data_5NPL # _model_server_result.job_id k-Xv1Ou4tYCHY0X291fVTQ _model_server_result.datetime_utc '2024-11-16 16:34:35' _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 5npl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":302}' # _entry.id 5NPL # _exptl.entry_id 5NPL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.459 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID' _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 5NPL _cell.length_a 79.89 _cell.length_b 120.734 _cell.length_c 117.548 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NPL _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,Q,R,S,T,U,V,W,X,Y _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' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -58.774 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N 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 disulf ? disulf1 A SG CYS 153 A CYS 153 1_555 A SG CYS 163 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf2 B SG CYS 153 B CYS 153 1_555 B SG CYS 163 B CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 C SG CYS 153 C CYS 153 1_555 C SG CYS 163 C CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc1 A NH2 ARG 37 A ARG 37 1_555 I YB YB . A YB 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.444 ? metalc ? metalc2 A OE2 GLU 42 A GLU 42 1_555 H YB YB . A YB 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.141 ? metalc ? metalc3 D YB YB . A YB 301 1_555 E N4 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.413 ? metalc ? metalc4 D YB YB . A YB 301 1_555 E O5 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.39 ? metalc ? metalc5 D YB YB . A YB 301 1_555 E O7 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.485 ? metalc ? metalc6 D YB YB . A YB 301 1_555 E O1 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.116 ? metalc ? metalc7 D YB YB . A YB 301 1_555 E N3 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.388 ? metalc ? metalc8 D YB YB . A YB 301 1_555 E N2 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.413 ? metalc ? metalc9 D YB YB . A YB 301 1_555 E O4 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.214 ? metalc ? metalc10 F YB YB . A YB 303 1_555 G N2 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.341 ? metalc ? metalc11 F YB YB . A YB 303 1_555 G N3 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.388 ? metalc ? metalc12 F YB YB . A YB 303 1_555 G O5 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.86 ? metalc ? metalc13 F YB YB . A YB 303 1_555 G N4 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.359 ? metalc ? metalc14 F YB YB . A YB 303 1_555 G N1 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.422 ? metalc ? metalc15 F YB YB . A YB 303 1_555 G O4 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.599 ? metalc ? metalc16 F YB YB . A YB 303 1_555 G O1 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.055 ? metalc ? metalc17 F YB YB . A YB 303 1_555 G O7 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.307 ? # _chem_comp.formula 'C17 H32 N4 O7' _chem_comp.formula_weight 404.459 _chem_comp.id DO3 _chem_comp.mon_nstd_flag . _chem_comp.name '10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID' _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 C1 DO3 sing 83 n n N1 C8 DO3 sing 84 n n N1 C10 DO3 sing 85 n n N2 C2 DO3 sing 86 n n N2 C3 DO3 sing 87 n n N2 C12 DO3 sing 88 n n N3 C4 DO3 sing 89 n n N3 C5 DO3 sing 90 n n N3 C14 DO3 sing 91 n n N4 C6 DO3 sing 92 n n N4 C7 DO3 sing 93 n n N4 C16 DO3 sing 94 n n O1 C9 DO3 sing 95 n n O1 HO1 DO3 sing 96 n n O3 C11 DO3 sing 97 n n O3 HO3 DO3 sing 98 n n O5 C13 DO3 sing 99 n n O5 HO5 DO3 sing 100 n n O7 C15 DO3 sing 101 n n O7 HO7 DO3 sing 102 n n C1 C2 DO3 sing 103 n n C1 HC11 DO3 sing 104 n n C1 HC12 DO3 sing 105 n n C2 HC21 DO3 sing 106 n n C2 HC22 DO3 sing 107 n n C3 C4 DO3 sing 108 n n C3 HC31 DO3 sing 109 n n C3 HC32 DO3 sing 110 n n C4 HC41 DO3 sing 111 n n C4 HC42 DO3 sing 112 n n C5 C6 DO3 sing 113 n n C5 HC51 DO3 sing 114 n n C5 HC52 DO3 sing 115 n n C6 HC61 DO3 sing 116 n n C6 HC62 DO3 sing 117 n n C7 C8 DO3 sing 118 n n C7 HC71 DO3 sing 119 n n C7 HC72 DO3 sing 120 n n C8 HC81 DO3 sing 121 n n C8 HC82 DO3 sing 122 n n C9 C10 DO3 sing 123 n n C9 O2 DO3 doub 124 n n C10 H101 DO3 sing 125 n n C10 H102 DO3 sing 126 n n C11 C12 DO3 sing 127 n n C11 O4 DO3 doub 128 n n C12 H121 DO3 sing 129 n n C12 H122 DO3 sing 130 n n C13 C14 DO3 sing 131 n n C13 O6 DO3 doub 132 n n C14 H141 DO3 sing 133 n n C14 H142 DO3 sing 134 n n C15 C16 DO3 sing 135 n n C15 C17 DO3 sing 136 n n C15 HA DO3 sing 137 n n C16 H161 DO3 sing 138 n n C16 H162 DO3 sing 139 n n C17 H171 DO3 sing 140 n n C17 H172 DO3 sing 141 n n C17 H173 DO3 sing 142 n n # _atom_sites.entry_id 5NPL _atom_sites.fract_transf_matrix[1][1] 0.012517 _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] 0.008283 _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] 0.008507 _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 D 2 YB A 1 301 301 YB YB . E 3 DO3 A 1 302 302 DO3 DO3 . F 2 YB A 1 303 303 YB YB . G 3 DO3 A 1 304 304 DO3 DO3 . H 2 YB A 1 305 305 YB YB . I 2 YB A 1 306 306 YB YB . J 2 YB A 1 307 307 YB YB . K 2 YB A 1 308 309 YB YB . L 2 YB B 1 301 301 YB YB . M 2 YB B 1 302 302 YB YB . N 2 YB B 1 303 303 YB YB . O 2 YB C 1 301 301 YB YB . P 2 YB C 1 302 303 YB YB . Q 2 YB C 1 303 304 YB YB . R 2 YB C 1 304 305 YB YB . S 2 YB C 1 305 306 YB YB . T 2 YB C 1 306 307 YB YB . U 2 YB C 1 307 308 YB YB . V 2 YB C 1 308 310 YB YB . W 4 HOH A 1 401 1 HOH HOH . W 4 HOH A 2 402 2 HOH HOH . W 4 HOH A 3 403 18 HOH HOH . W 4 HOH A 4 404 5 HOH HOH . W 4 HOH A 5 405 7 HOH HOH . W 4 HOH A 6 406 3 HOH HOH . W 4 HOH A 7 407 4 HOH HOH . W 4 HOH A 8 408 9 HOH HOH . W 4 HOH A 9 409 6 HOH HOH . W 4 HOH A 10 410 10 HOH HOH . W 4 HOH A 11 411 8 HOH HOH . W 4 HOH A 12 412 11 HOH HOH . W 4 HOH A 13 413 12 HOH HOH . W 4 HOH A 14 414 13 HOH HOH . W 4 HOH A 15 415 27 HOH HOH . W 4 HOH A 16 416 14 HOH HOH . X 4 HOH B 1 401 16 HOH HOH . X 4 HOH B 2 402 17 HOH HOH . X 4 HOH B 3 403 15 HOH HOH . X 4 HOH B 4 404 19 HOH HOH . X 4 HOH B 5 405 20 HOH HOH . X 4 HOH B 6 406 21 HOH HOH . X 4 HOH B 7 407 22 HOH HOH . X 4 HOH B 8 408 24 HOH HOH . X 4 HOH B 9 409 23 HOH HOH . X 4 HOH B 10 410 25 HOH HOH . X 4 HOH B 11 411 26 HOH HOH . X 4 HOH B 12 412 28 HOH HOH . X 4 HOH B 13 413 29 HOH HOH . X 4 HOH B 14 414 30 HOH HOH . X 4 HOH B 15 415 31 HOH HOH . X 4 HOH B 16 416 32 HOH HOH . X 4 HOH B 17 417 33 HOH HOH . Y 4 HOH C 1 401 34 HOH HOH . Y 4 HOH C 2 402 36 HOH HOH . Y 4 HOH C 3 403 37 HOH HOH . Y 4 HOH C 4 404 38 HOH HOH . Y 4 HOH C 5 405 35 HOH HOH . Y 4 HOH C 6 406 40 HOH HOH . Y 4 HOH C 7 407 39 HOH HOH . Y 4 HOH C 8 408 42 HOH HOH . Y 4 HOH C 9 409 43 HOH HOH . Y 4 HOH C 10 410 41 HOH HOH . Y 4 HOH C 11 411 46 HOH HOH . Y 4 HOH C 12 412 47 HOH HOH . Y 4 HOH C 13 413 48 HOH HOH . Y 4 HOH C 14 414 45 HOH HOH . Y 4 HOH C 15 415 44 HOH HOH . Y 4 HOH C 16 416 49 HOH HOH . Y 4 HOH C 17 417 50 HOH HOH . Y 4 HOH C 18 418 51 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 DO3 . A . E 3 15.332 -38.049 14.31 1 67.32 ? N1 DO3 302 A 1 HETATM 2 N N2 DO3 . A . E 3 15.86 -38.142 18.136 1 65.6 ? N2 DO3 302 A 1 HETATM 3 N N3 DO3 . A . E 3 17.116 -41.686 18.171 1 67.36 ? N3 DO3 302 A 1 HETATM 4 N N4 DO3 . A . E 3 15.929 -41.409 14.909 1 67.41 ? N4 DO3 302 A 1 HETATM 5 O O1 DO3 . A . E 3 13.302 -38.988 15.882 1 56.48 ? O1 DO3 302 A 1 HETATM 6 O O3 DO3 . A . E 3 12.628 -38.505 19.848 1 64.61 ? O3 DO3 302 A 1 HETATM 7 O O5 DO3 . A . E 3 14.348 -42.974 17.372 1 72.31 ? O5 DO3 302 A 1 HETATM 8 O O7 DO3 . A . E 3 13.254 -41.738 14.535 1 60.66 ? O7 DO3 302 A 1 HETATM 9 C C1 DO3 . A . E 3 15.492 -37.406 15.66 1 65.17 ? C1 DO3 302 A 1 HETATM 10 C C2 DO3 . A . E 3 16.15 -38.305 16.696 1 64.4 ? C2 DO3 302 A 1 HETATM 11 C C3 DO3 . A . E 3 16.532 -39.181 19.001 1 65.95 ? C3 DO3 302 A 1 HETATM 12 C C4 DO3 . A . E 3 17.492 -40.242 18.385 1 65.64 ? C4 DO3 302 A 1 HETATM 13 C C5 DO3 . A . E 3 17.432 -42.307 16.831 1 63.1 ? C5 DO3 302 A 1 HETATM 14 C C6 DO3 . A . E 3 17.289 -41.538 15.507 1 65.92 ? C6 DO3 302 A 1 HETATM 15 C C7 DO3 . A . E 3 15.976 -40.522 13.731 1 64.7 ? C7 DO3 302 A 1 HETATM 16 C C8 DO3 . A . E 3 16.342 -39.06 13.877 1 65.77 ? C8 DO3 302 A 1 HETATM 17 C C9 DO3 . A . E 3 12.907 -38.523 14.796 1 63.34 ? C9 DO3 302 A 1 HETATM 18 C C10 DO3 . A . E 3 13.937 -38.071 13.783 1 64.56 ? C10 DO3 302 A 1 HETATM 19 C C11 DO3 . A . E 3 13.491 -38.819 18.986 1 68.71 ? C11 DO3 302 A 1 HETATM 20 C C12 DO3 . A . E 3 14.463 -37.727 18.538 1 68.55 ? C12 DO3 302 A 1 HETATM 21 C C13 DO3 . A . E 3 15.108 -43.313 18.305 1 73.4 ? C13 DO3 302 A 1 HETATM 22 C C14 DO3 . A . E 3 15.934 -42.217 18.933 1 70.13 ? C14 DO3 302 A 1 HETATM 23 C C15 DO3 . A . E 3 14.009 -42.811 13.955 1 63.16 ? C15 DO3 302 A 1 HETATM 24 C C16 DO3 . A . E 3 15.481 -42.732 14.392 1 65.92 ? C16 DO3 302 A 1 HETATM 25 C C17 DO3 . A . E 3 13.361 -44.15 14.301 1 66.61 ? C17 DO3 302 A 1 HETATM 26 O O2 DO3 . A . E 3 11.692 -38.395 14.526 1 64.59 ? O2 DO3 302 A 1 HETATM 27 O O4 DO3 . A . E 3 13.57 -39.979 18.503 1 61.78 ? O4 DO3 302 A 1 HETATM 28 O O6 DO3 . A . E 3 15.205 -44.482 18.758 1 74.58 ? O6 DO3 302 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #