data_8AGC # _model_server_result.job_id GfcM9Tj6hGTocxIpKeYbWg _model_server_result.datetime_utc '2024-11-22 10:33:47' _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 8agc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":101}' # _entry.id 8AGC # _exptl.entry_id 8AGC _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 414.453 _entity.id 18 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate _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 8AGC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AGC _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _pdbx_struct_assembly.details author_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 _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 ? _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 18 _struct_asym.id X _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 10 oligosaccharide 11 oligosaccharide 12 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 ? 10 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 10 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 10 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 10 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 10 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 10 7 3 MAN BMA C1 O1 . O6 HO6 . sing 7 ? 11 2 1 NAG NAG C1 O1 . O4 HO4 . sing 8 ? 12 2 1 NAG NDG C1 O1 . O4 HO4 . sing 9 ? 12 3 2 BMA NAG C1 O1 . O4 HO4 . sing 10 ? 12 4 3 MAN BMA C1 O1 . O3 HO3 . sing 11 ? 12 5 4 MAN MAN C1 O1 . O2 HO2 . sing 12 ? 12 6 5 MAN MAN C1 O1 . O2 HO2 . sing 13 ? 12 7 6 GLC MAN C1 O1 . O3 HO3 . sing 14 ? 12 8 7 GLC GLC C1 O1 . O3 HO3 . sing 15 ? 12 9 8 GLC GLC C1 O1 . O2 HO2 . sing 16 ? 12 10 3 MAN BMA C1 O1 . O6 HO6 . sing 17 ? 12 11 10 MAN MAN C1 O1 . O3 HO3 . 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 10 n J NAG 1 I 1 NAG A 1002 NAG 10 n J NAG 2 I 2 NAG A 1009 NAG 10 n J BMA 3 I 3 BMA A 1010 BMA 10 n J MAN 4 I 4 MAN A 1011 MAN 10 n J MAN 5 I 5 MAN A 1006 MAN 10 n J MAN 6 I 6 MAN A 1007 MAN 10 n J MAN 7 I 7 MAN A 1008 MAN 11 n K NAG 1 J 1 NAG I 1 NAG 11 n K NAG 2 J 2 NAG I 2 NAG 11 n L NAG 1 K 1 NAG J 1 NAG 11 n L NAG 2 K 2 NAG J 2 NAG 12 n M NDG 1 L 1 NDG K 1 NDG 12 n M NAG 2 L 2 NAG K 2 NAG 12 n M BMA 3 L 3 BMA K 3 BMA 12 n M MAN 4 L 4 MAN K 4 MAN 12 n M MAN 5 L 5 MAN K 5 MAN 12 n M MAN 6 L 6 MAN K 6 MAN 12 n M GLC 7 L 7 GLC K 7 GLC 12 n M GLC 8 L 8 GLC K 8 GLC 12 n M GLC 9 L 9 GLC K 9 GLC 12 n M MAN 10 L 10 MAN K 10 MAN 12 n M MAN 11 L 11 MAN K 11 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 covale ? covale1 A ND2 ASN 539 A ASN 539 1_555 J C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 N O1B ELU . A ELU 1001 1_555 M C1 NDG . L NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale3 E ND2 ASN 336 E ASN 336 1_555 K C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 E ND2 ASN 400 E ASN 400 1_555 L C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale5 G ND2 ASN 60 G ASN 60 1_555 V C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale6 G ND2 ASN 332 G ASN 332 1_555 U C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 I N TYR 1 P TYR 2 1_555 X C25 323 . P 323 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale8 I C ALA 2 P ALA 3 1_555 I N DAB 3 P DAB 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 I C DAB 3 P DAB 4 1_555 I N ALA 4 P ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 J O4 NAG . I NAG 1 1_555 J C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale11 J O4 NAG . I NAG 2 1_555 J C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 J O3 BMA . I BMA 3 1_555 J C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 J O6 BMA . I BMA 3 1_555 J C1 MAN . I MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 J O2 MAN . I MAN 4 1_555 J C1 MAN . I MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale15 J O2 MAN . I MAN 5 1_555 J C1 MAN . I MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale16 K O4 NAG . J NAG 1 1_555 K C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale17 L O4 NAG . K NAG 1 1_555 L C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale18 M O4 NDG . L NDG 1 1_555 M C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 M O4 NAG . L NAG 2 1_555 M C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale20 M O3 BMA . L BMA 3 1_555 M C1 MAN . L MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale21 M O6 BMA . L BMA 3 1_555 M C1 MAN . L MAN 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale22 M O2 MAN . L MAN 4 1_555 M C1 MAN . L MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale23 M O2 MAN . L MAN 5 1_555 M C1 MAN . L MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale24 M O3 MAN . L MAN 6 1_555 M C1 GLC . L GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale25 M O3 GLC . L GLC 7 1_555 M C1 GLC . L GLC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale26 M O2 GLC . L GLC 8 1_555 M C1 GLC . L GLC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale27 M O3 MAN . L MAN 10 1_555 M C1 MAN . L MAN 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A OD2 ASP 166 A ASP 166 1_555 Q MN MN . A MN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 N O2B ELU . A ELU 1001 1_555 Q MN MN . A MN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? # _chem_comp.formula 'C25 H22 N2 O4' _chem_comp.formula_weight 414.453 _chem_comp.id 323 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "5-Carboxy-N,N'-tetramethyl rhodamine" # 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 O4 C25 323 doub 1 n n C25 C21 323 sing 2 n n C21 C22 323 doub 3 n y C21 C20 323 sing 4 n y C22 C23 323 sing 5 n y C20 C19 323 doub 6 n y O3 C24 323 doub 7 n n C23 C24 323 sing 8 n n C23 C18 323 doub 9 n y C19 C18 323 sing 10 n y C24 O2 323 sing 11 n n C18 C1 323 sing 12 n n C10 C11 323 doub 13 n y C10 C2 323 sing 14 n y C1 C2 323 doub 15 n n C1 C5 323 sing 16 n n C11 C12 323 sing 17 n y C2 C3 323 sing 18 n y C9 C5 323 doub 19 n y C9 C8 323 sing 20 n y C5 C4 323 sing 21 n y C17 N1 323 sing 22 n n C12 N1 323 doub 23 n n C12 C13 323 sing 24 n y C8 C7 323 doub 25 n y C3 C13 323 doub 26 n y C3 O1 323 sing 27 n n N1 C16 323 sing 28 n n C4 O1 323 sing 29 n n C4 C6 323 doub 30 n y C7 C6 323 sing 31 n y C7 N2 323 sing 32 n n C15 N2 323 sing 33 n n N2 C14 323 sing 34 n n C10 H10 323 sing 35 n n C11 H11 323 sing 36 n n C13 H13 323 sing 37 n n C14 H114 323 sing 38 n n C14 H214 323 sing 39 n n C14 H314 323 sing 40 n n C15 H115 323 sing 41 n n C15 H215 323 sing 42 n n C15 H315 323 sing 43 n n C16 H116 323 sing 44 n n C16 H216 323 sing 45 n n C16 H316 323 sing 46 n n C17 H117 323 sing 47 n n C17 H217 323 sing 48 n n C17 H317 323 sing 49 n n C19 H19 323 sing 50 n n C20 H20 323 sing 51 n n C22 H22 323 sing 52 n n C25 H25 323 sing 53 n n C6 H6 323 sing 54 n n C8 H8 323 sing 55 n n C9 H9 323 sing 56 n n # _atom_sites.entry_id 8AGC _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 N 13 ELU A 1 1001 1001 ELU ELU . O 14 CPL A 1 1002 1003 CPL CPL . P 15 PTY A 1 1003 1004 PTY PTY . Q 16 MN A 1 1004 1005 MN MN . R 14 CPL C 1 101 101 CPL CPL . S 14 CPL E 1 501 501 CPL CPL . T 14 CPL F 1 301 301 CPL CPL . U 17 NAG G 1 501 501 NAG NAG . V 17 NAG G 1 502 502 NAG NAG . W 15 PTY H 1 901 901 PTY PTY . X 18 323 P 1 101 1 323 323 . # 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 323 . . . X 18 175.065 143.834 148.856 1 93.44 ? C1 323 101 P 1 HETATM 2 O O1 323 . . . X 18 177.904 143.661 148.544 1 93.44 ? O1 323 101 P 1 HETATM 3 N N1 323 . . . X 18 177.618 146.377 144.583 1 93.44 ? N1 323 101 P 1 HETATM 4 C C10 323 . . . X 18 174.989 145.251 146.773 1 93.44 ? C10 323 101 P 1 HETATM 5 C C11 323 . . . X 18 175.624 145.883 145.711 1 93.44 ? C11 323 101 P 1 HETATM 6 C C12 323 . . . X 18 177.017 145.789 145.572 1 93.44 ? C12 323 101 P 1 HETATM 7 C C13 323 . . . X 18 177.763 145.059 146.503 1 93.44 ? C13 323 101 P 1 HETATM 8 C C14 323 . . . X 18 177.437 139.057 152.844 1 93.44 ? C14 323 101 P 1 HETATM 9 C C15 323 . . . X 18 179.584 140.393 152.295 1 93.44 ? C15 323 101 P 1 HETATM 10 C C16 323 . . . X 18 176.981 146.442 143.265 1 93.44 ? C16 323 101 P 1 HETATM 11 C C17 323 . . . X 18 178.992 147.001 144.794 1 93.44 ? C17 323 101 P 1 HETATM 12 C C18 323 . . . X 18 173.569 144.093 149.122 1 93.44 ? C18 323 101 P 1 HETATM 13 C C19 323 . . . X 18 173.158 145.15 149.939 1 93.44 ? C19 323 101 P 1 HETATM 14 O O2 323 . . . X 18 173.348 140.928 148.13 1 93.44 ? O2 323 101 P 1 HETATM 15 N N2 323 . . . X 18 178.109 140.191 152.151 1 93.44 ? N2 323 101 P 1 HETATM 16 C C2 323 . . . X 18 175.739 144.519 147.708 1 93.44 ? C2 323 101 P 1 HETATM 17 C C20 323 . . . X 18 171.78 145.371 150.165 1 93.44 ? C20 323 101 P 1 HETATM 18 C C21 323 . . . X 18 170.846 144.545 149.579 1 93.44 ? C21 323 101 P 1 HETATM 19 C C22 323 . . . X 18 171.256 143.485 148.757 1 93.44 ? C22 323 101 P 1 HETATM 20 C C23 323 . . . X 18 172.626 143.264 148.531 1 93.44 ? C23 323 101 P 1 HETATM 21 C C24 323 . . . X 18 173.106 142.081 147.615 1 93.44 ? C24 323 101 P 1 HETATM 22 C C25 323 . . . X 18 169.324 144.785 149.824 1 93.44 ? C25 323 101 P 1 HETATM 23 O O3 323 . . . X 18 173.26 142.263 146.361 1 93.44 ? O3 323 101 P 1 HETATM 24 C C3 323 . . . X 18 177.126 144.425 147.568 1 93.44 ? C3 323 101 P 1 HETATM 25 O O4 323 . . . X 18 168.518 144.05 149.315 1 93.44 ? O4 323 101 P 1 HETATM 26 C C4 323 . . . X 18 177.216 142.81 149.557 1 93.44 ? C4 323 101 P 1 HETATM 27 C C5 323 . . . X 18 175.839 142.892 149.712 1 93.44 ? C5 323 101 P 1 HETATM 28 C C6 323 . . . X 18 177.958 141.929 150.353 1 93.44 ? C6 323 101 P 1 HETATM 29 C C7 323 . . . X 18 177.306 141.131 151.306 1 93.44 ? C7 323 101 P 1 HETATM 30 C C8 323 . . . X 18 175.916 141.209 151.465 1 93.44 ? C8 323 101 P 1 HETATM 31 C C9 323 . . . X 18 175.181 142.082 150.675 1 93.44 ? C9 323 101 P 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #