1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kurniawan, N.D. Aliabadizadeh, K. Brereton, I.M. Kroon, P.A. Smith, R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 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 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 311 341 356 10.1006/jmbi.2001.4867 11478865 NMR structure and backbone dynamics of a concatemer of epidermal growth factor homology modules of the human low-density lipoprotein receptor. 2001 US Protein Sci. PRCIEI 0795 0961-8368 9 1282 1293 NMR Structure of a Concatemer of the First and Second Ligand-Binding Modules of the Human Low-Density Lipoprotein Receptor 2000 UK J.Mol.Biol. JMOBAK 0070 0022-2836 283 837 862 10.1006/jmbi.1998.2115 An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components. An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components 1998 10.2210/pdb1i0u/pdb pdb_00001i0u 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 9001.013 LOW DENSITY LIPOPROTEIN RECEPTOR EGF-AB CONCATEMER(RESIDUES 314-395) 1 man polymer 40.078 CALCIUM ION 2 syn non-polymer LDL RECEPTOR no no GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACK AV GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACK AV 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 human Homo LIVER Escherichia sample 9606 Homo sapiens 562 Escherichia coli DH5-ALPHA; BL21-DE3 PLASMID PGEX-4T; PET-30A+ 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 2001-08-15 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 1F5Y contains ligand binding modules (LB1-2) of the human LDL receptor 1LRX contains YWTD modules of the human LDL receptor 1HZ8 is the ensemble of 30 structures RCSB Y PDBJ 2001-01-29 REL REL CA CALCIUM ION 15N T1, T2, and NOE relaxations to obtain backbone dynamics information T1/T2 data were not used for structure refinement Energy minimised average structure from 30 selected structure with lowest energy 100 1 HNHA 2D NOESY 2D NOESY 2D NOESY DQF-COSY 3D_15N-separated_NOESY 0.060 5.5 ambient 310 K 0.060 5.5 ambient 283 K 0.060 5.5 ambient 295 K The structures are based on: 874 NOE restraints, 64 phi dihedral angles, 14 chi1 dihedral angles, 14 hydrogen bonds, 9 calcium ion ligand restraints 1. Torsion angles dynamics 2. Restrained molecular dynamics with calcium 3. Energy minimisation 1mM EGF-AB, 20mM CaCl2 95% H2O/5% D2O 1mM EGF-AB, 20mM CaCl2 99% D2O 1mM 15N-EGF-AB, 20mM CaCl2 95% H2O/5% D2O 1.5mM EGF-A, 20mM CaCl2 99% D2O 1.5mM EGF-A, 20mM CaCl2 95% H2O/5% D2O Bruker collection XwinNMR 2.6 T. Goddard & D. G. Kneller processing Sparky 3.95 P. Guntert structure solution DYANA 1.5 A. Brunger refinement X-PLOR 3.85 R. Koradi data analysis MOLMOL 2.6 750 Bruker DMX CA 83 2 CA CA 83 A CA 84 2 CA CA 84 A GLY 1 n 1 GLY 1 A THR 2 n 2 THR 2 A ASN 3 n 3 ASN 3 A GLU 4 n 4 GLU 4 A CYS 5 n 5 CYS 5 A LEU 6 n 6 LEU 6 A ASP 7 n 7 ASP 7 A ASN 8 n 8 ASN 8 A ASN 9 n 9 ASN 9 A GLY 10 n 10 GLY 10 A GLY 11 n 11 GLY 11 A CYS 12 n 12 CYS 12 A SER 13 n 13 SER 13 A HIS 14 n 14 HIS 14 A VAL 15 n 15 VAL 15 A CYS 16 n 16 CYS 16 A ASN 17 n 17 ASN 17 A ASP 18 n 18 ASP 18 A LEU 19 n 19 LEU 19 A LYS 20 n 20 LYS 20 A ILE 21 n 21 ILE 21 A GLY 22 n 22 GLY 22 A TYR 23 n 23 TYR 23 A GLU 24 n 24 GLU 24 A CYS 25 n 25 CYS 25 A LEU 26 n 26 LEU 26 A CYS 27 n 27 CYS 27 A PRO 28 n 28 PRO 28 A ASP 29 n 29 ASP 29 A GLY 30 n 30 GLY 30 A PHE 31 n 31 PHE 31 A GLN 32 n 32 GLN 32 A LEU 33 n 33 LEU 33 A VAL 34 n 34 VAL 34 A ALA 35 n 35 ALA 35 A GLN 36 n 36 GLN 36 A ARG 37 n 37 ARG 37 A ARG 38 n 38 ARG 38 A CYS 39 n 39 CYS 39 A GLU 40 n 40 GLU 40 A ASP 41 n 41 ASP 41 A ILE 42 n 42 ILE 42 A ASP 43 n 43 ASP 43 A GLU 44 n 44 GLU 44 A CYS 45 n 45 CYS 45 A GLN 46 n 46 GLN 46 A ASP 47 n 47 ASP 47 A PRO 48 n 48 PRO 48 A ASP 49 n 49 ASP 49 A THR 50 n 50 THR 50 A CYS 51 n 51 CYS 51 A SER 52 n 52 SER 52 A GLN 53 n 53 GLN 53 A LEU 54 n 54 LEU 54 A CYS 55 n 55 CYS 55 A VAL 56 n 56 VAL 56 A ASN 57 n 57 ASN 57 A LEU 58 n 58 LEU 58 A GLU 59 n 59 GLU 59 A GLY 60 n 60 GLY 60 A GLY 61 n 61 GLY 61 A TYR 62 n 62 TYR 62 A LYS 63 n 63 LYS 63 A CYS 64 n 64 CYS 64 A GLN 65 n 65 GLN 65 A CYS 66 n 66 CYS 66 A GLU 67 n 67 GLU 67 A GLU 68 n 68 GLU 68 A GLY 69 n 69 GLY 69 A PHE 70 n 70 PHE 70 A GLN 71 n 71 GLN 71 A LEU 72 n 72 LEU 72 A ASP 73 n 73 ASP 73 A PRO 74 n 74 PRO 74 A HIS 75 n 75 HIS 75 A THR 76 n 76 THR 76 A LYS 77 n 77 LYS 77 A ALA 78 n 78 ALA 78 A CYS 79 n 79 CYS 79 A LYS 80 n 80 LYS 80 A ALA 81 n 81 ALA 81 A VAL 82 n 82 VAL 82 A author_defined_assembly 1 monomeric A THR 2 A O THR 2 1_555 A CA 83 B CA CA 1_555 A GLU 4 A OE1 GLU 4 1_555 104.2 A THR 2 A O THR 2 1_555 A CA 83 B CA CA 1_555 A GLU 4 A OE2 GLU 4 1_555 58.2 A GLU 4 A OE1 GLU 4 1_555 A CA 83 B CA CA 1_555 A GLU 4 A OE2 GLU 4 1_555 46.9 A THR 2 A O THR 2 1_555 A CA 83 B CA CA 1_555 A GLU 4 A N GLU 4 1_555 78.1 A GLU 4 A OE1 GLU 4 1_555 A CA 83 B CA CA 1_555 A GLU 4 A N GLU 4 1_555 75.3 A GLU 4 A OE2 GLU 4 1_555 A CA 83 B CA CA 1_555 A GLU 4 A N GLU 4 1_555 59.9 A THR 2 A O THR 2 1_555 A CA 83 B CA CA 1_555 A ASP 18 A OD1 ASP 18 1_555 61.9 A GLU 4 A OE1 GLU 4 1_555 A CA 83 B CA CA 1_555 A ASP 18 A OD1 ASP 18 1_555 76.6 A GLU 4 A OE2 GLU 4 1_555 A CA 83 B CA CA 1_555 A ASP 18 A OD1 ASP 18 1_555 64.2 A GLU 4 A N GLU 4 1_555 A CA 83 B CA CA 1_555 A ASP 18 A OD1 ASP 18 1_555 122.6 A ASP 41 A OD2 ASP 41 1_555 A CA 84 C CA CA 1_555 A ILE 42 A O ILE 42 1_555 65.9 A ASP 41 A OD2 ASP 41 1_555 A CA 84 C CA CA 1_555 A GLU 44 A OE1 GLU 44 1_555 106.4 A ILE 42 A O ILE 42 1_555 A CA 84 C CA CA 1_555 A GLU 44 A OE1 GLU 44 1_555 89.8 A ASP 41 A OD2 ASP 41 1_555 A CA 84 C CA CA 1_555 A GLU 44 A OE2 GLU 44 1_555 62.8 A ILE 42 A O ILE 42 1_555 A CA 84 C CA CA 1_555 A GLU 44 A OE2 GLU 44 1_555 58.1 A GLU 44 A OE1 GLU 44 1_555 A CA 84 C CA CA 1_555 A GLU 44 A OE2 GLU 44 1_555 46.6 A ASP 41 A OD2 ASP 41 1_555 A CA 84 C CA CA 1_555 A ASN 57 A OD1 ASN 57 1_555 162.2 A ILE 42 A O ILE 42 1_555 A CA 84 C CA CA 1_555 A ASN 57 A OD1 ASN 57 1_555 101.4 A GLU 44 A OE1 GLU 44 1_555 A CA 84 C CA CA 1_555 A ASN 57 A OD1 ASN 57 1_555 59.5 A GLU 44 A OE2 GLU 44 1_555 A CA 84 C CA CA 1_555 A ASN 57 A OD1 ASN 57 1_555 100.2 A ASP 41 A OD2 ASP 41 1_555 A CA 84 C CA CA 1_555 A LEU 58 A O LEU 58 1_555 131.0 A ILE 42 A O ILE 42 1_555 A CA 84 C CA CA 1_555 A LEU 58 A O LEU 58 1_555 144.2 A GLU 44 A OE1 GLU 44 1_555 A CA 84 C CA CA 1_555 A LEU 58 A O LEU 58 1_555 109.5 A GLU 44 A OE2 GLU 44 1_555 A CA 84 C CA CA 1_555 A LEU 58 A O LEU 58 1_555 153.8 A ASN 57 A OD1 ASN 57 1_555 A CA 84 C CA CA 1_555 A LEU 58 A O LEU 58 1_555 66.7 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 O ASN 17 A O ASN 17 A N GLU 24 A N GLU 24 A O ALA 35 A O ALA 35 A N ARG 38 A N ARG 38 A N VAL 56 A N VAL 56 A O LYS 63 A O LYS 63 A N GLN 71 A N GLN 71 A O LYS 80 A O LYS 80 1 8.58 1.10 114.20 122.78 A A A CA CB SG CYS CYS CYS 55 55 55 N 1 7.12 1.10 114.20 121.32 A A A CA CB SG CYS CYS CYS 64 64 64 N 1 12.01 1.10 114.20 126.21 A A A CA CB SG CYS CYS CYS 66 66 66 N 1 A THR 2 -64.57 -172.40 1 A ASN 9 -41.75 87.69 1 A CYS 12 -105.01 -129.77 1 A SER 13 -159.98 35.05 1 A HIS 14 -109.78 -104.48 1 A ASP 18 -52.36 86.55 1 A TYR 23 -34.32 154.44 1 A VAL 34 -79.74 -76.11 1 A GLN 36 65.01 -66.96 1 A ASP 49 -140.77 -40.84 1 A THR 50 -75.57 -102.30 1 A GLN 53 -111.79 -113.69 1 A LEU 58 -176.35 -152.91 1 A GLU 68 47.75 -79.00 1 A THR 76 -140.05 -37.79 SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR 1 N N 2 N N 2 N N A ASN 8 A ASN 8 HELX_P A CYS 12 A CYS 12 5 1 5 disulf 2.018 A CYS 5 A SG CYS 5 1_555 A CYS 16 A SG CYS 16 1_555 disulf 2.016 A CYS 12 A SG CYS 12 1_555 A CYS 25 A SG CYS 25 1_555 disulf 2.017 A CYS 27 A SG CYS 27 1_555 A CYS 39 A SG CYS 39 1_555 disulf 2.017 A CYS 45 A SG CYS 45 1_555 A CYS 55 A SG CYS 55 1_555 disulf 2.022 A CYS 51 A SG CYS 51 1_555 A CYS 64 A SG CYS 64 1_555 disulf 2.018 A CYS 66 A SG CYS 66 1_555 A CYS 79 A SG CYS 79 1_555 metalc 2.834 A THR 2 A O THR 2 1_555 A CA 83 B CA CA 1_555 metalc 2.693 A GLU 4 A OE1 GLU 4 1_555 A CA 83 B CA CA 1_555 metalc 2.749 A GLU 4 A OE2 GLU 4 1_555 A CA 83 B CA CA 1_555 metalc 3.165 A GLU 4 A N GLU 4 1_555 A CA 83 B CA CA 1_555 metalc 2.705 A ASP 18 A OD1 ASP 18 1_555 A CA 83 B CA CA 1_555 metalc 2.724 A ASP 41 A OD2 ASP 41 1_555 A CA 84 C CA CA 1_555 metalc 2.698 A ILE 42 A O ILE 42 1_555 A CA 84 C CA CA 1_555 metalc 2.713 A GLU 44 A OE1 GLU 44 1_555 A CA 84 C CA CA 1_555 metalc 2.759 A GLU 44 A OE2 GLU 44 1_555 A CA 84 C CA CA 1_555 metalc 2.669 A ASN 57 A OD1 ASN 57 1_555 A CA 84 C CA CA 1_555 metalc 2.760 A LEU 58 A O LEU 58 1_555 A CA 84 C CA CA 1_555 LIPID BINDING PROTEIN anti-parallel beta strands, calcium binding sites, LIPID BINDING PROTEIN LDLR_HUMAN UNP 1 314 P01130 314 395 1I0U 1 82 P01130 A 1 1 82 2 2 2 2 anti-parallel anti-parallel anti-parallel anti-parallel A VAL 15 A VAL 15 A ASN 17 A ASN 17 A GLU 24 A GLU 24 A LEU 26 A LEU 26 A GLN 32 A GLN 32 A ALA 35 A ALA 35 A ARG 38 A ARG 38 A GLU 40 A GLU 40 A CYS 55 A CYS 55 A VAL 56 A VAL 56 A LYS 63 A LYS 63 A CYS 64 A CYS 64 A PHE 70 A PHE 70 A LEU 72 A LEU 72 A CYS 79 A CYS 79 A ALA 81 A ALA 81 BINDING SITE FOR RESIDUE CA A 83 A CA 83 Software 4 BINDING SITE FOR RESIDUE CA A 84 A CA 84 Software 6 A THR 2 A THR 2 4 1_555 A ASN 3 A ASN 3 4 1_555 A GLU 4 A GLU 4 4 1_555 A ASP 18 A ASP 18 4 1_555 A ASP 41 A ASP 41 6 1_555 A ILE 42 A ILE 42 6 1_555 A GLU 44 A GLU 44 6 1_555 A ASN 57 A ASN 57 6 1_555 A LEU 58 A LEU 58 6 1_555 A GLY 60 A GLY 60 6 1_555