEEDLNHHHHH A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n llama Lama Escherichia sample 9844 Lama glama 562 Escherichia coli database_2 pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2002-08-07 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_spectrometer.model NMR data RCSB Y RCSB 2001-04-09 REL REL structures with the lowest energy 150 10 3D combined 13C/15N-separated NOESY 0.16 6.8 1 atm 303 K NO MANUAL ASSIGNMENTS OF NOE PEAKS WERE INITIALLY PERFORMED - THE GLOBAL FOLD OF THE PROTEIN WAS DETERMINED USING RESTRAINTS WITH LOW AMBIGUITY. THE SET OF GLOBAL FOLD STRUCTURES SERVED AS AN ASSIGNMENT FILTER TO REDUCE THE AMBIGUITY OF THE OTHER RESTRAINTS. THE RESTRAINT LIST AND STRUCTURES WERE FURTHER REFINED BY MANUALLY CHOOSING POSSIBILITIES FROM THE RESTRAINTS WITH LOW AMBIGUITY (BASED ON THE SPECTRA). simulated annealing using torsion angle and cartesian dynamics 1 lowest energy 10mM sodium phosphate 150mM NaCl 0.2mM EDTA 90% H2O/10% D2O Frank Delaglio, Stephan Grzesiek, Ad Bax, Geerten W. Vuister, Guang Zhu, John Pfeifer processing NMRPipe Bruce Johnson and Richard Blevins data analysis NMRView 4.1.2 J. Linge and M. Nilges structure solution ARIA 1.0 AT Brunger, PD Adams, GM Clore, WL DeLano, P Gros, RW Grosse-Kunstleve, JS Jiang, J Kuszewski, M Nilges, NS Pannu, RJ Read, LM Rice, T Simonson, GL Warren structure solution CNS 1.0 Linge, Nilges refinement ARIA 1.0 800 Bruker AVANCE ASP 1 n 1 ASP 1 A VAL 2 n 2 VAL 2 A GLN 3 n 3 GLN 3 A LEU 4 n 4 LEU 4 A GLN 5 n 5 GLN 5 A ALA 6 n 6 ALA 6 A SER 7 n 7 SER 7 A GLY 8 n 8 GLY 8 A GLY 9 n 9 GLY 9 A GLY 10 n 10 GLY 10 A LEU 11 n 11 LEU 11 A VAL 12 n 12 VAL 12 A GLN 13 n 13 GLN 13 A PRO 14 n 14 PRO 14 A GLY 15 n 15 GLY 15 A GLY 16 n 16 GLY 16 A SER 17 n 17 SER 17 A LEU 18 n 18 LEU 18 A ARG 19 n 19 ARG 19 A VAL 20 n 20 VAL 20 A SER 21 n 21 SER 21 A CYS 22 n 22 CYS 22 A ALA 23 n 23 ALA 23 A ALA 24 n 24 ALA 24 A SER 25 n 25 SER 25 A GLY 26 n 26 GLY 26 A PHE 27 n 27 PHE 27 A THR 28 n 28 THR 28 A PHE 29 n 29 PHE 29 A SER 30 n 30 SER 30 A SER 31 n 31 SER 31 A TYR 32 n 32 TYR 32 A HIS 33 n 33 HIS 33 A MET 34 n 34 MET 34 A ALA 35 n 35 ALA 35 A TRP 36 n 36 TRP 36 A VAL 37 n 37 VAL 37 A ARG 38 n 38 ARG 38 A GLN 39 n 39 GLN 39 A ALA 40 n 40 ALA 40 A PRO 41 n 41 PRO 41 A GLY 42 n 42 GLY 42 A LYS 43 n 43 LYS 43 A GLY 44 n 44 GLY 44 A LEU 45 n 45 LEU 45 A GLU 46 n 46 GLU 46 A TRP 47 n 47 TRP 47 A VAL 48 n 48 VAL 48 A SER 49 n 49 SER 49 A THR 50 n 50 THR 50 A ILE 51 n 51 ILE 51 A ASN 52 n 52 ASN 52 A PRO 53 n 53 PRO 53 A GLY 54 n 54 GLY 54 A ASP 55 n 55 ASP 55 A GLY 56 n 56 GLY 56 A SER 57 n 57 SER 57 A THR 58 n 58 THR 58 A TYR 59 n 59 TYR 59 A TYR 60 n 60 TYR 60 A ALA 61 n 61 ALA 61 A ASP 62 n 62 ASP 62 A SER 63 n 63 SER 63 A VAL 64 n 64 VAL 64 A LYS 65 n 65 LYS 65 A GLY 66 n 66 GLY 66 A ARG 67 n 67 ARG 67 A PHE 68 n 68 PHE 68 A THR 69 n 69 THR 69 A ILE 70 n 70 ILE 70 A SER 71 n 71 SER 71 A ARG 72 n 72 ARG 72 A ASP 73 n 73 ASP 73 A ASN 74 n 74 ASN 74 A ALA 75 n 75 ALA 75 A LYS 76 n 76 LYS 76 A ASN 77 n 77 ASN 77 A THR 78 n 78 THR 78 A LEU 79 n 79 LEU 79 A TYR 80 n 80 TYR 80 A LEU 81 n 81 LEU 81 A GLN 82 n 82 GLN 82 A MET 83 n 83 MET 83 A ASN 84 n 84 ASN 84 A SER 85 n 85 SER 85 A LEU 86 n 86 LEU 86 A LYS 87 n 87 LYS 87 A SER 88 n 88 SER 88 A GLU 89 n 89 GLU 89 A ASP 90 n 90 ASP 90 A THR 91 n 91 THR 91 A ALA 92 n 92 ALA 92 A VAL 93 n 93 VAL 93 A TYR 94 n 94 TYR 94 A TYR 95 n 95 TYR 95 A CYS 96 n 96 CYS 96 A ALA 97 n 97 ALA 97 A LYS 98 n 98 LYS 98 A TYR 99 n 99 TYR 99 A SER 100 n 100 SER 100 A GLY 101 n 101 GLY 101 A GLY 102 n 102 GLY 102 A ALA 103 n 103 ALA 103 A LEU 104 n 104 LEU 104 A ASP 105 n 105 ASP 105 A ALA 106 n 106 ALA 106 A TRP 107 n 107 TRP 107 A GLY 108 n 108 GLY 108 A GLN 109 n 109 GLN 109 A GLY 110 n 110 GLY 110 A THR 111 n 111 THR 111 A GLN 112 n 112 GLN 112 A VAL 113 n 113 VAL 113 A THR 114 n 114 THR 114 A VAL 115 n 115 VAL 115 A SER 116 n 116 SER 116 A SER 117 n 117 SER 117 A GLN 118 n 118 GLN 118 A SER 119 n 119 SER 119 A GLU 120 n 120 GLU 120 A GLN 121 n 121 GLN 121 A LYS 122 n 122 LYS 122 A LEU 123 n 123 LEU 123 A ILE 124 n 124 ILE 124 A SER 125 n 125 SER 125 A GLU 126 n 126 GLU 126 A GLU 127 n 127 GLU 127 A ASP 128 n 128 ASP 128 A LEU 129 n 129 LEU 129 A ASN 130 n 130 ASN 130 A HIS 131 n 131 HIS 131 A HIS 132 n 132 HIS 132 A HIS 133 n 133 HIS 133 A HIS 134 n 134 HIS 134 A HIS 135 n 135 HIS 135 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N SER 7 A N SER 7 A O SER 21 A O SER 21 A N LEU 18 A N LEU 18 A O MET 83 A O MET 83 A O TYR 80 A O TYR 80 A N SER 71 A N SER 71 A N VAL 12 A N VAL 12 A O THR 114 A O THR 114 A O VAL 113 A O VAL 113 A N ALA 92 A N ALA 92 A O TYR 95 A O TYR 95 A N VAL 37 A N VAL 37 A N TRP 36 A N TRP 36 A O SER 49 A O SER 49 A N THR 50 A N THR 50 A O TYR 59 A O TYR 59 2 A A HB3 H SER SER 116 117 1.32 3 A A HB3 H LEU ASN 129 130 1.33 5 A A H H