data_5IYV # _model_server_result.job_id cdPlVmmIjdCNSpKXnqCRjw _model_server_result.datetime_utc '2024-11-15 23:24:54' _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 5iyv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":2000}' # _entry.id 5IYV # _exptl.entry_id 5IYV _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 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 5IYV _cell.length_a 150.181 _cell.length_b 150.181 _cell.length_c 60.07 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IYV _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,K _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . 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 3 n C NAG 1 C 1 NAG A 1098 NAG 3 n C NAG 2 C 2 NAG A 1099 NAG 3 n D NAG 1 D 1 NAG A 1150 NAG 3 n D NAG 2 D 2 NAG A 1151 NAG 4 n E NAG 1 E 1 NAG A 1269 NAG 4 n E NAG 2 E 2 NAG A 1270 NAG 4 n E BMA 3 E 3 BMA A 1271 BMA 4 n E MAN 4 E 4 MAN A 1272 MAN 3 n F NAG 1 F 1 NAG A 1576 NAG 3 n F NAG 2 F 2 NAG A 1577 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 40 A CYS 54 1_555 A SG CYS 47 A CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf2 A SG CYS 72 A CYS 86 1_555 A SG CYS 99 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf3 A SG CYS 362 A CYS 376 1_555 A SG CYS 388 A CYS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? covale ? covale1 A ND2 ASN 84 A ASN 98 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 88 A ASN 102 1_555 G C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 A ND2 ASN 136 A ASN 150 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 171 A ASN 185 1_555 H C1 NAG . A NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 255 A ASN 269 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 A ND2 ASN 268 A ASN 282 1_555 I C1 NAG . A NAG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale7 A ND2 ASN 562 A ASN 576 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 B C GLY 6 B GLY 72 1_555 B N HYP 7 B HYP 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale9 B C HYP 7 B HYP 73 1_555 B N SER 8 B SER 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale10 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale13 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale14 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale15 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 5IYV _atom_sites.fract_transf_matrix[1][1] 0.006659 _atom_sites.fract_transf_matrix[1][2] 0.003844 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007689 _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] 0.016647 _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 G 5 NAG A 1 703 1102 NAG NAG . H 5 NAG A 1 706 1185 NAG NAG . I 5 NAG A 1 711 1282 NAG NAG . J 6 EDO B 1 2000 2000 EDO EDO . K 7 HOH A 1 801 3 HOH HOH . K 7 HOH A 2 802 6 HOH HOH . K 7 HOH A 3 803 4 HOH HOH . K 7 HOH A 4 804 7 HOH HOH . K 7 HOH A 5 805 2 HOH HOH . K 7 HOH A 6 806 8 HOH HOH . K 7 HOH A 7 807 1 HOH HOH . K 7 HOH A 8 808 5 HOH HOH . K 7 HOH A 9 809 9 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 . . . J 6 -2.941 46.749 7.984 1 129.28 ? C1 EDO 2000 B 1 HETATM 2 O O1 EDO . . . J 6 -2.192 47.853 7.446 1 128.53 ? O1 EDO 2000 B 1 HETATM 3 C C2 EDO . . . J 6 -2.405 45.419 7.454 1 124.59 ? C2 EDO 2000 B 1 HETATM 4 O O2 EDO . . . J 6 -0.967 45.392 7.425 1 115.82 ? O2 EDO 2000 B 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 4 #