1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Miyamoto, K. Tomizawa, T. Koshiba, S. Inoue, M. Kigawa, T. Yokoyama, S. RIKEN Structural Genomics/Proteomics Initiative (RSGI) 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 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 Zn 2 65.409 ZINC ION non-polymer To be Published 0353 Solution Structure of the zinc finger BED domain of the zinc finger BED domain containing protein 1 10.2210/pdb2ct5/pdb pdb_00002ct5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 8072.971 Zinc finger BED domain containing protein 1 zinc finger BED domain 1 man polymer 65.409 ZINC ION 1 syn non-polymer dREF homolog, Putative Ac-like transposable element no no GSSGSSGSKVWKYFGFDTNAEGCILQWKKIYCRICMAQIAYSGNTSNLSYHLEKNHPEEFCEFVKSNSGPSSG GSSGSSGSKVWKYFGFDTNAEGCILQWKKIYCRICMAQIAYSGNTSNLSYHLEKNHPEEFCEFVKSNSGPSSG A hsk002000767.1 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 human Homo sample Cell-free protein synthesis ZBED1X 9606 Homo sapiens PLASMID P040308-29 RIKEN Structural Genomics/Proteomics Initiative RSGI NPPSFA, National Project on Protein Structural and Functional Analyses database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2005-11-23 1 1 2008-04-30 1 2 2011-07-13 1 3 2022-03-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _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_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y PDBJ Y PDBJ 2005-05-23 REL ZN ZINC ION target function, structures with the least restraint violations 100 20 3D_15N-separated_NOESY 3D_13C-separated_NOESY 120 7.0 ambient 296 K torsion angle dynamics 1 lowest energy 1.09mM zinc finger BED domain U-13C, 15N; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZNCl2; 90% H2O, 10% D2O 90% H2O/10% D2O Bruker collection XwinNMR 2.6 Delaglio, F. processing NMRPipe 20031121 Johnson, B. A. data analysis NMRView 5.0.4 Kobayashi, N. data analysis KUJIRA 0.925 Guntert, P. structure solution CYANA 2.0.17 Guntert, P. refinement CYANA 2.0.17 800 Bruker AVANCE ZN 201 2 ZN ZN 201 A GLY 1 n 1 GLY 1 A SER 2 n 2 SER 2 A SER 3 n 3 SER 3 A GLY 4 n 4 GLY 4 A SER 5 n 5 SER 5 A SER 6 n 6 SER 6 A GLY 7 n 7 GLY 7 A SER 8 n 8 SER 8 A LYS 9 n 9 LYS 9 A VAL 10 n 10 VAL 10 A TRP 11 n 11 TRP 11 A LYS 12 n 12 LYS 12 A TYR 13 n 13 TYR 13 A PHE 14 n 14 PHE 14 A GLY 15 n 15 GLY 15 A PHE 16 n 16 PHE 16 A ASP 17 n 17 ASP 17 A THR 18 n 18 THR 18 A ASN 19 n 19 ASN 19 A ALA 20 n 20 ALA 20 A GLU 21 n 21 GLU 21 A GLY 22 n 22 GLY 22 A CYS 23 n 23 CYS 23 A ILE 24 n 24 ILE 24 A LEU 25 n 25 LEU 25 A GLN 26 n 26 GLN 26 A TRP 27 n 27 TRP 27 A LYS 28 n 28 LYS 28 A LYS 29 n 29 LYS 29 A ILE 30 n 30 ILE 30 A TYR 31 n 31 TYR 31 A CYS 32 n 32 CYS 32 A ARG 33 n 33 ARG 33 A ILE 34 n 34 ILE 34 A CYS 35 n 35 CYS 35 A MET 36 n 36 MET 36 A ALA 37 n 37 ALA 37 A GLN 38 n 38 GLN 38 A ILE 39 n 39 ILE 39 A ALA 40 n 40 ALA 40 A TYR 41 n 41 TYR 41 A SER 42 n 42 SER 42 A GLY 43 n 43 GLY 43 A ASN 44 n 44 ASN 44 A THR 45 n 45 THR 45 A SER 46 n 46 SER 46 A ASN 47 n 47 ASN 47 A LEU 48 n 48 LEU 48 A SER 49 n 49 SER 49 A TYR 50 n 50 TYR 50 A HIS 51 n 51 HIS 51 A LEU 52 n 52 LEU 52 A GLU 53 n 53 GLU 53 A LYS 54 n 54 LYS 54 A ASN 55 n 55 ASN 55 A HIS 56 n 56 HIS 56 A PRO 57 n 57 PRO 57 A GLU 58 n 58 GLU 58 A GLU 59 n 59 GLU 59 A PHE 60 n 60 PHE 60 A CYS 61 n 61 CYS 61 A GLU 62 n 62 GLU 62 A PHE 63 n 63 PHE 63 A VAL 64 n 64 VAL 64 A LYS 65 n 65 LYS 65 A SER 66 n 66 SER 66 A ASN 67 n 67 ASN 67 A SER 68 n 68 SER 68 A GLY 69 n 69 GLY 69 A PRO 70 n 70 PRO 70 A SER 71 n 71 SER 71 A SER 72 n 72 SER 72 A GLY 73 n 73 GLY 73 A author_defined_assembly 1 monomeric A CYS 32 A SG CYS 32 1_555 A ZN 201 B ZN ZN 1_555 A CYS 35 A SG CYS 35 1_555 106.9 A CYS 32 A SG CYS 32 1_555 A ZN 201 B ZN ZN 1_555 A HIS 51 A NE2 HIS 51 1_555 92.4 A CYS 35 A SG CYS 35 1_555 A ZN 201 B ZN ZN 1_555 A HIS 51 A NE2 HIS 51 1_555 117.5 A CYS 32 A SG CYS 32 1_555 A ZN 201 B ZN ZN 1_555 A HIS 56 A NE2 HIS 56 1_555 117.9 A CYS 35 A SG CYS 35 1_555 A ZN 201 B ZN ZN 1_555 A HIS 56 A NE2 HIS 56 1_555 104.0 A HIS 51 A NE2 HIS 51 1_555 A ZN 201 B ZN ZN 1_555 A HIS 56 A NE2 HIS 56 1_555 118.1 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 CYS 32 A N CYS 32 A O ALA 37 A O ALA 37 1 A SER 2 -124.33 -50.31 1 A VAL 10 -85.80 36.46 1 A ASP 17 -105.92 79.79 1 A TRP 27 -59.28 172.45 1 A MET 36 36.91 44.81 1 A THR 45 -86.63 38.40 1 A GLU 53 -38.81 -32.18 1 A ASN 55 -71.15 -76.39 2 A SER 5 -82.36 43.61 2 A LYS 12 -37.57 -37.74 2 A ASN 19 71.94 36.83 2 A GLN 26 -82.54 41.06 2 A ARG 33 -86.06 33.01 2 A MET 36 34.67 48.15 2 A ASN 44 -46.56 155.05 2 A ASN 55 -83.24 -70.50 2 A VAL 64 -97.54 48.17 2 A SER 71 -168.35 105.27 3 A SER 5 -54.68 96.10 3 A LYS 9 47.59 27.99 3 A CYS 23 -36.81 152.59 3 A SER 42 -124.04 -54.61 3 A ASN 44 38.44 39.53 3 A THR 45 35.36 52.07 3 A GLU 53 -49.77 -18.68 3 A ASN 55 -111.08 -70.91 3 A LYS 65 -96.44 40.13 3 A PRO 70 -69.78 -174.61 3 A SER 72 -39.39 138.90 4 A SER 3 -65.77 82.00 4 A TRP 11 -91.63 39.79 4 A GLN 26 -33.99 141.11 4 A THR 45 35.07 45.81 4 A ASN 55 -95.09 -60.39 5 A SER 5 -64.44 91.02 5 A TRP 11 -94.13 34.06 5 A ASP 17 -55.01 -73.99 5 A ASN 19 -35.27 102.74 5 A GLU 21 -66.44 78.15 5 A CYS 23 -41.64 152.13 5 A ILE 24 -35.34 144.98 5 A LYS 28 -174.98 115.48 5 A MET 36 35.51 45.01 5 A THR 45 37.08 42.20 5 A ASN 55 -93.67 -73.88 5 A ASN 67 -34.99 108.21 5 A SER 72 70.98 42.12 6 A LYS 12 -34.37 -39.13 6 A ASP 17 -63.91 94.61 6 A ILE 24 -35.41 139.83 6 A LEU 25 -133.09 -34.43 6 A MET 36 39.11 53.63 6 A THR 45 -94.12 48.12 6 A ASN 55 -109.65 -67.95 6 A SER 68 -36.03 151.92 7 A GLN 26 -46.28 173.58 7 A MET 36 37.56 39.64 7 A ASN 44 -109.25 79.74 7 A THR 45 35.68 45.00 7 A ASN 55 -101.52 -66.32 7 A SER 68 -52.65 172.40 7 A PRO 70 -69.79 86.30 8 A SER 6 37.76 40.45 8 A LYS 9 -80.85 42.07 8 A ASP 17 -60.98 -71.86 8 A THR 18 38.35 44.02 8 A ASN 19 -43.94 100.93 8 A LEU 25 -106.91 41.22 8 A GLN 26 -171.02 149.73 8 A TRP 27 -35.00 140.40 8 A LYS 28 -69.61 94.56 8 A MET 36 38.32 39.04 8 A THR 45 -86.21 45.54 8 A ASN 55 -108.94 -60.81 8 A LYS 65 -102.88 41.51 8 A ASN 67 -51.04 86.68 9 A TRP 11 -88.62 37.51 9 A ASP 17 -103.74 75.35 9 A GLU 21 34.11 41.73 9 A GLN 26 -82.02 41.10 9 A MET 36 33.99 37.06 9 A SER 42 -160.49 112.53 9 A THR 45 -84.22 40.83 9 A GLU 53 -29.44 -49.77 9 A ASN 55 -71.81 -74.57 9 A LYS 65 33.16 47.61 10 A ASP 17 -90.83 38.45 10 A MET 36 39.02 42.56 10 A SER 42 -115.89 -71.67 10 A THR 45 -82.12 48.94 10 A ASN 55 -90.80 -67.26 10 A ASN 67 -86.29 40.59 10 A SER 71 -44.96 165.30 11 A SER 3 -174.18 147.74 11 A GLU 21 -42.29 155.14 11 A CYS 23 -45.93 166.91 11 A TRP 27 34.23 42.95 11 A LYS 28 -55.45 177.90 11 A THR 45 34.58 42.04 11 A LEU 48 -40.24 -70.38 11 A PRO 70 -69.79 -176.74 12 A SER 2 -101.95 42.56 12 A LYS 12 -34.27 -35.63 12 A ILE 24 -37.74 149.04 12 A TRP 27 -37.93 128.82 12 A ASN 44 -49.44 178.77 12 A THR 45 -85.01 43.92 12 A ASN 55 -98.41 -70.25 12 A LYS 65 -67.08 97.82 13 A SER 8 -54.89 108.38 13 A ILE 24 -49.61 175.21 13 A MET 36 39.26 50.63 13 A ASN 44 -62.40 85.45 13 A ASN 55 -80.91 -75.33 13 A ASN 67 -59.83 87.85 13 A SER 68 -166.72 107.73 13 A PRO 70 -69.78 -174.75 14 A SER 3 -42.13 151.59 14 A SER 5 -124.54 -54.39 14 A CYS 23 -52.46 -177.69 14 A ILE 24 38.55 45.58 14 A TRP 27 -40.93 150.77 14 A LYS 28 -60.14 76.38 14 A MET 36 34.07 44.90 14 A THR 45 -86.71 41.67 14 A ASN 67 -59.96 172.53 14 A SER 68 -174.61 144.22 15 A LYS 9 -82.57 38.50 15 A TRP 11 -85.04 30.35 15 A ILE 24 39.33 53.03 15 A LEU 25 -45.58 155.73 15 A ARG 33 -81.47 40.10 15 A THR 45 -81.64 40.19 15 A ASN 55 -102.08 -70.12 15 A SER 71 -108.00 41.79 16 A TRP 11 -93.67 33.58 16 A TRP 27 -76.11 48.33 16 A LYS 28 33.82 47.76 16 A MET 36 34.49 45.59 16 A SER 42 -122.75 -57.88 16 A THR 45 36.21 44.14 16 A GLU 53 -35.41 -37.25 16 A ASN 55 -77.40 -74.10 16 A PRO 70 -69.75 -176.84 17 A TRP 11 -35.11 -38.06 17 A TRP 27 -59.11 171.31 17 A LYS 28 -64.29 85.63 17 A THR 45 -86.07 48.87 17 A SER 71 38.04 44.51 18 A TRP 11 -89.28 31.39 18 A CYS 23 -170.73 -176.74 18 A ILE 24 -64.04 98.60 18 A GLN 26 -82.45 38.55 18 A TRP 27 33.72 46.39 18 A LYS 28 -49.47 -179.44 18 A MET 36 34.90 49.25 18 A ASN 44 39.13 37.68 18 A THR 45 34.36 40.40 18 A GLU 58 -63.79 -71.21 18 A GLU 59 -35.42 -34.31 18 A ASN 67 -92.54 42.30 18 A SER 71 34.66 42.27 19 A LYS 9 -97.98 38.27 19 A ASP 17 -106.42 48.06 19 A LYS 28 -38.03 116.42 19 A SER 42 -109.46 -68.44 19 A ASN 44 -66.18 90.81 19 A THR 45 38.92 45.19 19 A LEU 48 -48.14 -73.74 19 A GLU 53 -39.12 -29.71 19 A ASN 55 -81.16 -76.25 19 A PRO 70 -69.72 93.88 20 A SER 3 -37.96 138.34 20 A LYS 9 -79.88 45.72 20 A ASN 19 -40.71 162.61 20 A GLN 26 -49.48 176.03 20 A TRP 27 -34.04 116.01 20 A SER 42 -113.92 77.36 20 A THR 45 -80.98 42.01 20 A SER 66 -81.14 43.73 Solution Structure of the zinc finger BED domain of the zinc finger BED domain containing protein 1 1 N N 2 N N A VAL 10 A VAL 10 HELX_P A LYS 12 A LYS 12 5 1 3 A SER 46 A SER 46 HELX_P A LYS 54 A LYS 54 1 2 9 A PRO 57 A PRO 57 HELX_P A PHE 63 A PHE 63 1 3 7 metalc 2.331 A CYS 32 A SG CYS 32 1_555 A ZN 201 B ZN ZN 1_555 metalc 2.329 A CYS 35 A SG CYS 35 1_555 A ZN 201 B ZN ZN 1_555 metalc 2.345 A HIS 51 A NE2 HIS 51 1_555 A ZN 201 B ZN ZN 1_555 metalc 2.328 A HIS 56 A NE2 HIS 56 1_555 A ZN 201 B ZN ZN 1_555 TRANSCRIPTION Zinc finger BED domain containing protein 1, dREF homolog, Putative c-like transposable element, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, transcription ZBED1_HUMAN UNP 1 23 O96006 SKVWKYFGFDTNAEGCILQWKKIYCRICMAQIAYSGNTSNLSYHLEKNHPEEFCEFVKSN 23 82 2CT5 8 67 O96006 A 1 8 67 1 cloning artifact GLY 1 2CT5 A O96006 UNP 1 1 cloning artifact SER 2 2CT5 A O96006 UNP 2 1 cloning artifact SER 3 2CT5 A O96006 UNP 3 1 cloning artifact GLY 4 2CT5 A O96006 UNP 4 1 cloning artifact SER 5 2CT5 A O96006 UNP 5 1 cloning artifact SER 6 2CT5 A O96006 UNP 6 1 cloning artifact GLY 7 2CT5 A O96006 UNP 7 1 cloning artifact SER 68 2CT5 A O96006 UNP 68 1 cloning artifact GLY 69 2CT5 A O96006 UNP 69 1 cloning artifact PRO 70 2CT5 A O96006 UNP 70 1 cloning artifact SER 71 2CT5 A O96006 UNP 71 1 cloning artifact SER 72 2CT5 A O96006 UNP 72 1 cloning artifact GLY 73 2CT5 A O96006 UNP 73 3 anti-parallel anti-parallel A PHE 14 A PHE 14 A GLY 15 A GLY 15 A ILE 30 A ILE 30 A CYS 32 A CYS 32 A ALA 37 A ALA 37 A ILE 39 A ILE 39 BINDING SITE FOR RESIDUE ZN A 201 A ZN 201 Software 4 A CYS 32 A CYS 32 4 1_555 A CYS 35 A CYS 35 4 1_555 A HIS 51 A HIS 51 4 1_555 A HIS 56 A HIS 56 4 1_555 1 P 1