data_4DY8 # _model_server_result.job_id dGK-pVSVn4Vap_F-G9c2sg _model_server_result.datetime_utc '2024-11-22 05:54:35' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4dy8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 4DY8 # _exptl.entry_id 4DY8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4DY8 _cell.length_a 35.213 _cell.length_b 35.213 _cell.length_c 44.452 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G 1 1 C,D,H,I 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _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_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A O6 DG 4 A DG 4 1_555 E MN MN . A MN 101 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.74 ? metalc ? metalc2 E MN MN . A MN 101 1_555 D O6 DG 2 D DG 16 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.57 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DA 2 A DA 2 1_555 B N3 DT 5 B DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 DA 2 A DA 2 1_555 B O4 DT 5 B DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 DC 3 A DC 3 1_555 B N1 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 DC 3 A DC 3 1_555 B O6 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 DC 3 A DC 3 1_555 B N2 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DG 4 A DG 4 1_555 B N3 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 DG 4 A DG 4 1_555 B O2 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 DG 4 A DG 4 1_555 B N4 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DG MISPAIR' hydrog18 C O2 DT 1 C DT 13 1_555 D N2 DG 2 D DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog19 C N2 DG 2 C DG 14 1_555 D O2 DT 1 D DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4DY8 _atom_sites.fract_transf_matrix[1][1] 0.028399 _atom_sites.fract_transf_matrix[1][2] 0.016396 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.032792 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.022496 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 4 MN A 1 101 1 MN MN . F 5 HOH A 1 201 3 HOH HOH . F 5 HOH A 2 202 4 HOH HOH . F 5 HOH A 3 203 9 HOH HOH . F 5 HOH A 4 204 13 HOH HOH . F 5 HOH A 5 205 16 HOH HOH . F 5 HOH A 6 206 18 HOH HOH . F 5 HOH A 7 207 21 HOH HOH . F 5 HOH A 8 208 23 HOH HOH . F 5 HOH A 9 209 25 HOH HOH . F 5 HOH A 10 210 29 HOH HOH . F 5 HOH A 11 211 30 HOH HOH . F 5 HOH A 12 212 32 HOH HOH . F 5 HOH A 13 213 5 HOH HOH . F 5 HOH A 14 214 10 HOH HOH . F 5 HOH A 15 215 26 HOH HOH . G 5 HOH B 1 101 2 HOH HOH . G 5 HOH B 2 102 6 HOH HOH . G 5 HOH B 3 103 11 HOH HOH . G 5 HOH B 4 104 12 HOH HOH . G 5 HOH B 5 105 17 HOH HOH . G 5 HOH B 6 106 20 HOH HOH . G 5 HOH B 7 107 27 HOH HOH . G 5 HOH B 8 108 28 HOH HOH . G 5 HOH B 9 109 34 HOH HOH . H 5 HOH C 1 101 7 HOH HOH . H 5 HOH C 2 102 8 HOH HOH . H 5 HOH C 3 103 14 HOH HOH . H 5 HOH C 4 104 15 HOH HOH . H 5 HOH C 5 105 19 HOH HOH . H 5 HOH C 6 106 33 HOH HOH . I 5 HOH D 1 101 1 HOH HOH . I 5 HOH D 2 102 22 HOH HOH . I 5 HOH D 3 103 24 HOH HOH . I 5 HOH D 4 104 31 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 MN MN MN . A . E 4 -4.236 8.935 -0.708 0.65 24.81 ? MN MN 101 A 1 HETATM 2 MN MN MN . B . E 4 -3.516 7.372 -1.489 0.35 26.77 ? MN MN 101 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 2 #