1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Dagil, R. Kragelund, B. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE 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 Ca 2 40.078 CALCIUM ION non-polymer 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 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 J.Biol.Chem. JBCHA3 0071 0021-9258 288 4424 4435 10.1074/jbc.M112.434159 23275343 Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin. 2013 10.2210/pdb2m0p/pdb pdb_00002m0p 5874.158 Low-density lipoprotein receptor-related protein 2 1 man polymer 40.078 CALCIUM ION 1 syn non-polymer LRP-2, Glycoprotein 330, gp330, Megalin no no THAPASCLDTQYTCDNHQCISKNWVCDTDNDCGDGSDEKNCNSTETHHHHHH THAPASCLDTQYTCDNHQCISKNWVCDTDNDCGDGSDEKNCNSTETHHHHHH 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 human sample LRP2 9606 Homo sapiens 4922 Komagataella pastoris plasmid pPICaC database_2 pdbx_database_status pdbx_nmr_spectrometer pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Database references Data collection Database references Derived calculations Other 1 0 2013-01-09 1 1 2013-06-19 1 2 2023-06-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data _pdbx_nmr_spectrometer.model _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Solution structure of the twelfth cysteine-rich ligand-binding repeat in rat megalin NMR Solution structure of calcium-loaded LRP double module BMRB Y RCSB 2012-11-01 REL REL REL REL CA CALCIUM ION 555 273 101 87 94 3 15 21 17 structures with the lowest energy 200 20 2D 1H-15N HSQC 2D 1H-13C HSQC 2D 1H-1H TOCSY aromatic 3D HNCO 3D HNCA 3D HNCACB 3D C(CO)NH 3D CBCA(CO)NH 3D HCCH-TOCSY 3D HN(CO)CA 3D 1H-13C NOESY aliphatic 2D 1H-13C NOESY aromatic 3D H(CCO)NH 3D 1H-15N NOESY 3D 1H-15N TOCSY 0.6 mM [U-100% 13C; U-100% 15N] 100 mM 50 mM 50 mM 0.1 mM 0.1 % 0.6 mM [U-100% 13C; U-100% 15N] 50 mM 100 mM 50 mM 0.1 mM 0.1 % 0.2 6.5 ambient 298 K simulated annealing 1 lowest energy 0.6 mM [U-100% 13C; U-100% 15N] CR10, 100 mM sodium chloride, 50 mM calcium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 90% H2O/10% D2O 90% H2O/10% D2O 0.6 mM [U-100% 13C; U-100% 15N] CR10, 50 mM calcium chloride, 100 mM sodium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 100% D2O 100% D2O CCPN chemical shift assignment Analysis 2.2 CCPN peak picking Analysis 2.2 Linge, O'Donoghue and Nilges structure solution ARIA Linge, O'Donoghue and Nilges refinement ARIA Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRDraw 750 Varian INOVA Varian INOVA 800 Varian INOVA Varian INOVA 800 Bruker AVANCE Bruker Avance CA 1149 2 CA CA 1201 A THR 1103 n 1 THR 1103 A HIS 1104 n 2 HIS 1104 A ALA 1105 n 3 ALA 1105 A PRO 1106 n 4 PRO 1106 A ALA 1107 n 5 ALA 1107 A SER 1108 n 6 SER 1108 A CYS 1109 n 7 CYS 1109 A LEU 1110 n 8 LEU 1110 A ASP 1111 n 9 ASP 1111 A THR 1112 n 10 THR 1112 A GLN 1113 n 11 GLN 1113 A TYR 1114 n 12 TYR 1114 A THR 1115 n 13 THR 1115 A CYS 1116 n 14 CYS 1116 A ASP 1117 n 15 ASP 1117 A ASN 1118 n 16 ASN 1118 A HIS 1119 n 17 HIS 1119 A GLN 1120 n 18 GLN 1120 A CYS 1121 n 19 CYS 1121 A ILE 1122 n 20 ILE 1122 A SER 1123 n 21 SER 1123 A LYS 1124 n 22 LYS 1124 A ASN 1125 n 23 ASN 1125 A TRP 1126 n 24 TRP 1126 A VAL 1127 n 25 VAL 1127 A CYS 1128 n 26 CYS 1128 A ASP 1129 n 27 ASP 1129 A THR 1130 n 28 THR 1130 A ASP 1131 n 29 ASP 1131 A ASN 1132 n 30 ASN 1132 A ASP 1133 n 31 ASP 1133 A CYS 1134 n 32 CYS 1134 A GLY 1135 n 33 GLY 1135 A ASP 1136 n 34 ASP 1136 A GLY 1137 n 35 GLY 1137 A SER 1138 n 36 SER 1138 A ASP 1139 n 37 ASP 1139 A GLU 1140 n 38 GLU 1140 A LYS 1141 n 39 LYS 1141 A ASN 1142 n 40 ASN 1142 A CYS 1143 n 41 CYS 1143 A ASN 1144 n 42 ASN 1144 A SER 1145 n 43 SER 1145 A THR 1146 n 44 THR 1146 A GLU 1147 n 45 GLU 1147 A THR 1148 n 46 THR 1148 A n 47 1149 A n 48 1150 A n 49 1151 A n 50 1152 A n 51 1153 A n 52 1154 A author_defined_assembly 1 monomeric A TRP 1126 A O TRP 24 1_555 A CA 1201 B CA CA 1_555 A ASP 1129 A OD1 ASP 27 1_555 76.0 A TRP 1126 A O TRP 24 1_555 A CA 1201 B CA CA 1_555 A ASP 1131 A O ASP 29 1_555 156.8 A ASP 1129 A OD1 ASP 27 1_555 A CA 1201 B CA CA 1_555 A ASP 1131 A O ASP 29 1_555 80.9 A TRP 1126 A O TRP 24 1_555 A CA 1201 B CA CA 1_555 A ASP 1133 A OD2 ASP 31 1_555 95.8 A ASP 1129 A OD1 ASP 27 1_555 A CA 1201 B CA CA 1_555 A ASP 1133 A OD2 ASP 31 1_555 93.1 A ASP 1131 A O ASP 29 1_555 A CA 1201 B CA CA 1_555 A ASP 1133 A OD2 ASP 31 1_555 82.9 A TRP 1126 A O TRP 24 1_555 A CA 1201 B CA CA 1_555 A ASP 1139 A OD2 ASP 37 1_555 86.1 A ASP 1129 A OD1 ASP 27 1_555 A CA 1201 B CA CA 1_555 A ASP 1139 A OD2 ASP 37 1_555 152.5 A ASP 1131 A O ASP 29 1_555 A CA 1201 B CA CA 1_555 A ASP 1139 A OD2 ASP 37 1_555 116.3 A ASP 1133 A OD2 ASP 31 1_555 A CA 1201 B CA CA 1_555 A ASP 1139 A OD2 ASP 37 1_555 109.6 A TRP 1126 A O TRP 24 1_555 A CA 1201 B CA CA 1_555 A GLU 1140 A OE2 GLU 38 1_555 97.1 A ASP 1129 A OD1 ASP 27 1_555 A CA 1201 B CA CA 1_555 A GLU 1140 A OE2 GLU 38 1_555 84.2 A ASP 1131 A O ASP 29 1_555 A CA 1201 B CA CA 1_555 A GLU 1140 A OE2 GLU 38 1_555 82.9 A ASP 1133 A OD2 ASP 31 1_555 A CA 1201 B CA CA 1_555 A GLU 1140 A OE2 GLU 38 1_555 165.8 A ASP 1139 A OD2 ASP 37 1_555 A CA 1201 B CA CA 1_555 A GLU 1140 A OE2 GLU 38 1_555 77.4 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 TYR 1114 A N TYR 12 A O ILE 1122 A O ILE 20 1 A HIS 1149 A HIS 47 1 Y 1 A HIS 1150 A HIS 48 1 Y 1 A HIS 1151 A HIS 49 1 Y 1 A HIS 1152 A HIS 50 1 Y 1 A HIS 1153 A HIS 51 1 Y 1 A HIS 1154 A HIS 52 1 Y 2 A HIS 1149 A HIS 47 1 Y 2 A HIS 1150 A HIS 48 1 Y 2 A HIS 1151 A HIS 49 1 Y 2 A HIS 1152 A HIS 50 1 Y 2 A HIS 1153 A HIS 51 1 Y 2 A HIS 1154 A HIS 52 1 Y 3 A HIS 1149 A HIS 47 1 Y 3 A HIS 1150 A HIS 48 1 Y 3 A HIS 1151 A HIS 49 1 Y 3 A HIS 1152 A HIS 50 1 Y 3 A HIS 1153 A HIS 51 1 Y 3 A HIS 1154 A HIS 52 1 Y 4 A HIS 1149 A HIS 47 1 Y 4 A HIS 1150 A HIS 48 1 Y 4 A HIS 1151 A HIS 49 1 Y 4 A HIS 1152 A HIS 50 1 Y 4 A HIS 1153 A HIS 51 1 Y 4 A HIS 1154 A HIS 52 1 Y 5 A HIS 1149 A HIS 47 1 Y 5 A HIS 1150 A HIS 48 1 Y 5 A HIS 1151 A HIS 49 1 Y 5 A HIS 1152 A HIS 50 1 Y 5 A HIS 1153 A HIS 51 1 Y 5 A HIS 1154 A HIS 52 1 Y 6 A HIS 1149 A HIS 47 1 Y 6 A HIS 1150 A HIS 48 1 Y 6 A HIS 1151 A HIS 49 1 Y 6 A HIS 1152 A HIS 50 1 Y 6 A HIS 1153 A HIS 51 1 Y 6 A HIS 1154 A HIS 52 1 Y 7 A HIS 1149 A HIS 47 1 Y 7 A HIS 1150 A HIS 48 1 Y 7 A HIS 1151 A HIS 49 1 Y 7 A HIS 1152 A HIS 50 1 Y 7 A HIS 1153 A HIS 51 1 Y 7 A HIS 1154 A HIS 52 1 Y 8 A HIS 1149 A HIS 47 1 Y 8 A HIS 1150 A HIS 48 1 Y 8 A HIS 1151 A HIS 49 1 Y 8 A HIS 1152 A HIS 50 1 Y 8 A HIS 1153 A HIS 51 1 Y 8 A HIS 1154 A HIS 52 1 Y 9 A HIS 1149 A HIS 47 1 Y 9 A HIS 1150 A HIS 48 1 Y 9 A HIS 1151 A HIS 49 1 Y 9 A HIS 1152 A HIS 50 1 Y 9 A HIS 1153 A HIS 51 1 Y 9 A HIS 1154 A HIS 52 1 Y 10 A HIS 1149 A HIS 47 1 Y 10 A HIS 1150 A HIS 48 1 Y 10 A HIS 1151 A HIS 49 1 Y 10 A HIS 1152 A HIS 50 1 Y 10 A HIS 1153 A HIS 51 1 Y 10 A HIS 1154 A HIS 52 1 Y 11 A HIS 1149 A HIS 47 1 Y 11 A HIS 1150 A HIS 48 1 Y 11 A HIS 1151 A HIS 49 1 Y 11 A HIS 1152 A HIS 50 1 Y 11 A HIS 1153 A HIS 51 1 Y 11 A HIS 1154 A HIS 52 1 Y 12 A HIS 1149 A HIS 47 1 Y 12 A HIS 1150 A HIS 48 1 Y 12 A HIS 1151 A HIS 49 1 Y 12 A HIS 