data_8AGE # _model_server_result.job_id t_db_bcvfsc7oDxPogvS0A _model_server_result.datetime_utc '2025-03-04 09:37:41' _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 8age # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":101}' # _entry.id 8AGE # _exptl.entry_id 8AGE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 414.453 _entity.id 17 _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 8AGE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AGE _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 PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,Z,AA,BA,CA,DA,EA,FA,GA _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 17 _struct_asym.id CA _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 # 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 # 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 K 1 NAG A 801 NAG 10 n J NAG 2 K 2 NAG A 802 NAG 10 n J BMA 3 K 3 BMA A 803 BMA 10 n J MAN 4 K 4 MAN A 804 MAN 10 n J MAN 5 K 5 MAN A 805 MAN 10 n J MAN 6 K 6 MAN A 806 MAN 10 n J MAN 7 K 7 MAN A 807 MAN 11 n K NAG 1 I 1 NAG E 501 NAG 11 n K NAG 2 I 2 NAG E 502 NAG 11 n L NAG 1 J 1 NAG E 504 NAG 11 n L NAG 2 J 2 NAG E 505 NAG # 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 . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 E ND2 ASN 336 E ASN 336 1_555 K C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 E ND2 ASN 400 E ASN 400 1_555 L C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 G ND2 ASN 60 G ASN 60 1_555 AA C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 G ND2 ASN 332 G ASN 332 1_555 Z C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 G SG CYS 400 G CYS 400 1_555 BA C01 KZB . G KZB 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.768 ? covale ? covale7 I N TYR 1 P TYR 2 1_555 CA C25 323 . P 323 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale8 J O4 NAG . K NAG 1 1_555 J C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale9 J O4 NAG . K NAG 2 1_555 J C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 J O3 BMA . K BMA 3 1_555 J C1 MAN . K MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 J O6 BMA . K BMA 3 1_555 J C1 MAN . K MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale12 J O2 MAN . K MAN 4 1_555 J C1 MAN . K MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 J O2 MAN . K MAN 5 1_555 J C1 MAN . K MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale14 K O4 NAG . I NAG 1 1_555 K C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale15 L O4 NAG . J NAG 1 1_555 L C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A OD2 ASP 166 A ASP 166 1_555 M MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? # _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 8AGE _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 M 12 MN A 1 801 1 MN MN . N 13 CPL A 1 802 809 CPL CPL . O 14 PTY A 1 803 901 PTY PTY . P 15 KZB A 1 804 1001 KZB DIG . Q 15 KZB A 1 805 1201 KZB DIG . R 15 KZB A 1 806 1401 KZB DIG . S 15 KZB B 1 101 101 KZB DIG . T 15 KZB B 1 102 201 KZB DIG . U 13 CPL B 1 103 501 CPL CPL . V 13 CPL E 1 501 506 CPL CPL . W 13 CPL F 1 301 298 CPL CPL . X 15 KZB F 1 302 401 KZB DIG . Y 15 KZB F 1 303 601 KZB DIG . Z 16 NAG G 1 501 503 NAG NAG . AA 16 NAG G 1 502 504 NAG NAG . BA 15 KZB G 1 503 701 KZB DIG . CA 17 323 P 1 101 101 323 323 . DA 18 HOH A 1 901 8 HOH HOH . DA 18 HOH A 2 902 9 HOH HOH . DA 18 HOH A 3 903 1 HOH HOH . DA 18 HOH A 4 904 2 HOH HOH . EA 18 HOH C 1 101 4 HOH HOH . FA 18 HOH E 1 601 3 HOH HOH . FA 18 HOH E 2 602 5 HOH HOH . GA 18 HOH G 1 601 7 HOH HOH . GA 18 HOH G 2 602 6 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 C1 323 . . . CA 17 175.353 143.668 148.847 1 46.75 ? C1 323 101 P 1 HETATM 2 O O1 323 . . . CA 17 178.115 143.195 148.219 1 46.75 ? O1 323 101 P 1 HETATM 3 N N1 323 . . . CA 17 177.964 146.643 144.906 1 46.75 ? N1 323 101 P 1 HETATM 4 C C10 323 . . . CA 17 175.351 145.467 147.084 1 46.75 ? C10 323 101 P 1 HETATM 5 C C11 323 . . . CA 17 176 146.205 146.106 1 46.75 ? C11 323 101 P 1 HETATM 6 C C12 323 . . . CA 17 177.347 145.956 145.815 1 46.75 ? C12 323 101 P 1 HETATM 7 C C13 323 . . . CA 17 178.036 144.965 146.514 1 46.75 ? C13 323 101 P 1 HETATM 8 C C14 323 . . . CA 17 178.003 138.928 152.735 1 46.75 ? C14 323 101 P 1 HETATM 9 C C15 323 . . . CA 17 180.025 140.488 152.304 1 46.75 ? C15 323 101 P 1 HETATM 10 C C16 323 . . . CA 17 177.408 146.753 143.557 1 46.75 ? C16 323 101 P 1 HETATM 11 C C17 323 . . . CA 17 179.273 147.341 145.255 1 46.75 ? C17 323 101 P 1 HETATM 12 C C18 323 . . . CA 17 173.852 143.91 149.115 1 46.75 ? C18 323 101 P 1 HETATM 13 C C19 323 . . . CA 17 173.437 144.977 149.916 1 46.75 ? C19 323 101 P 1 HETATM 14 O O2 323 . . . CA 17 173.53 140.702 148.138 1 46.75 ? O2 323 101 P 1 HETATM 15 N N2 323 . . . CA 17 178.579 140.151 152.116 1 46.75 ? N2 323 101 P 1 HETATM 16 C C2 323 . . . CA 17 176.042 144.471 147.788 1 46.75 ? C2 323 101 P 1 HETATM 17 C C20 323 . . . CA 17 172.06 145.192 150.146 1 46.75 ? C20 323 101 P 1 HETATM 18 C C21 323 . . . CA 17 171.128 144.354 149.578 1 46.75 ? C21 323 101 P 1 HETATM 19 C C22 323 . . . CA 17 171.537 143.286 148.77 1 46.75 ? C22 323 101 P 1 HETATM 20 C C23 323 . . . CA 17 172.906 143.069 148.539 1 46.75 ? C23 323 101 P 1 HETATM 21 C C24 323 . . . CA 17 173.366 141.872 147.632 1 46.75 ? C24 323 101 P 1 HETATM 22 C C25 323 . . . CA 17 169.611 144.597 149.834 1 46.75 ? C25 323 101 P 1 HETATM 23 O O3 323 . . . CA 17 173.574 142.069 146.388 1 46.75 ? O3 323 101 P 1 HETATM 24 C C3 323 . . . CA 17 177.385 144.227 147.495 1 46.75 ? C3 323 101 P 1 HETATM 25 O O4 323 . . . CA 17 168.791 143.856 149.357 1 46.75 ? O4 323 101 P 1 HETATM 26 C C4 323 . . . CA 17 177.492 142.533 149.395 1 46.75 ? C4 323 101 P 1 HETATM 27 C C5 323 . . . CA 17 176.159 142.755 149.71 1 46.75 ? C5 323 101 P 1 HETATM 28 C C6 323 . . . CA 17 178.271 141.686 150.181 1 46.75 ? C6 323 101 P 1 HETATM 29 C C7 323 . . . CA 17 177.711 141.052 151.295 1 46.75 ? C7 323 101 P 1 HETATM 30 C C8 323 . . . CA 17 176.366 141.267 151.623 1 46.75 ? C8 323 101 P 1 HETATM 31 C C9 323 . . . CA 17 175.589 142.111 150.84 1 46.75 ? C9 323 101 P 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #