1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Clayton, D.J. Brereton, I.M. Kroon, P.A. Smith, R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 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 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking NE FEBS Lett. FEBLAL 0165 0014-5793 479 118 122 10.1016/S0014-5793(00)01842-1 10981718 Three-dimensional NMR structure of the sixth ligand-binding module of the human LDL receptor: comparison of two adjacent modules with different ligand binding specificities. 2000 10.2210/pdb1f8z/pdb pdb_00001f8z 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 4392.759 LOW-DENSITY LIPOPROTEIN RECEPTOR SIXTH LIGAND-BINDING MODULE 1 syn polymer 40.078 CALCIUM ION 1 syn non-polymer no no ATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVN ATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVN 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 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2000-10-18 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_software.name _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_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1LDL contains the first ligand-binding module of the LDL receptor 1LDR contains the second ligand-binding module of the LDL receptor RCSB Y RCSB 2000-07-05 REL REL CA CALCIUM ION Peptide synthesis - based on the human sequence sample structures with the least restraint violations, structures with the lowest energy 50 20 2D NOESY DQF-COSY E-COSY 10 mM 5.50 1 atm 298 K Structures are based on 552 distance constraints, 18 backbone angle restraints and 14 sidechain angle restraints Structure determination by Torsion angle dynamics, Molecular dynamics 3 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate 90% H2O/10% D2O 3 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate 100% D2O Bruker collection XwinNMR Bruker processing AURELIA Xia & Bartels processing XEASY Peter Guntert structure solution DYANA 1.5 Axel Brunger structure solution X-PLOR 3.1 Axel Brunger refinement X-PLOR 3.1 750 Bruker DMX CA 40 2 CA CA 40 A ALA 1 n 1 ALA 1 A THR 2 n 2 THR 2 A CYS 3 n 3 CYS 3 A ARG 4 n 4 ARG 4 A PRO 5 n 5 PRO 5 A ASP 6 n 6 ASP 6 A GLU 7 n 7 GLU 7 A PHE 8 n 8 PHE 8 A GLN 9 n 9 GLN 9 A CYS 10 n 10 CYS 10 A SER 11 n 11 SER 11 A ASP 12 n 12 ASP 12 A GLY 13 n 13 GLY 13 A ASN 14 n 14 ASN 14 A CYS 15 n 15 CYS 15 A ILE 16 n 16 ILE 16 A HIS 17 n 17 HIS 17 A GLY 18 n 18 GLY 18 A SER 19 n 19 SER 19 A ARG 20 n 20 ARG 20 A GLN 21 n 21 GLN 21 A CYS 22 n 22 CYS 22 A ASP 23 n 23 ASP 23 A ARG 24 n 24 ARG 24 A GLU 25 n 25 GLU 25 A TYR 26 n 26 TYR 26 A ASP 27 n 27 ASP 27 A CYS 28 n 28 CYS 28 A LYS 29 n 29 LYS 29 A ASP 30 n 30 ASP 30 A MET 31 n 31 MET 31 A SER 32 n 32 SER 32 A ASP 33 n 33 ASP 33 A GLU 34 n 34 GLU 34 A VAL 35 n 35 VAL 35 A GLY 36 n 36 GLY 36 A CYS 37 n 37 CYS 37 A VAL 38 n 38 VAL 38 A ASN 39 n 39 ASN 39 A author_defined_assembly 1 monomeric A ARG 20 A O ARG 20 1_555 A CA 40 B CA CA 1_555 A ASP 23 A OD1 ASP 23 1_555 61.5 A ARG 20 A O ARG 20 1_555 A CA 40 B CA CA 1_555 A GLU 25 A O GLU 25 1_555 138.9 A ASP 23 A OD1 ASP 23 1_555 A CA 40 B CA CA 1_555 A GLU 25 A O GLU 25 1_555 117.7 A ARG 20 A O ARG 20 1_555 A CA 40 B CA CA 1_555 A GLU 25 A N GLU 25 1_555 129.9 A ASP 23 A OD1 ASP 23 1_555 A CA 40 B CA CA 1_555 A GLU 25 A N GLU 25 1_555 68.5 A GLU 25 A O GLU 25 1_555 A CA 40 B CA CA 1_555 A GLU 25 A N GLU 25 1_555 69.3 A ARG 20 A O ARG 20 1_555 A CA 40 B CA CA 1_555 A TYR 26 A N TYR 26 1_555 179.5 A ASP 23 A OD1 ASP 23 1_555 A CA 40 B CA CA 1_555 A TYR 26 A N TYR 26 1_555 118.0 A GLU 25 A O GLU 25 1_555 A CA 40 B CA CA 1_555 A TYR 26 A N TYR 26 1_555 41.0 A GLU 25 A N GLU 25 1_555 A CA 40 B CA CA 1_555 A TYR 26 A N TYR 26 1_555 49.7 A ARG 20 A O ARG 20 1_555 A CA 40 B CA CA 1_555 A ASP 27 A OD2 ASP 27 1_555 62.9 A ASP 23 A OD1 ASP 23 1_555 A CA 40 B CA CA 1_555 A ASP 27 A OD2 ASP 27 1_555 113.1 A GLU 25 A O GLU 25 1_555 A CA 40 B CA CA 1_555 A ASP 27 A OD2 ASP 27 1_555 84.2 A GLU 25 A N GLU 25 1_555 A CA 40 B CA CA 1_555 A ASP 27 A OD2 ASP 27 1_555 148.8 A TYR 26 A N TYR 26 1_555 A CA 40 B CA CA 1_555 A ASP 27 A OD2 ASP 27 1_555 117.3 A ARG 20 A O ARG 20 1_555 A CA 40 B CA CA 1_555 A ASP 33 A OD2 ASP 33 1_555 87.2 A ASP 23 A OD1 ASP 23 1_555 A CA 40 B CA CA 1_555 A ASP 33 A OD2 ASP 33 1_555 140.9 A GLU 25 A O GLU 25 1_555 A CA 40 B CA CA 1_555 A ASP 33 A OD2 ASP 33 1_555 101.2 A GLU 25 A N GLU 25 1_555 A CA 40 B CA CA 1_555 A ASP 33 A OD2 ASP 33 1_555 134.6 A TYR 26 A N TYR 26 1_555 A CA 40 B CA CA 1_555 A ASP 33 A OD2 ASP 33 1_555 93.3 A ASP 27 A OD2 ASP 27 1_555 A CA 40 B CA CA 1_555 A ASP 33 A OD2 ASP 33 1_555 65.0 A ARG 20 A O ARG 20 1_555 A CA 40 B CA CA 1_555 A GLU 34 A OE2 GLU 34 1_555 70.2 A ASP 23 A OD1 ASP 23 1_555 A CA 40 B CA CA 1_555 A GLU 34 A OE2 GLU 34 1_555 66.2 A GLU 25 A O GLU 25 1_555 A CA 40 B CA CA 1_555 A GLU 34 A OE2 GLU 34 1_555 150.4 A GLU 25 A N GLU 25 1_555 A CA 40 B CA CA 1_555 A GLU 34 A OE2 GLU 34 1_555 87.3 A TYR 26 A N TYR 26 1_555 A CA 40 B CA CA 1_555 A GLU 34 A OE2 GLU 34 1_555 109.8 A ASP 27 A OD2 ASP 27 1_555 A CA 40 B CA CA 1_555 A GLU 34 A OE2 GLU 34 1_555 122.7 A ASP 33 A OD2 ASP 33 1_555 A CA 40 B CA CA 1_555 A GLU 34 A OE2 GLU 34 1_555 82.1 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 PHE 8 A N PHE 8 A O ILE 16 A O ILE 16 1 6.70 1.10 114.20 120.90 A A A CA CB SG CYS CYS CYS 15 15 15 N 1 7.66 1.10 114.20 121.86 A A A CA CB SG CYS CYS CYS 22 22 22 N 2 7.84 1.10 114.20 122.04 A A A CA CB SG CYS CYS CYS 22 22 22 N 3 6.78 1.10 114.20 120.98 A A A CA CB SG CYS CYS CYS 15 15 15 N 3 7.22 1.10 114.20 121.42 A A A CA CB SG CYS CYS CYS 22 22 22 N 4 6.80 1.10 114.20 121.00 A A A CA CB SG CYS CYS CYS 22 22 22 N 6 -3.05 0.50 120.30 117.25 A A A NE CZ NH2 ARG ARG ARG 20 20 20 N 7 7.83 1.10 114.20 122.03 A A A CA CB SG CYS CYS CYS 22 22 22 N 8 7.47 1.10 114.20 121.67 A A A CA CB SG CYS CYS CYS 22 22 22 N 9 7.34 1.10 114.20 121.54 A A A CA CB SG CYS CYS CYS 22 22 22 N 11 7.48 1.10 114.20 121.68 A A A CA CB SG CYS CYS CYS 22 22 22 N 12 7.31 1.10 114.20 121.51 A A A CA CB SG CYS CYS CYS 22 22 22 N 13 7.03 1.10 114.20 121.23 A A A CA CB SG CYS CYS CYS 15 15 15 N 13 6.87 1.10 114.20 121.07 A A A CA CB SG CYS CYS CYS 22 22 22 N 14 7.84 1.10 114.20 122.04 A A A CA CB SG CYS CYS CYS 22 22 22 N 15 7.22 1.10 114.20 121.42 A A A CA CB SG CYS CYS CYS 15 15 15 N 15 8.28 1.10 114.20 122.48 A A A CA CB SG CYS CYS CYS 22 22 22 N 16 7.45 1.10 114.20 121.65 A A A CA CB SG CYS CYS CYS 22 22 22 N 17 8.30 1.10 114.20 122.50 A A A CA CB SG CYS CYS CYS 22 22 22 N 18 7.65 1.10 114.20 121.85 A A A CA CB SG CYS CYS CYS 22 22 22 N 19 6.69 1.10 114.20 120.89 A A A CA CB SG CYS CYS CYS 15 15 15 N 19 7.28 1.10 114.20 121.48 A A A CA CB SG CYS CYS CYS 22 22 22 N 20 7.71 1.10 114.20 121.91 A A A CA CB SG CYS CYS CYS 22 22 22 N 1 A ASP 23 -150.33 3.39 1 A GLU 25 -92.60 38.03 1 A TYR 26 -2.20 75.85 1 A MET 31 56.81 17.15 2 A CYS 22 68.06 63.86 2 A ASP 23 -150.42 9.97 2 A ARG 24 43.10 28.23 2 A GLU 25 -101.65 41.38 2 A TYR 26 1.07 80.39 2 A MET 31 55.80 17.41 3 A ASP 23 -150.61 3.64 3 A GLU 25 -93.95 39.82 3 A TYR 26 -3.96 79.06 3 A MET 31 51.23 11.17 4 A ASP 23 -141.70 -5.07 4 A GLU 25 -98.48 44.71 4 A TYR 26 -2.60 82.95 4 A MET 31 46.11 16.46 5 A CYS 22 67.67 65.00 5 A ASP 23 -150.48 1.11 5 A GLU 25 -89.99 40.48 5 A TYR 26 1.40 76.31 5 A MET 31 57.51 12.54 5 A VAL 38 -102.93 46.80 6 A ASP 23 -150.18 2.49 6 A GLU 25 -98.37 43.65 6 A TYR 26 -3.66 83.97 6 A MET 31 53.72 14.48 6 A CYS 37 -52.57 -75.50 7 A ASP 23 -150.45 6.44 7 A ARG 24 48.95 29.96 7 A GLU 25 -92.29 41.92 7 A TYR 26 -5.74 79.79 7 A MET 31 59.42 15.90 8 A ASP 23 -150.60 6.64 8 A GLU 25 -92.12 41.76 8 A TYR 26 -6.52 76.96 8 A MET 31 54.65 13.40 8 A VAL 38 -95.19 43.16 9 A ASP 23 -150.43 9.32 9 A GLU 25 -97.83 45.38 9 A TYR 26 -11.39 85.73 9 A MET 31 52.17 15.65 10 A ASP 23 -150.56 12.17 10 A ARG 24 39.90 33.62 10 A GLU 25 -96.73 40.15 10 A TYR 26 1.36 76.82 10 A CYS 37 -68.87 -73.42 11 A CYS 22 63.48 61.59 11 A ASP 23 -143.53 -0.20 11 A ARG 24 45.09 26.95 11 A GLU 25 -100.53 46.36 11 A TYR 26 4.29 76.68 11 A MET 31 58.40 13.17 12 A ASP 23 -150.64 3.58 12 A GLU 25 -92.16 39.62 12 A TYR 26 -2.35 76.68 12 A MET 31 54.76 16.26 13 A ASP 23 -150.37 6.45 13 A GLU 25 -94.34 40.16 13 A TYR 26 -3.44 77.92 13 A MET 31 57.21 13.28 14 A CYS 22 65.18 60.04 14 A ASP 23 -150.28 8.03 14 A ARG 24 44.39 29.93 14 A GLU 25 -94.76 42.91 14 A TYR 26 -2.94 78.90 14 A MET 31 55.99 13.62 15 A CYS 22 67.70 60.85 15 A ASP 23 -142.34 -5.38 15 A GLU 25 -99.93 41.58 15 A TYR 26 9.76 70.78 15 A CYS 37 -77.36 -74.32 15 A VAL 38 -101.35 45.94 16 A ASP 23 -150.52 2.85 16 A GLU 25 -94.19 42.76 16 A TYR 26 -6.25 82.72 16 A MET 31 51.23 13.45 17 A CYS 22 65.39 60.08 17 A ASP 23 -147.49 -4.39 17 A GLU 25 -96.77 36.00 17 A TYR 26 5.84 73.87 17 A MET 31 59.13 14.72 17 A CYS 37 -59.53 -71.94 17 A VAL 38 -96.40 43.35 18 A ASP 23 -150.39 5.47 18 A GLU 25 -93.98 41.45 18 A TYR 26 -5.40 77.35 18 A MET 31 55.44 15.89 19 A ASP 23 -150.36 4.65 19 A GLU 25 -93.93 39.35 19 A TYR 26 0.35 76.89 19 A MET 31 56.49 14.36 20 A GLU 25 -98.49 44.69 20 A TYR 26 -11.66 80.12 20 A MET 31 57.42 6.67 20 A CYS 37 -69.01 -70.49 NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR 1 N N 2 N N A MET 31 A MET 31 HELX_P A VAL 35 A VAL 35 5 1 5 disulf 2.019 A CYS 3 A SG CYS 3 1_555 A CYS 15 A SG CYS 15 1_555 disulf 2.019 A CYS 10 A SG CYS 10 1_555 A CYS 28 A SG CYS 28 1_555 disulf 2.020 A CYS 22 A SG CYS 22 1_555 A CYS 37 A SG CYS 37 1_555 metalc 2.791 A ARG 20 A O ARG 20 1_555 A CA 40 B CA CA 1_555 metalc 2.647 A ASP 23 A OD1 ASP 23 1_555 A CA 40 B CA CA 1_555 metalc 3.186 A GLU 25 A O GLU 25 1_555 A CA 40 B CA CA 1_555 metalc 3.021 A GLU 25 A N GLU 25 1_555 A CA 40 B CA CA 1_555 metalc 3.248 A TYR 26 A N TYR 26 1_555 A CA 40 B CA CA 1_555 metalc 2.635 A ASP 27 A OD2 ASP 27 1_555 A CA 40 B CA CA 1_555 metalc 2.632 A ASP 33 A OD2 ASP 33 1_555 A CA 40 B CA CA 1_555 metalc 2.619 A GLU 34 A OE2 GLU 34 1_555 A CA 40 B CA CA 1_555 LIPID BINDING PROTEIN LDL receptor, ligand-binding domain, calcium-binding, familial hypercholesterolemia, LIPID BINDING PROTEIN LDLR_HUMAN UNP 1 234 P01130 ATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVN 234 272 1F8Z 1 39 P01130 A 1 1 39 2 anti-parallel A GLU 7 A GLU 7 A GLN 9 A GLN 9 A CYS 15 A CYS 15 A HIS 17 A HIS 17 BINDING SITE FOR RESIDUE CA A 40 A CA 40 Software 7 A ARG 20 A ARG 20 7 1_555 A ASP 23 A ASP 23 7 1_555 A GLU 25 A GLU 25 7 1_555 A TYR 26 A TYR 26 7 1_555 A ASP 27 A ASP 27 7 1_555 A ASP 33 A ASP 33 7 1_555 A GLU 34 A GLU 34 7 1_555 1 P 1