data_5DGM # _model_server_result.job_id 2vArukx4qbBxK-M8pq2MIQ _model_server_result.datetime_utc '2025-02-05 18:09:31' _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 5dgm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5DGM # _exptl.entry_id 5DGM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 362.274 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '{2-[(phosphonomethyl)carbamoyl]-1H-benzo[g]indol-1-yl}acetic acid' _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 5DGM _cell.length_a 110.723 _cell.length_b 110.723 _cell.length_c 76.775 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DGM _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 software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 110.723 110.723 38.3875 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C16 H15 N2 O6 P' _chem_comp.formula_weight 362.274 _chem_comp.id 59Z _chem_comp.mon_nstd_flag . _chem_comp.name '{2-[(phosphonomethyl)carbamoyl]-1H-benzo[g]indol-1-yl}acetic 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 O2 P1 59Z doub 1 n n O38 C37 59Z doub 2 n n O3 P1 59Z sing 3 n n P1 O5 59Z sing 4 n n P1 C7 59Z sing 5 n n O13 C12 59Z doub 6 n n C37 O39 59Z sing 7 n n C37 C34 59Z sing 8 n n C21 C19 59Z doub 9 n y C21 C23 59Z sing 10 n y C24 C23 59Z sing 11 n y C24 C14 59Z doub 12 n y C19 C18 59Z sing 13 n y C23 C16 59Z doub 14 n y C12 C14 59Z sing 15 n n C12 N10 59Z sing 16 n n C14 N15 59Z sing 17 n y C18 C17 59Z doub 18 n y C18 C26 59Z sing 19 n y C16 N15 59Z sing 20 n y C16 C17 59Z sing 21 n y N15 C34 59Z sing 22 n n C17 C32 59Z sing 23 n y C7 N10 59Z sing 24 n n C26 C28 59Z doub 25 n y C32 C30 59Z doub 26 n y C28 C30 59Z sing 27 n y C7 H1 59Z sing 28 n n C7 H2 59Z sing 29 n n C21 H3 59Z sing 30 n n C24 H4 59Z sing 31 n n C26 H5 59Z sing 32 n n C28 H6 59Z sing 33 n n O3 H7 59Z sing 34 n n O5 H8 59Z sing 35 n n N10 H9 59Z sing 36 n n C19 H10 59Z sing 37 n n C30 H11 59Z sing 38 n n C32 H12 59Z sing 39 n n C34 H13 59Z sing 40 n n C34 H14 59Z sing 41 n n O39 H15 59Z sing 42 n n # _atom_sites.entry_id 5DGM _atom_sites.fract_transf_matrix[1][1] 0.009032 _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] 0.009032 _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] 0.013025 _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 B 2 59Z F 1 401 1 59Z LIG . C 3 PO4 F 1 402 1 PO4 PO4 . D 4 HOH F 1 501 5 HOH HOH . D 4 HOH F 2 502 20 HOH HOH . D 4 HOH F 3 503 26 HOH HOH . D 4 HOH F 4 504 31 HOH HOH . D 4 HOH F 5 505 8 HOH HOH . D 4 HOH F 6 506 14 HOH HOH . D 4 HOH F 7 507 17 HOH HOH . D 4 HOH F 8 508 11 HOH HOH . D 4 HOH F 9 509 10 HOH HOH . D 4 HOH F 10 510 29 HOH HOH . D 4 HOH F 11 511 1 HOH HOH . D 4 HOH F 12 512 12 HOH HOH . D 4 HOH F 13 513 9 HOH HOH . D 4 HOH F 14 514 19 HOH HOH . D 4 HOH F 15 515 2 HOH HOH . D 4 HOH F 16 516 15 HOH HOH . D 4 HOH F 17 517 27 HOH HOH . D 4 HOH F 18 518 25 HOH HOH . D 4 HOH F 19 519 6 HOH HOH . D 4 HOH F 20 520 30 HOH HOH . D 4 HOH F 21 521 23 HOH HOH . D 4 HOH F 22 522 32 HOH HOH . D 4 HOH F 23 523 21 HOH HOH . D 4 HOH F 24 524 4 HOH HOH . D 4 HOH F 25 525 22 HOH HOH . D 4 HOH F 26 526 16 HOH HOH . D 4 HOH F 27 527 33 HOH HOH . D 4 HOH F 28 528 13 HOH HOH . D 4 HOH F 29 529 18 HOH HOH . D 4 HOH F 30 530 28 HOH HOH . D 4 HOH F 31 531 24 HOH HOH . D 4 HOH F 32 532 3 HOH HOH . D 4 HOH F 33 533 7 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 C7 59Z . . . B 2 2.016 68.822 27.94 1 93.99 ? C7 59Z 401 F 1 HETATM 2 C C17 59Z . . . B 2 3.316 76.166 27.932 1 70.35 ? C17 59Z 401 F 1 HETATM 3 C C21 59Z . . . B 2 0.533 75.629 27.317 1 71.47 ? C21 59Z 401 F 1 HETATM 4 C C24 59Z . . . B 2 1.321 73.128 27.369 1 73.91 ? C24 59Z 401 F 1 HETATM 5 C C26 59Z . . . B 2 2.743 78.563 27.971 1 63.86 ? C26 59Z 401 F 1 HETATM 6 C C28 59Z . . . B 2 4.061 78.907 28.287 1 61.79 ? C28 59Z 401 F 1 HETATM 7 P P1 59Z . . . B 2 1.434 68.318 26.293 1 100.32 ? P1 59Z 401 F 1 HETATM 8 O O2 59Z . . . B 2 1.756 69.253 25.169 1 102.53 ? O2 59Z 401 F 1 HETATM 9 O O3 59Z . . . B 2 2.02 66.838 26.157 1 100.62 ? O3 59Z 401 F 1 HETATM 10 O O5 59Z . . . B 2 -0.14 68.06 26.427 1 101.83 ? O5 59Z 401 F 1 HETATM 11 N N10 59Z . . . B 2 1.885 70.271 28.119 1 89.15 ? N10 59Z 401 F 1 HETATM 12 C C12 59Z . . . B 2 2.73 71.15 27.512 1 81.76 ? C12 59Z 401 F 1 HETATM 13 O O13 59Z . . . B 2 3.634 70.786 26.777 1 79.85 ? O13 59Z 401 F 1 HETATM 14 C C14 59Z . . . B 2 2.522 72.611 27.653 1 76.59 ? C14 59Z 401 F 1 HETATM 15 N N15 59Z . . . B 2 3.419 73.581 27.844 1 73.89 ? N15 59Z 401 F 1 HETATM 16 C C16 59Z . . . B 2 2.827 74.819 27.783 1 73.02 ? C16 59Z 401 F 1 HETATM 17 C C18 59Z . . . B 2 2.363 77.217 27.78 1 68.03 ? C18 59Z 401 F 1 HETATM 18 C C19 59Z . . . B 2 1.012 76.944 27.454 1 70.36 ? C19 59Z 401 F 1 HETATM 19 C C23 59Z . . . B 2 1.471 74.61 27.492 1 72.75 ? C23 59Z 401 F 1 HETATM 20 C C30 59Z . . . B 2 5.018 77.901 28.423 1 63.49 ? C30 59Z 401 F 1 HETATM 21 C C32 59Z . . . B 2 4.643 76.563 28.262 1 67.22 ? C32 59Z 401 F 1 HETATM 22 C C34 59Z . . . B 2 4.852 73.326 28.103 1 70.52 ? C34 59Z 401 F 1 HETATM 23 C C37 59Z . . . B 2 5.753 73.57 26.901 1 67.87 ? C37 59Z 401 F 1 HETATM 24 O O38 59Z . . . B 2 5.362 73.962 25.798 1 63.87 ? O38 59Z 401 F 1 HETATM 25 O O39 59Z . . . B 2 7.045 73.312 27.146 1 69.55 ? O39 59Z 401 F 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #