data_4BDV # _model_server_result.job_id sqf23T5vu08PpPqNikDzCw _model_server_result.datetime_utc '2024-11-05 04:21:59' _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 4bdv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":3333}' # _entry.id 4BDV # _exptl.entry_id 4BDV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 7 _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 90 _cell.entry_id 4BDV _cell.length_a 133.84 _cell.length_b 133.84 _cell.length_c 355.81 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BDV _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 ? 7 G N N ? 7 I N 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 BMA BMA C1 O1 . O3 HO3 . sing 5 ? 4 5 3 BMA BMA 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 3 n C NAG 1 C 1 NAG A 1755 NAG 3 n C NAG 2 C 2 NAG A 1756 NAG 4 n D NAG 1 D 1 NAG B 2334 NAG 4 n D NAG 2 D 2 NAG B 2335 NAG 4 n D BMA 3 D 3 BMA B 2336 BMA 4 n D BMA 4 D 4 BMA B 2337 BMA 4 n D BMA 5 D 5 BMA B 2338 BMA # 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 153 A CYS 153 1_555 A SG CYS 179 A CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 248 A CYS 248 1_555 A SG CYS 329 A CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf3 A SG CYS 528 A CYS 528 1_555 A SG CYS 554 A CYS 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf4 A SG CYS 630 A CYS 630 1_555 A SG CYS 711 A CYS 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf5 B SG CYS 185 B CYS 1832 1_555 B SG CYS 211 B CYS 1858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf6 B SG CYS 374 B CYS 2021 1_555 B SG CYS 522 B CYS 2169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf7 B SG CYS 527 B CYS 2174 1_555 B SG CYS 679 B CYS 2326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 239 A ASN 239 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale2 B ND2 ASN 471 B ASN 2118 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale4 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale6 D O3 BMA . D BMA 3 1_555 D C1 BMA . D BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 D O6 BMA . D BMA 3 1_555 D C1 BMA . D BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? metalc ? metalc1 A O LYS 107 A LYS 107 1_555 F CA CA . A CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 A OD2 ASP 116 A ASP 116 1_555 F CA CA . A CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc3 A OD1 ASP 125 A ASP 125 1_555 F CA CA . A CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc4 A OD2 ASP 125 A ASP 125 1_555 F CA CA . A CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc5 A OD1 ASP 126 A ASP 126 1_555 F CA CA . A CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc6 A ND1 HIS 267 A HIS 267 1_555 E ZN ZN . A ZN 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc7 A SG CYS 310 A CYS 310 1_555 E ZN ZN . A ZN 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc8 A ND1 HIS 315 A HIS 315 1_555 E ZN ZN . A ZN 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc9 H CU CU1 . B CU1 1 1_555 B ND1 HIS 307 B HIS 1954 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc10 H CU CU1 . B CU1 1 1_555 B SG CYS 353 B CYS 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc11 H CU CU1 . B CU1 1 1_555 B ND1 HIS 358 B HIS 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? # _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 4BDV _atom_sites.fract_transf_matrix[1][1] 0.007472 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007472 _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] 0.00281 _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 5 ZN A 1 800 800 ZN ZN . F 6 CA A 1 801 801 CA CA . G 7 EDO A 1 3333 3333 EDO EDO . H 8 CU1 B 1 1 1 CU1 CU1 . I 7 EDO B 1 3333 3333 EDO EDO . # 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 . . . I 7 -17.242 -41.636 56.88 1 134.2 ? C1 EDO 3333 B 1 HETATM 2 O O1 EDO . . . I 7 -16.925 -40.886 55.693 1 129.02 ? O1 EDO 3333 B 1 HETATM 3 C C2 EDO . . . I 7 -18.553 -42.409 56.718 1 143.66 ? C2 EDO 3333 B 1 HETATM 4 O O2 EDO . . . I 7 -19.491 -41.745 55.847 1 141.61 ? O2 EDO 3333 B 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 4 #