ALA GLN 6 109 1.34 1 A SER 7 -171.82 -178.21 1 A PRO 14 -51.69 90.55 1 A SER 30 -78.23 30.24 1 A SER 31 -150.71 -34.85 1 A PRO 41 -31.80 93.35 1 A LYS 43 41.38 -155.74 1 A LEU 45 66.55 142.58 1 A ASP 62 75.55 -56.33 1 A ALA 75 -162.57 69.71 1 A LYS 76 -167.64 -16.21 1 A LYS 87 -162.24 45.85 1 A THR 91 -60.31 95.57 1 A ALA 92 -175.06 -163.93 1 A SER 100 -143.49 57.79 1 A ALA 106 63.43 111.97 1 A LYS 122 -157.80 -13.21 1 A LEU 123 63.33 111.60 1 A ILE 124 -131.38 -58.74 1 A GLU 126 -164.75 16.76 1 A GLU 127 61.31 109.04 1 A LEU 129 56.48 -147.24 1 A ASN 130 -152.70 -59.67 1 A HIS 131 -163.42 29.39 2 A PRO 14 -48.83 91.26 2 A SER 25 -172.60 111.35 2 A PHE 27 -168.06 -11.79 2 A THR 28 65.10 144.01 2 A SER 30 58.38 14.59 2 A LEU 45 64.66 153.38 2 A VAL 48 59.04 -75.94 2 A ASP 55 52.10 73.90 2 A SER 57 -65.05 -165.99 2 A ASP 62 71.41 -12.80 2 A ARG 67 -122.29 -65.01 2 A ALA 75 -168.93 -62.24 2 A LYS 87 -135.30 -57.68 2 A SER 88 -173.42 -20.91 2 A THR 91 -60.71 90.70 2 A ALA 92 -172.58 -171.06 2 A ALA 106 67.61 96.74 2 A SER 116 -159.70 -117.92 2 A SER 117 69.62 -13.75 2 A LYS 122 -90.00 48.53 2 A SER 125 57.83 -177.61 2 A GLU 126 55.66 -93.69 2 A HIS 133 59.61 -178.65 2 A HIS 134 55.40 85.66 3 A PRO 14 -49.03 91.33 3 A THR 28 -72.53 -116.09 3 A PHE 29 -177.52 -54.90 3 A PRO 41 -49.88 97.65 3 A LEU 45 65.72 124.97 3 A VAL 48 56.58 -77.98 3 A ASP 55 -76.62 -76.45 3 A SER 57 -59.71 -178.68 3 A ASP 62 75.79 -43.50 3 A ASN 74 -88.41 31.67 3 A ALA 75 -149.79 16.45 3 A LYS 87 -158.38 51.21 3 A THR 91 -61.44 95.09 3 A ALA 92 -177.34 -167.60 3 A ALA 106 76.52 -56.03 3 A TRP 107 44.53 -151.90 3 A GLN 118 -150.28 63.10 3 A ILE 124 54.80 86.29 3 A GLU 127 -132.39 -45.68 3 A LEU 129 -128.95 -129.55 3 A ASN 130 60.69 -97.85 4 A PRO 14 -51.91 92.76 4 A SER 25 -171.18 137.32 4 A PHE 27 -158.90 -12.69 4 A THR 28 65.14 141.92 4 A SER 31 -146.35 -28.62 4 A PRO 41 -57.89 91.91 4 A LEU 45 62.85 160.54 4 A VAL 48 56.57 -78.40 4 A PRO 53 -53.49 -73.42 4 A ASP 55 63.95 -80.30 4 A ASP 62 76.00 -48.30 4 A ARG 67 -145.20 -55.97 4 A LYS 76 -138.76 -155.79 4 A LYS 87 -159.61 61.60 4 A THR 91 -59.21 90.73 4 A SER 100 -131.87 -31.54 4 A ALA 106 63.29 89.87 4 A SER 116 -120.34 -104.14 4 A SER 117 -173.34 58.80 4 A GLN 118 64.41 158.34 4 A SER 119 -148.07 -29.54 4 A GLU 120 61.24 -85.12 4 A LEU 123 55.57 75.94 4 A ILE 124 -175.13 148.22 4 A SER 125 -113.05 -71.93 4 A GLU 127 55.15 -162.53 4 A ASP 128 63.26 113.65 4 A LEU 129 59.58 -147.01 4 A HIS 131 64.75 125.09 5 A PRO 14 -52.91 90.72 5 A SER 17 -175.03 149.58 5 A PHE 29 -76.01 -169.77 5 A SER 30 57.58 18.44 5 A SER 31 -151.54 -22.40 5 A ALA 40 165.57 -54.25 5 A PRO 41 -63.18 -73.46 5 A LYS 43 47.23 -168.27 5 A LEU 45 68.15 160.06 5 A PRO 53 -51.09 -83.82 5 A ASP 62 74.70 -31.36 5 A SER 85 70.47 -71.77 5 A LEU 86 61.23 153.89 5 A LYS 87 -172.08 -67.99 5 A SER 88 -151.07 -44.54 5 A THR 91 -67.61 89.73 5 A LEU 104 61.52 171.02 5 A ALA 106 64.97 117.59 5 A TRP 107 -129.65 -134.18 5 A GLN 118 60.62 -179.05 5 A LEU 129 -131.42 -87.05 5 A HIS 131 -166.85 15.99 5 A HIS 132 -128.92 -78.50 5 A HIS 133 -157.80 -7.83 5 A HIS 134 61.89 -87.04 6 A PRO 14 -69.94 30.90 6 A SER 25 -162.50 103.41 6 A THR 28 -85.13 -106.72 6 A PHE 29 -173.81 -62.35 6 A PRO 41 -49.37 -18.05 6 A LEU 45 66.42 149.44 6 A ASP 62 76.53 -51.11 6 A ALA 75 58.07 19.01 6 A THR 91 -63.95 90.55 6 A ALA 92 -170.24 -179.49 6 A ALA 103 66.62 159.63 6 A ALA 106 64.34 108.97 6 A LYS 122 -104.11 -72.30 6 A LEU 123 57.11 91.42 6 A GLU 127 57.74 97.68 6 A LEU 129 63.06 -82.04 6 A ASN 130 61.06 68.86 7 A PRO 14 -58.17 82.90 7 A SER 17 -174.75 136.45 7 A THR 28 -72.57 -119.05 7 A PHE 29 -169.70 -60.04 7 A TYR 32 -112.75 -168.98 7 A PRO 41 -54.21 92.54 7 A LYS 43 -142.86 -99.29 7 A LEU 45 64.19 162.92 7 A VAL 48 55.99 -76.79 7 A ASP 62 73.04 -27.93 7 A ALA 75 -171.44 51.91 7 A LYS 76 -158.85 -8.25 7 A ASN 77 54.99 73.37 7 A LYS 87 -162.32 -49.94 7 A SER 88 -175.85 -46.03 7 A THR 91 -63.79 92.74 7 A ALA 92 -172.39 -166.58 7 A SER 100 -153.21 -47.33 7 A ALA 106 67.17 111.14 7 A GLN 118 38.58 -152.06 7 A SER 119 -142.25 31.64 7 A GLN 121 -157.63 -30.72 7 A LEU 123 -165.06 70.01 7 A ILE 124 52.43 -95.57 7 A SER 125 57.53 15.78 7 A GLU 126 -160.52 19.06 7 A ASP 128 60.33 -178.93 7 A HIS 131 -114.11 -166.37 7 A HIS 133 -105.06 -64.21 8 A PRO 14 -34.14 93.97 8 A SER 25 179.52 114.94 8 A PHE 27 -154.64 -24.55 8 A THR 28 61.80 161.20 8 A PHE 29 -105.25 -160.05 8 A SER 30 66.62 -7.24 8 A PRO 41 -50.59 98.89 8 A LEU 45 64.05 166.44 8 A VAL 48 58.52 -77.98 8 A ASP 55 57.66 83.86 8 A ASP 62 73.35 -24.57 8 A ASN 77 -104.28 66.93 8 A SER 85 -176.39 -93.87 8 A LEU 86 53.07 94.24 8 A SER 88 57.44 17.19 8 A ASP 90 -59.47 -98.94 8 A THR 91 44.07 91.05 8 A ALA 106 61.27 109.99 8 A TRP 107 -128.70 -128.62 8 A SER 116 -161.34 109.31 8 A SER 117 -165.47 109.51 8 A GLN 118 56.00 177.96 8 A GLN 121 -146.99 -15.58 8 A ILE 124 -53.92 105.53 8 A SER 125 -170.39 7.84 8 A GLU 126 -143.38 -68.61 8 A ASP 128 -95.34 51.87 8 A LEU 129 -147.50 -32.93 8 A ASN 130 63.39 111.90 8 A HIS 132 -70.16 -162.37 9 A GLN 3 61.80 160.13 9 A PRO 14 -45.76 94.49 9 A SER 17 -164.54 112.29 9 A PHE 27 -158.27 -13.21 9 A THR 28 65.65 144.70 9 A SER 30 59.59 5.68 9 A LEU 45 161.98 165.73 9 A ASP 55 -161.48 -63.00 9 A ASP 62 76.29 -42.54 9 A ARG 67 -99.09 -65.77 9 A LYS 87 -153.11 -48.55 9 A SER 88 -175.46 -49.55 9 A SER 100 -127.18 -69.67 9 A ALA 103 -170.70 142.03 9 A ALA 106 63.96 119.10 9 A TRP 107 -111.61 -85.88 9 A GLN 109 76.75 -132.54 9 A GLN 118 -129.07 -70.50 9 A SER 119 59.02 -90.88 9 A GLU 120 58.77 -175.24 9 A GLN 121 -126.66 -72.06 9 A GLU 127 -167.31 9.44 9 A ASP 128 -96.13 -74.01 9 A LEU 129 61.85 109.66 9 A HIS 131 57.61 -165.61 10 A PRO 14 -49.21 106.14 10 A SER 17 -167.92 112.56 10 A PHE 27 -167.88 -14.14 10 A THR 28 64.06 159.88 10 A PHE 29 -100.52 -164.97 10 A SER 30 59.61 14.17 10 A SER 31 -136.17 -37.57 10 A LYS 43 54.94 -176.94 10 A LEU 45 62.24 134.76 10 A VAL 48 55.13 -77.84 10 A ALA 61 -76.61 20.60 10 A ASP 62 75.90 -57.07 10 A SER 63 -81.05 30.71 10 A VAL 64 -148.44 -11.14 10 A ARG 67 -96.42 -65.66 10 A ASN 74 -88.66 46.87 10 A ALA 75 -155.46 -69.71 10 A SER 88 177.93 -34.15 10 A THR 91 -46.69 99.25 10 A ALA 92 179.74 174.14 10 A SER 100 -171.04 136.02 10 A ALA 106 65.85 115.91 10 A TRP 107 -124.44 -130.26 10 A SER 116 -119.63 -116.95 10 A SER 117 -158.23 25.33 10 A GLN 118 -129.92 -164.29 10 A GLU 120 -148.29 46.74 10 A GLN 121 -159.95 -63.29 10 A LEU 123 62.59 112.29 10 A GLU 127 63.59 119.02 10 A LEU 129 -162.73 6.55 10 A HIS 132 -100.69 -168.46 SOLUTION STRUCTURE OF A SOLUBLE SINGLE-DOMAIN ANTIBODY WITH HYDROPHOBIC RESIDUES TYPICAL OF A VL/VH INTERFACE 1 N N disulf 2.027 A CYS 22 A SG CYS 22 1_555 A CYS 96 A SG CYS 96 1_555 IMMUNE SYSTEM two pleated beta-sheet, immunoglobulin beta-barrel, IMMUNE SYSTEM 1IEH PDB 1 1IEH 1 135 1IEH 1 135 1IEH A 1 1 135 4 6 anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel A GLN 3 A GLN 3 A SER 7 A SER 7 A SER 17 A SER 17 A SER 25 A SER 25 A LEU 79 A LEU 79 A ASN 84 A ASN 84 A PHE 68 A PHE 68 A ARG 72 A ARG 72 A LEU 11 A LEU 11 A VAL 12 A VAL 12 A THR 111 A THR 111 A VAL 115 A VAL 115 A ALA 92 A ALA 92 A LYS 98 A LYS 98 A MET 34 A MET 34 A GLN 39 A GLN 39 A GLU 46 A GLU 46 A ILE 51 A ILE 51 A THR 58 A THR 58 A TYR 60 A TYR 60