data_5H6O # _model_server_result.job_id -9qTSC9GnRL-weE2k-ps3Q _model_server_result.datetime_utc '2025-02-20 01:01:17' _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 5h6o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5H6O # _exptl.entry_id 5H6O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 420.413 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic 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 5H6O _cell.length_a 94.23 _cell.length_b 94.23 _cell.length_c 165.34 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5H6O _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 248 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 248 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id CHA _struct_conn.ptnr2_label_comp_id DPM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id DPM _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 1.78 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C20 H24 N2 O8' _chem_comp.formula_weight 420.413 _chem_comp.id DPM _chem_comp.mon_nstd_flag . _chem_comp.name '3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'DIPYRROMETHANE COFACTOR' # 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 C1A C2A DPM doub 83 n y C1A CHA DPM sing 84 n n C1A NA DPM sing 85 n y C2A C3A DPM sing 86 n y C2A C5A DPM sing 87 n n C3A C4A DPM doub 88 n y C3A C7A DPM sing 89 n n C4A NA DPM sing 90 n y C4A CHB DPM sing 91 n n C5A C6A DPM sing 92 n n C6A O1A DPM doub 93 n n C6A O2A DPM sing 94 n n C7A C8A DPM sing 95 n n C8A C9A DPM sing 96 n n C9A O3A DPM doub 97 n n C9A O4A DPM sing 98 n n C1B C2B DPM doub 99 n y C1B CHB DPM sing 100 n n C1B NB DPM sing 101 n y C2B C3B DPM sing 102 n y C2B C5B DPM sing 103 n n C3B C4B DPM doub 104 n y C3B C7B DPM sing 105 n n C4B NB DPM sing 106 n y C5B C6B DPM sing 107 n n C6B O1B DPM doub 108 n n C6B O2B DPM sing 109 n n C7B C8B DPM sing 110 n n C8B C9B DPM sing 111 n n C9B O3B DPM doub 112 n n C9B O4B DPM sing 113 n n C5A H5A1 DPM sing 114 n n C5A H5A2 DPM sing 115 n n C7A H7A1 DPM sing 116 n n C7A H7A2 DPM sing 117 n n C8A H8A1 DPM sing 118 n n C8A H8A2 DPM sing 119 n n CHA HCA1 DPM sing 120 n n CHA HCA2 DPM sing 121 n n CHA HCA3 DPM sing 122 n n NA H10 DPM sing 123 n n O2A HOA2 DPM sing 124 n n O4A HOA4 DPM sing 125 n n C4B H4B1 DPM sing 126 n n C5B H5B1 DPM sing 127 n n C5B H5B2 DPM sing 128 n n C7B H7B1 DPM sing 129 n n C7B H7B2 DPM sing 130 n n C8B H8B1 DPM sing 131 n n C8B H8B2 DPM sing 132 n n CHB HCB1 DPM sing 133 n n CHB HCB2 DPM sing 134 n n NB H22 DPM sing 135 n n O2B HOB2 DPM sing 136 n n O4B HOB4 DPM sing 137 n n # _atom_sites.entry_id 5H6O _atom_sites.fract_transf_matrix[1][1] 0.010612 _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] 0.010612 _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] 0.006048 _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 DPM A 1 401 1 DPM DPM . C 3 MG A 1 402 1 MG MG . D 4 HOH A 1 501 18 HOH HOH . D 4 HOH A 2 502 10 HOH HOH . D 4 HOH A 3 503 4 HOH HOH . D 4 HOH A 4 504 20 HOH HOH . D 4 HOH A 5 505 3 HOH HOH . D 4 HOH A 6 506 2 HOH HOH . D 4 HOH A 7 507 9 HOH HOH . D 4 HOH A 8 508 19 HOH HOH . D 4 HOH A 9 509 11 HOH HOH . D 4 HOH A 10 510 12 HOH HOH . D 4 HOH A 11 511 5 HOH HOH . D 4 HOH A 12 512 1 HOH HOH . D 4 HOH A 13 513 14 HOH HOH . D 4 HOH A 14 514 15 HOH HOH . D 4 HOH A 15 515 17 HOH HOH . D 4 HOH A 16 516 16 HOH HOH . D 4 HOH A 17 517 7 HOH HOH . D 4 HOH A 18 518 6 HOH HOH . D 4 HOH A 19 519 13 HOH HOH . D 4 HOH A 20 520 8 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 C1A DPM . . . B 2 56.568 21.202 64.901 1 65.62 ? C1A DPM 401 A 1 HETATM 2 C C2A DPM . . . B 2 56.278 19.641 65.053 1 73.88 ? C2A DPM 401 A 1 HETATM 3 C C3A DPM . . . B 2 56.605 19.023 63.681 1 73.25 ? C3A DPM 401 A 1 HETATM 4 C C4A DPM . . . B 2 56.88 20.049 62.865 1 76.3 ? C4A DPM 401 A 1 HETATM 5 C C5A DPM . . . B 2 57.026 19.069 66.12 1 79.46 ? C5A DPM 401 A 1 HETATM 6 C C6A DPM . . . B 2 56.24 18.035 66.896 1 70.09 ? C6A DPM 401 A 1 HETATM 7 C C7A DPM . . . B 2 57.825 18.022 63.758 1 67.08 ? C7A DPM 401 A 1 HETATM 8 C C8A DPM . . . B 2 57.798 17.012 62.634 1 74.95 ? C8A DPM 401 A 1 HETATM 9 C C9A DPM . . . B 2 59.133 16.324 62.464 1 68.67 ? C9A DPM 401 A 1 HETATM 10 C CHA DPM . . . B 2 55.587 22.015 65.725 1 79.35 ? CHA DPM 401 A 1 HETATM 11 N NA DPM . . . B 2 56.464 21.455 63.63 1 64.16 ? NA DPM 401 A 1 HETATM 12 O O1A DPM . . . B 2 55.131 17.623 66.462 1 54.45 ? O1A DPM 401 A 1 HETATM 13 O O2A DPM . . . B 2 56.694 17.585 67.981 1 59.85 ? O2A DPM 401 A 1 HETATM 14 O O3A DPM . . . B 2 60.023 16.456 63.345 1 77.63 ? O3A DPM 401 A 1 HETATM 15 O O4A DPM . . . B 2 59.356 15.62 61.442 1 70.51 ? O4A DPM 401 A 1 HETATM 16 C C1B DPM . . . B 2 54.835 20.184 61.408 1 73.18 ? C1B DPM 401 A 1 HETATM 17 C C2B DPM . . . B 2 53.918 19.421 60.687 1 83.71 ? C2B DPM 401 A 1 HETATM 18 C C3B DPM . . . B 2 52.669 20.062 60.844 1 70.96 ? C3B DPM 401 A 1 HETATM 19 C C4B DPM . . . B 2 52.907 21.177 61.643 1 73.3 ? C4B DPM 401 A 1 HETATM 20 C C5B DPM . . . B 2 54.199 18.16 59.903 1 80.49 ? C5B DPM 401 A 1 HETATM 21 C C6B DPM . . . B 2 54.335 16.949 60.798 1 74.42 ? C6B DPM 401 A 1 HETATM 22 C C7B DPM . . . B 2 51.347 19.628 60.256 1 69.32 ? C7B DPM 401 A 1 HETATM 23 C C8B DPM . . . B 2 50.44 18.985 61.279 1 63.9 ? C8B DPM 401 A 1 HETATM 24 C C9B DPM . . . B 2 49.322 19.92 61.682 1 72.09 ? C9B DPM 401 A 1 HETATM 25 C CHB DPM . . . B 2 56.313 19.878 61.518 1 73.07 ? CHB DPM 401 A 1 HETATM 26 N NB DPM . . . B 2 54.192 21.205 61.946 1 81.79 ? NB DPM 401 A 1 HETATM 27 O O1B DPM . . . B 2 54.893 15.906 60.366 1 76.65 ? O1B DPM 401 A 1 HETATM 28 O O2B DPM . . . B 2 53.895 16.984 61.977 1 73.24 ? O2B DPM 401 A 1 HETATM 29 O O3B DPM . . . B 2 48.738 20.617 60.809 1 70 ? O3B DPM 401 A 1 HETATM 30 O O4B DPM . . . B 2 48.975 20.007 62.889 1 78.13 ? O4B DPM 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 30 #