1152 A HIS 50 1 Y 12 A HIS 1153 A HIS 51 1 Y 12 A HIS 1154 A HIS 52 1 Y 13 A HIS 1149 A HIS 47 1 Y 13 A HIS 1150 A HIS 48 1 Y 13 A HIS 1151 A HIS 49 1 Y 13 A HIS 1152 A HIS 50 1 Y 13 A HIS 1153 A HIS 51 1 Y 13 A HIS 1154 A HIS 52 1 Y 14 A HIS 1149 A HIS 47 1 Y 14 A HIS 1150 A HIS 48 1 Y 14 A HIS 1151 A HIS 49 1 Y 14 A HIS 1152 A HIS 50 1 Y 14 A HIS 1153 A HIS 51 1 Y 14 A HIS 1154 A HIS 52 1 Y 15 A HIS 1149 A HIS 47 1 Y 15 A HIS 1150 A HIS 48 1 Y 15 A HIS 1151 A HIS 49 1 Y 15 A HIS 1152 A HIS 50 1 Y 15 A HIS 1153 A HIS 51 1 Y 15 A HIS 1154 A HIS 52 1 Y 16 A HIS 1149 A HIS 47 1 Y 16 A HIS 1150 A HIS 48 1 Y 16 A HIS 1151 A HIS 49 1 Y 16 A HIS 1152 A HIS 50 1 Y 16 A HIS 1153 A HIS 51 1 Y 16 A HIS 1154 A HIS 52 1 Y 17 A HIS 1149 A HIS 47 1 Y 17 A HIS 1150 A HIS 48 1 Y 17 A HIS 1151 A HIS 49 1 Y 17 A HIS 1152 A HIS 50 1 Y 17 A HIS 1153 A HIS 51 1 Y 17 A HIS 1154 A HIS 52 1 Y 18 A HIS 1149 A HIS 47 1 Y 18 A HIS 1150 A HIS 48 1 Y 18 A HIS 1151 A HIS 49 1 Y 18 A HIS 1152 A HIS 50 1 Y 18 A HIS 1153 A HIS 51 1 Y 18 A HIS 1154 A HIS 52 1 Y 19 A HIS 1149 A HIS 47 1 Y 19 A HIS 1150 A HIS 48 1 Y 19 A HIS 1151 A HIS 49 1 Y 19 A HIS 1152 A HIS 50 1 Y 19 A HIS 1153 A HIS 51 1 Y 19 A HIS 1154 A HIS 52 1 Y 20 A HIS 1149 A HIS 47 1 Y 20 A HIS 1150 A HIS 48 1 Y 20 A HIS 1151 A HIS 49 1 Y 20 A HIS 1152 A HIS 50 1 Y 20 A HIS 1153 A HIS 51 1 Y 20 A HIS 1154 A HIS 52 1 Y 3 A A OD2 HG ASP SER 1136 1138 1.58 4 A A O HG1 ASP THR 1129 1130 1.60 12 A A HH HD21 TYR ASN 1114 1142 1.25 15 A A O HG ASN SER 1144 1145 1.57 1 A CYS 1109 61.73 -163.93 1 A THR 1146 -91.52 45.61 2 A HIS 1104 64.15 76.70 2 A CYS 1109 60.55 -168.48 2 A ASN 1132 -84.48 48.54 2 A ASN 1142 -114.26 74.16 2 A CYS 1143 -141.79 -63.79 2 A ASN 1144 -157.35 15.98 3 A ASN 1118 -79.16 25.56 3 A CYS 1143 -140.66 10.12 3 A THR 1146 -88.63 34.60 4 A ASN 1142 -93.39 53.80 4 A ASN 1144 50.45 -175.87 4 A SER 1145 53.43 -166.60 4 A THR 1146 -89.93 42.76 5 A ALA 1107 -80.31 39.63 5 A HIS 1119 66.72 83.79 5 A ASN 1132 -86.31 36.21 5 A CYS 1134 73.26 154.20 5 A ASP 1136 -158.25 -47.15 5 A SER 1145 58.94 168.50 6 A SER 1108 -85.19 37.33 6 A ASN 1142 -81.69 43.31 6 A CYS 1143 -171.76 -54.29 6 A THR 1146 -89.11 47.89 7 A HIS 1104 64.22 84.54 7 A LEU 1110 -48.01 151.26 7 A CYS 1143 -170.23 114.56 7 A ASN 1144 38.08 58.83 7 A SER 1145 -69.87 -81.69 8 A CYS 1143 -179.81 -42.59 9 A HIS 1104 64.20 93.70 9 A ASN 1118 -88.44 30.12 9 A ASP 1136 -164.91 -35.59 9 A ASN 1144 -150.83 36.55 10 A THR 1146 -79.50 45.92 11 A HIS 1104 61.80 94.94 11 A CYS 1143 -162.92 46.09 12 A HIS 1104 71.29 -58.25 12 A CYS 1143 -96.36 59.19 13 A ALA 1107 -93.99 37.35 13 A SER 1145 -77.50 -82.19 14 A HIS 1104 -168.91 -38.28 14 A CYS 1109 -101.88 -166.97 15 A ASN 1118 -92.60 33.37 15 A ASP 1133 -133.66 -39.14 15 A CYS 1134 -77.09 34.76 15 A ASN 1144 39.08 65.43 15 A SER 1145 60.20 133.97 15 A THR 1146 -68.30 98.24 16 A CYS 1109 60.51 -164.89 16 A SER 1145 -164.23 -58.91 16 A THR 1146 -91.05 46.65 18 A HIS 1104 65.91 104.80 18 A CYS 1109 -77.73 -167.47 18 A THR 1146 -91.45 31.88 19 A HIS 1119 61.13 77.53 19 A ASN 1142 -85.47 43.22 19 A CYS 1143 -141.01 10.13 19 A SER 1145 52.04 -160.50 20 A CYS 1143 -109.76 72.29 Solution structure of the tenth complement type repeat of human megalin 1 N N 2 N N A GLY 1137 A GLY 35 HELX_P A ASN 1142 A ASN 40 1 1 6 disulf 2.029 A CYS 1109 A SG CYS 7 1_555 A CYS 1121 A SG CYS 19 1_555 disulf 2.024 A CYS 1116 A SG CYS 14 1_555 A CYS 1134 A SG CYS 32 1_555 disulf 2.029 A CYS 1128 A SG CYS 26 1_555 A CYS 1143 A SG CYS 41 1_555 metalc 2.283 A TRP 1126 A O TRP 24 1_555 A CA 1201 B CA CA 1_555 metalc 2.188 A ASP 1129 A OD1 ASP 27 1_555 A CA 1201 B CA CA 1_555 metalc 2.253 A ASP 1131 A O ASP 29 1_555 A CA 1201 B CA CA 1_555 metalc 2.219 A ASP 1133 A OD2 ASP 31 1_555 A CA 1201 B CA CA 1_555 metalc 2.170 A ASP 1139 A OD2 ASP 37 1_555 A CA 1201 B CA CA 1_555 metalc 2.249 A GLU 1140 A OE2 GLU 38 1_555 A CA 1201 B CA CA 1_555 LIPID BINDING PROTEIN Complement type repeat, receptor, megalin, ldl receptor family, lrp2, LIPID BINDING PROTEIN LRP2_HUMAN UNP 1 1103 P98164 THAPASCLDTQYTCDNHQCISKNWVCDTDNDCGDGSDEKNCNSTET 1103 1148 2M0P 1103 1148 P98164 A 1 1 46 1 expression tag HIS 1149 2M0P A P98164 UNP 47 1 expression tag HIS 1150 2M0P A P98164 UNP 48 1 expression tag HIS 1151 2M0P A P98164 UNP 49 1 expression tag HIS 1152 2M0P A P98164 UNP 50 1 expression tag HIS 1153 2M0P A P98164 UNP 51 1 expression tag HIS 1154 2M0P A P98164 UNP 52 2 anti-parallel A GLN 1113 A GLN 11 A THR 1115 A THR 13 A CYS 1121 A CYS 19 A SER 1123 A SER 21 BINDING SITE FOR RESIDUE CA A 1201 A CA 1201 Software 6 A TRP 1126 A TRP 24 6 1_555 A ASP 1129 A ASP 27 6 1_555 A ASP 1131 A ASP 29 6 1_555 A ASP 1133 A ASP 31 6 1_555 A ASP 1139 A ASP 37 6 1_555 A GLU 1140 A GLU 38 6 1_555