data_9J1D # _model_server_result.job_id YPOhK54dszgwNqdxlmCs7w _model_server_result.datetime_utc '2024-12-23 18:17:39' _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 9j1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 9J1D # _exptl.entry_id 9J1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 766.746 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}2,~{N}9-bis[2-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethoxy]ethyl]-1,10-phenanthroline-2,9-dicarboxamide _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 90 _cell.entry_id 9J1D _cell.length_a 141.43 _cell.length_b 141.43 _cell.length_c 80.41 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9J1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 OE2 GLU 8 A GLU 8 1_555 E MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc2 A OD1 ASP 10 A ASP 10 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.185 ? metalc ? metalc3 A OD2 ASP 10 A ASP 10 1_555 E MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? metalc ? metalc4 A O TYR 12 A TYR 12 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc5 A OD1 ASN 14 A ASN 14 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc6 A OD2 ASP 19 A ASP 19 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc7 A OD1 ASP 19 A ASP 19 1_555 E MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc8 A NE2 HIS 24 A HIS 24 1_555 E MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc9 B OE1 GLU 8 B GLU 8 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc10 B OE2 GLU 8 B GLU 8 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc11 B OD1 ASP 10 B ASP 10 1_555 F CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc12 B OD2 ASP 10 B ASP 10 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc13 B O TYR 12 B TYR 12 1_555 F CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc14 B OD2 ASP 19 B ASP 19 1_555 F CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc15 B OD1 ASP 19 B ASP 19 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc16 B OD2 ASP 19 B ASP 19 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? # _chem_comp.formula 'C34 H46 N4 O16' _chem_comp.formula_weight 766.746 _chem_comp.id A1EAW _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}2,~{N}9-bis[2-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethoxy]ethyl]-1,10-phenanthroline-2,9-dicarboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,6-DI-O-PHOSPHONO-D-MANNITOL # 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 O3M C3M A1EAW sing 1 n n O2M C2M A1EAW sing 2 n n O6M C6M A1EAW sing 3 n n C4M O4M A1EAW sing 4 n n C4M C3M A1EAW sing 5 n n C4M C5M A1EAW sing 6 n n C3M C2M A1EAW sing 7 n n C2M C1M A1EAW sing 8 n n C6M C5M A1EAW sing 9 n n O5M C5M A1EAW sing 10 n n O5M C1M A1EAW sing 11 n n O3M2 C3M2 A1EAW sing 12 n n C1M O1M A1EAW sing 13 n n C33 C20 A1EAW sing 14 n n C33 O1M2 A1EAW sing 15 n n C3M2 C2M2 A1EAW sing 16 n n C3M2 C4M2 A1EAW sing 17 n n C18 C17 A1EAW sing 18 n n C18 O1 A1EAW sing 19 n n C2M2 O2M2 A1EAW sing 20 n n C2M2 C1M2 A1EAW sing 21 n n C20 O1 A1EAW sing 22 n n O1M2 C1M2 A1EAW sing 23 n n C17 N2 A1EAW sing 24 n n O1M C21 A1EAW sing 25 n n O4M2 C4M2 A1EAW sing 26 n n C1M2 O5M2 A1EAW sing 27 n n C22 C21 A1EAW sing 28 n n C22 O8 A1EAW sing 29 n n C4M2 C5M2 A1EAW sing 30 n n C19 O8 A1EAW sing 31 n n C19 C16 A1EAW sing 32 n n N2 C15 A1EAW sing 33 n n C5M2 O5M2 A1EAW sing 34 n n C5M2 C6M2 A1EAW sing 35 n n O C15 A1EAW doub 36 n n C16 N3 A1EAW sing 37 n n C15 C5 A1EAW sing 38 n n O6M2 C6M2 A1EAW sing 39 n n O7 C13 A1EAW doub 40 n n N3 C13 A1EAW sing 41 n n C5 N A1EAW doub 42 n y C5 C A1EAW sing 43 n y C13 C12 A1EAW sing 44 n n N C3 A1EAW sing 45 n y C C1 A1EAW doub 46 n y N1 C12 A1EAW doub 47 n y N1 C9 A1EAW sing 48 n y C12 C11 A1EAW sing 49 n y C3 C9 A1EAW doub 50 n y C3 C2 A1EAW sing 51 n y C9 C8 A1EAW sing 52 n y C1 C2 A1EAW sing 53 n y C2 C6 A1EAW doub 54 n y C11 C10 A1EAW doub 55 n y C8 C10 A1EAW sing 56 n y C8 C7 A1EAW doub 57 n y C6 C7 A1EAW sing 58 n y C1 H1 A1EAW sing 59 n n C6 H2 A1EAW sing 60 n n C H3 A1EAW sing 61 n n C10 H4 A1EAW sing 62 n n C11 H5 A1EAW sing 63 n n C16 H6 A1EAW sing 64 n n C16 H7 A1EAW sing 65 n n C17 H8 A1EAW sing 66 n n C17 H9 A1EAW sing 67 n n C18 H10 A1EAW sing 68 n n C18 H11 A1EAW sing 69 n n C19 H12 A1EAW sing 70 n n C19 H13 A1EAW sing 71 n n C1M H14 A1EAW sing 72 n n C20 H15 A1EAW sing 73 n n C20 H16 A1EAW sing 74 n n C21 H17 A1EAW sing 75 n n C21 H18 A1EAW sing 76 n n C22 H19 A1EAW sing 77 n n C22 H20 A1EAW sing 78 n n C2M H21 A1EAW sing 79 n n C33 H22 A1EAW sing 80 n n C33 H23 A1EAW sing 81 n n C3M H24 A1EAW sing 82 n n C4M H25 A1EAW sing 83 n n C5M H26 A1EAW sing 84 n n C6M H27 A1EAW sing 85 n n C6M H28 A1EAW sing 86 n n C7 H29 A1EAW sing 87 n n N2 H30 A1EAW sing 88 n n N3 H31 A1EAW sing 89 n n O2M H32 A1EAW sing 90 n n O3M H33 A1EAW sing 91 n n O4M H34 A1EAW sing 92 n n O6M H35 A1EAW sing 93 n n C1M2 H36 A1EAW sing 94 n n C2M2 H37 A1EAW sing 95 n n C3M2 H38 A1EAW sing 96 n n C4M2 H39 A1EAW sing 97 n n C5M2 H40 A1EAW sing 98 n n C6M2 H41 A1EAW sing 99 n n C6M2 H42 A1EAW sing 100 n n O2M2 H43 A1EAW sing 101 n n O3M2 H44 A1EAW sing 102 n n O4M2 H45 A1EAW sing 103 n n O6M2 H46 A1EAW sing 104 n n # _atom_sites.entry_id 9J1D _atom_sites.fract_transf_matrix[1][1] 0.007071 _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] 0.007071 _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] 0.012436 _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 2 A1EAW A 1 301 301 A1EAW M2P . D 3 CA A 1 302 1 CA CA . E 4 MN A 1 303 1 MN MN . F 3 CA B 1 301 2 CA CA . G 4 MN B 1 302 2 MN MN . # 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 A1EAW . . . C 2 -25.894 23.704 0.947 1 151.25 ? C1 A1EAW 301 A 1 HETATM 2 C C5 A1EAW . . . C 2 -26.475 24.025 -1.36 1 148.62 ? C5 A1EAW 301 A 1 HETATM 3 C C6 A1EAW . . . C 2 -27.154 24.875 2.633 1 146.63 ? C6 A1EAW 301 A 1 HETATM 4 C C3 A1EAW . . . C 2 -27.693 25.159 0.301 1 154.08 ? C3 A1EAW 301 A 1 HETATM 5 C C2 A1EAW . . . C 2 -26.914 24.579 1.296 1 152 ? C2 A1EAW 301 A 1 HETATM 6 N N A1EAW . . . C 2 -27.462 24.874 -0.999 1 152.34 ? N A1EAW 301 A 1 HETATM 7 C C A1EAW . . . C 2 -25.674 23.425 -0.395 1 149.44 ? C A1EAW 301 A 1 HETATM 8 O O A1EAW . . . C 2 -25.106 23.772 -3.257 1 143.97 ? O A1EAW 301 A 1 HETATM 9 C C10 A1EAW . . . C 2 -29.98 27.21 2.317 1 159.24 ? C10 A1EAW 301 A 1 HETATM 10 C C11 A1EAW . . . C 2 -30.752 27.783 1.312 1 160.24 ? C11 A1EAW 301 A 1 HETATM 11 C C12 A1EAW . . . C 2 -30.5 27.478 -0.021 1 160.17 ? C12 A1EAW 301 A 1 HETATM 12 C C13 A1EAW . . . C 2 -31.36 28.119 -1.095 1 159.89 ? C13 A1EAW 301 A 1 HETATM 13 C C15 A1EAW . . . C 2 -26.241 23.727 -2.812 1 147.59 ? C15 A1EAW 301 A 1 HETATM 14 C C7 A1EAW . . . C 2 -28.176 25.752 2.978 1 149.08 ? C7 A1EAW 301 A 1 HETATM 15 C C8 A1EAW . . . C 2 -28.956 26.331 1.983 1 155.38 ? C8 A1EAW 301 A 1 HETATM 16 C C9 A1EAW . . . C 2 -28.714 26.036 0.648 1 155.26 ? C9 A1EAW 301 A 1 HETATM 17 N N1 A1EAW . . . C 2 -29.489 26.613 -0.318 1 158.8 ? N1 A1EAW 301 A 1 HETATM 18 O O7 A1EAW . . . C 2 -32.305 27.498 -1.554 1 153.09 ? O7 A1EAW 301 A 1 HETATM 19 C C33 A1EAW . . . C 2 -29.158 21.638 -5.704 1 141.18 ? C33 A1EAW 301 A 1 HETATM 20 C C20 A1EAW . . . C 2 -30.269 22.57 -5.236 1 141.12 ? C20 A1EAW 301 A 1 HETATM 21 C C18 A1EAW . . . C 2 -28.673 24.302 -5.415 1 153.49 ? C18 A1EAW 301 A 1 HETATM 22 C C17 A1EAW . . . C 2 -27.315 23.759 -4.988 1 153.96 ? C17 A1EAW 301 A 1 HETATM 23 N N2 A1EAW . . . C 2 -27.284 23.419 -3.579 1 151.38 ? N2 A1EAW 301 A 1 HETATM 24 O O1 A1EAW . . . C 2 -29.696 23.717 -4.612 1 146.58 ? O1 A1EAW 301 A 1 HETATM 25 O O1M2 A1EAW . . . C 2 -29.38 20.331 -5.178 1 136.93 ? O1M2 A1EAW 301 A 1 HETATM 26 C C1M2 A1EAW . . . C 2 -28.241 19.845 -4.47 1 137.69 ? C1M2 A1EAW 301 A 1 HETATM 27 C C2M2 A1EAW . . . C 2 -27.511 18.82 -5.326 1 128.54 ? C2M2 A1EAW 301 A 1 HETATM 28 C C3M2 A1EAW . . . C 2 -28.42 17.634 -5.618 1 124.51 ? C3M2 A1EAW 301 A 1 HETATM 29 C C4M2 A1EAW . . . C 2 -29.081 17.12 -4.345 1 126.3 ? C4M2 A1EAW 301 A 1 HETATM 30 C C5M2 A1EAW . . . C 2 -29.666 18.25 -3.505 1 131.69 ? C5M2 A1EAW 301 A 1 HETATM 31 C C6M2 A1EAW . . . C 2 -30.2 17.722 -2.179 1 144.12 ? C6M2 A1EAW 301 A 1 HETATM 32 O O2M2 A1EAW . . . C 2 -26.338 18.369 -4.641 1 123.6 ? O2M2 A1EAW 301 A 1 HETATM 33 O O3M2 A1EAW . . . C 2 -27.653 16.582 -6.215 1 137.23 ? O3M2 A1EAW 301 A 1 HETATM 34 O O4M2 A1EAW . . . C 2 -30.137 16.229 -4.706 1 124.95 ? O4M2 A1EAW 301 A 1 HETATM 35 O O5M2 A1EAW . . . C 2 -28.663 19.229 -3.257 1 141 ? O5M2 A1EAW 301 A 1 HETATM 36 O O6M2 A1EAW . . . C 2 -31.078 16.618 -2.426 1 145.61 ? O6M2 A1EAW 301 A 1 HETATM 37 C C21 A1EAW . . . C 2 -31.335 26.078 -4.301 1 166.28 ? C21 A1EAW 301 A 1 HETATM 38 C C22 A1EAW . . . C 2 -30.029 26.849 -4.454 1 163.46 ? C22 A1EAW 301 A 1 HETATM 39 C C19 A1EAW . . . C 2 -30.073 29.105 -3.755 1 166.07 ? C19 A1EAW 301 A 1 HETATM 40 C C16 A1EAW . . . C 2 -31.172 29.728 -2.902 1 162.04 ? C16 A1EAW 301 A 1 HETATM 41 N N3 A1EAW . . . C 2 -31.059 29.347 -1.508 1 162.11 ? N3 A1EAW 301 A 1 HETATM 42 O O8 A1EAW . . . C 2 -29.877 27.749 -3.358 1 177.16 ? O8 A1EAW 301 A 1 HETATM 43 O O1M A1EAW . . . C 2 -32.413 26.865 -4.805 1 167.55 ? O1M A1EAW 301 A 1 HETATM 44 C C1M A1EAW . . . C 2 -32.867 26.392 -6.071 1 158.15 ? C1M A1EAW 301 A 1 HETATM 45 C C2M A1EAW . . . C 2 -31.81 26.681 -7.13 1 156.23 ? C2M A1EAW 301 A 1 HETATM 46 C C3M A1EAW . . . C 2 -31.612 28.181 -7.311 1 151.97 ? C3M A1EAW 301 A 1 HETATM 47 C C4M A1EAW . . . C 2 -32.95 28.886 -7.495 1 148.73 ? C4M A1EAW 301 A 1 HETATM 48 C C5M A1EAW . . . C 2 -33.935 28.473 -6.408 1 145.95 ? C5M A1EAW 301 A 1 HETATM 49 C C6M A1EAW . . . C 2 -35.294 29.127 -6.625 1 150.17 ? C6M A1EAW 301 A 1 HETATM 50 O O2M A1EAW . . . C 2 -32.209 26.099 -8.376 1 150.29 ? O2M A1EAW 301 A 1 HETATM 51 O O3M A1EAW . . . C 2 -30.782 28.421 -8.453 1 169.43 ? O3M A1EAW 301 A 1 HETATM 52 O O4M A1EAW . . . C 2 -32.754 30.304 -7.45 1 149.54 ? O4M A1EAW 301 A 1 HETATM 53 O O5M A1EAW . . . C 2 -34.082 27.054 -6.417 1 157.61 ? O5M A1EAW 301 A 1 HETATM 54 O O6M A1EAW . . . C 2 -35.729 28.888 -7.968 1 156.86 ? O6M A1EAW 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 54 #