data_5MZO # _model_server_result.job_id SYld85gZhaISGu6uWmkqcQ _model_server_result.datetime_utc '2024-12-26 15:06:12' _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 5mzo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1614}' # _entry.id 5MZO # _exptl.entry_id 5MZO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 2 _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 5MZO _cell.length_a 163.57 _cell.length_b 163.57 _cell.length_c 248.584 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MZO _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H N N ? 6 I N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 3 5 4 MAN MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 1894 NAG 2 n B NAG 2 B 2 NAG A 1895 NAG 3 n C NAG 1 C 1 NAG A 2056 NAG 3 n C NAG 2 C 2 NAG A 2057 NAG 3 n C BMA 3 C 3 BMA A 2058 BMA 3 n C MAN 4 C 4 MAN A 2059 MAN 3 n C MAN 5 C 5 MAN A 2060 MAN 2 n D NAG 1 D 1 NAG A 2227 NAG 2 n D NAG 2 D 2 NAG A 2228 NAG 2 n E NAG 1 E 1 NAG A 2329 NAG 2 n E NAG 2 E 2 NAG A 2330 NAG # 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 disulf ? disulf1 A SG CYS 118 A CYS 138 1_555 A SG CYS 130 A CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 1310 A CYS 1330 1_555 A SG CYS 1403 A CYS 1423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 1399 A CYS 1419 1_555 A SG CYS 1417 A CYS 1437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A ND2 ASN 36 A ASN 56 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 A ND2 ASN 309 A ASN 329 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 618 A ASN 638 1_555 F C1 NAG . A NAG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 874 A ASN 894 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale5 A ND2 ASN 1207 A ASN 1227 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale6 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale8 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale10 C O6 MAN . C MAN 4 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale11 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 A OD2 ASP 1282 A ASP 1302 1_555 G CA CA . A CA 1613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc2 A OD1 ASP 1284 A ASP 1304 1_555 G CA CA . A CA 1613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc3 A OD2 ASP 1284 A ASP 1304 1_555 G CA CA . A CA 1613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc4 A OD1 ASP 1415 A ASP 1435 1_555 G CA CA . A CA 1613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc5 A OD2 ASP 1415 A ASP 1435 1_555 G CA CA . A CA 1613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 O1 EDO sing 107 n n C1 C2 EDO sing 108 n n C1 H11 EDO sing 109 n n C1 H12 EDO sing 110 n n O1 HO1 EDO sing 111 n n C2 O2 EDO sing 112 n n C2 H21 EDO sing 113 n n C2 H22 EDO sing 114 n n O2 HO2 EDO sing 115 n n # _atom_sites.entry_id 5MZO _atom_sites.fract_transf_matrix[1][1] 0.006114 _atom_sites.fract_transf_matrix[1][2] 0.00353 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007059 _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] 0.004023 _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 F 4 NAG A 1 1601 1638 NAG NAG . G 5 CA A 1 1613 9000 CA CA . H 6 EDO A 1 1614 9999 EDO EDO . I 6 EDO A 1 1615 9998 EDO EDO . J 7 HOH A 1 1701 9 HOH HOH . J 7 HOH A 2 1702 14 HOH HOH . J 7 HOH A 3 1703 4 HOH HOH . J 7 HOH A 4 1704 13 HOH HOH . J 7 HOH A 5 1705 1 HOH HOH . J 7 HOH A 6 1706 2 HOH HOH . J 7 HOH A 7 1707 6 HOH HOH . J 7 HOH A 8 1708 7 HOH HOH . J 7 HOH A 9 1709 12 HOH HOH . J 7 HOH A 10 1710 11 HOH HOH . J 7 HOH A 11 1711 10 HOH HOH . J 7 HOH A 12 1712 8 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 C C1 EDO . . . H 6 13.154 -51.565 1.955 1 122.16 ? C1 EDO 1614 A 1 HETATM 2 O O1 EDO . . . H 6 12.829 -51.935 3.297 1 121.85 ? O1 EDO 1614 A 1 HETATM 3 C C2 EDO . . . H 6 12.608 -50.155 1.663 1 122.07 ? C2 EDO 1614 A 1 HETATM 4 O O2 EDO . . . H 6 11.251 -50.084 2.081 1 121.65 ? O2 EDO 1614 A 1 HETATM 5 H H11 EDO . . . H 6 14.222 -51.619 1.747 1 122.19 ? H11 EDO 1614 A 1 HETATM 6 H H12 EDO . . . H 6 12.67 -52.31 1.325 1 122.05 ? H12 EDO 1614 A 1 HETATM 7 H HO1 EDO . . . H 6 11.841 -51.897 3.393 1 121.69 ? HO1 EDO 1614 A 1 HETATM 8 H H21 EDO . . . H 6 13.123 -49.403 2.258 1 122.05 ? H21 EDO 1614 A 1 HETATM 9 H H22 EDO . . . H 6 12.748 -49.889 0.616 1 122.03 ? H22 EDO 1614 A 1 HETATM 10 H HO2 EDO . . . H 6 11.04 -49.125 2.235 1 121.57 ? HO2 EDO 1614 A 1 # _model_server_stats.io_time_ms 83 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #