data_5E4J # _model_server_result.job_id KES1GeVh7b2l_EMxD6bkQg _model_server_result.datetime_utc '2024-11-28 01:20:12' _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 5e4j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":603}' # _entry.id 5E4J # _exptl.entry_id 5E4J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 258.486 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DECAMETHONIUM 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 5E4J _cell.length_a 111.21 _cell.length_b 111.21 _cell.length_c 137.03 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E4J _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,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 91.353333 # _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 # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O2 HO2 . 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 1539 NAG 2 n B NAG 2 B 2 NAG A 2107 NAG 2 n B BMA 3 B 3 BMA A 2108 BMA 2 n B MAN 4 B 4 MAN A 2109 MAN 2 n B MAN 5 B 5 MAN A 2110 MAN # 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 64 A CYS 67 1_555 A SG CYS 91 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf2 A SG CYS 251 A CYS 254 1_555 A SG CYS 262 A CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf3 A SG CYS 399 A CYS 402 1_555 A SG CYS 518 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? covale ? covale1 A ND2 ASN 56 A ASN 59 1_555 C C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale2 A ND2 ASN 413 A ASN 416 1_555 D C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale3 A ND2 ASN 454 A ASN 457 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale7 B O2 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _chem_comp.formula 'C16 H38 N2 2' _chem_comp.formula_weight 258.486 _chem_comp.id DME _chem_comp.mon_nstd_flag . _chem_comp.name 'DECAMETHONIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N1 C2 DME sing 107 n n N1 C13 DME sing 108 n n N1 C14 DME sing 109 n n N1 C15 DME sing 110 n n C2 C3 DME sing 111 n n C2 H21 DME sing 112 n n C2 H22 DME sing 113 n n C3 C4 DME sing 114 n n C3 H31 DME sing 115 n n C3 H32 DME sing 116 n n C4 C5 DME sing 117 n n C4 H41 DME sing 118 n n C4 H42 DME sing 119 n n C5 C6 DME sing 120 n n C5 H51 DME sing 121 n n C5 H52 DME sing 122 n n C6 C7 DME sing 123 n n C6 H61 DME sing 124 n n C6 H62 DME sing 125 n n C7 C8 DME sing 126 n n C7 H71 DME sing 127 n n C7 H72 DME sing 128 n n C8 C9 DME sing 129 n n C8 H81 DME sing 130 n n C8 H82 DME sing 131 n n C9 C10 DME sing 132 n n C9 H91 DME sing 133 n n C9 H92 DME sing 134 n n C10 C11 DME sing 135 n n C10 H101 DME sing 136 n n C10 H102 DME sing 137 n n C11 N12 DME sing 138 n n C11 H111 DME sing 139 n n C11 H112 DME sing 140 n n N12 C16 DME sing 141 n n N12 C17 DME sing 142 n n N12 C18 DME sing 143 n n C13 H131 DME sing 144 n n C13 H132 DME sing 145 n n C13 H133 DME sing 146 n n C14 H141 DME sing 147 n n C14 H142 DME sing 148 n n C14 H143 DME sing 149 n n C15 H151 DME sing 150 n n C15 H152 DME sing 151 n n C15 H153 DME sing 152 n n C16 H161 DME sing 153 n n C16 H162 DME sing 154 n n C16 H163 DME sing 155 n n C17 H171 DME sing 156 n n C17 H172 DME sing 157 n n C17 H173 DME sing 158 n n C18 H181 DME sing 159 n n C18 H182 DME sing 160 n n C18 H183 DME sing 161 n n # _atom_sites.entry_id 5E4J _atom_sites.fract_transf_matrix[1][1] 0.008992 _atom_sites.fract_transf_matrix[1][2] 0.005192 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010383 _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] 0.007298 _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 C 3 NAG A 1 601 1536 NAG NAG . D 3 NAG A 1 602 1537 NAG NAG . E 4 DME A 1 603 999 DME DME . F 5 SO4 A 1 604 701 SO4 SO4 . G 5 SO4 A 1 605 702 SO4 SO4 . H 5 SO4 A 1 606 703 SO4 SO4 . I 5 SO4 A 1 607 704 SO4 SO4 . J 5 SO4 A 1 608 705 SO4 SO4 . K 5 SO4 A 1 609 706 SO4 SO4 . L 5 SO4 A 1 610 707 SO4 SO4 . M 5 SO4 A 1 611 708 SO4 SO4 . N 5 SO4 A 1 612 709 SO4 SO4 . O 5 SO4 A 1 613 710 SO4 SO4 . P 6 HOH A 1 701 2011 HOH HOH . P 6 HOH A 2 702 2005 HOH HOH . P 6 HOH A 3 703 2013 HOH HOH . P 6 HOH A 4 704 2007 HOH HOH . P 6 HOH A 5 705 2002 HOH HOH . P 6 HOH A 6 706 2010 HOH HOH . P 6 HOH A 7 707 2003 HOH HOH . P 6 HOH A 8 708 2001 HOH HOH . P 6 HOH A 9 709 2006 HOH HOH . P 6 HOH A 10 710 2012 HOH HOH . P 6 HOH A 11 711 2015 HOH HOH . P 6 HOH A 12 712 2004 HOH HOH . P 6 HOH A 13 713 2014 HOH HOH . P 6 HOH A 14 714 2008 HOH HOH . P 6 HOH A 15 715 2009 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 N N1 DME . . . E 4 49.838 -30.392 39.83 1 65.74 ? N1 DME 603 A 1 HETATM 2 C C2 DME . . . E 4 50.696 -29.7 40.8 1 66.67 ? C2 DME 603 A 1 HETATM 3 C C3 DME . . . E 4 50.035 -29.807 42.169 1 62.76 ? C3 DME 603 A 1 HETATM 4 C C4 DME . . . E 4 50.271 -31.179 42.785 1 60.32 ? C4 DME 603 A 1 HETATM 5 C C5 DME . . . E 4 50.44 -31.108 44.301 1 58.62 ? C5 DME 603 A 1 HETATM 6 C C6 DME . . . E 4 51.846 -30.689 44.727 1 55.73 ? C6 DME 603 A 1 HETATM 7 C C7 DME . . . E 4 51.916 -29.198 45.035 1 54.32 ? C7 DME 603 A 1 HETATM 8 C C8 DME . . . E 4 52.701 -28.899 46.3 1 52.26 ? C8 DME 603 A 1 HETATM 9 C C9 DME . . . E 4 54.181 -28.674 46.018 1 50.78 ? C9 DME 603 A 1 HETATM 10 C C10 DME . . . E 4 55.013 -29.675 46.8 1 50.24 ? C10 DME 603 A 1 HETATM 11 C C11 DME . . . E 4 56.458 -29.221 46.884 1 50.02 ? C11 DME 603 A 1 HETATM 12 N N12 DME . . . E 4 57.416 -30.349 46.943 1 52.8 ? N12 DME 603 A 1 HETATM 13 C C13 DME . . . E 4 50.073 -31.874 39.588 1 69.2 ? C13 DME 603 A 1 HETATM 14 C C14 DME . . . E 4 48.705 -29.676 39.212 1 65.33 ? C14 DME 603 A 1 HETATM 15 C C15 DME . . . E 4 50.728 -30.032 38.673 1 65.16 ? C15 DME 603 A 1 HETATM 16 C C16 DME . . . E 4 58.828 -30.028 46.659 1 57.16 ? C16 DME 603 A 1 HETATM 17 C C17 DME . . . E 4 57.03 -31.765 47.134 1 51.97 ? C17 DME 603 A 1 HETATM 18 C C18 DME . . . E 4 57.629 -30.183 48.427 1 51.59 ? C18 DME 603 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #