data_7DSI # _model_server_result.job_id vozoPat6at2WLjDxZ67moQ _model_server_result.datetime_utc '2024-12-26 16:49:53' _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 7dsi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1601}' # _entry.id 7DSI # _exptl.entry_id 7DSI _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 505.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 7DSI _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DSI _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 5 2 1 NAG NAG C1 O1 . O6 HO6 . 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 3 n C NAG 1 C 1 NAG B 412 NAG 3 n C NAG 2 C 2 NAG B 413 NAG 4 n D NAG 1 D 1 NAG B 414 NAG 4 n D NAG 2 D 2 NAG B 415 NAG 4 n D BMA 3 D 3 BMA B 416 BMA 5 n E NAG 1 E 1 NAG B 419 NAG 5 n E NAG 2 E 2 NAG B 420 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 disulf ? disulf1 A SG CYS 777 A CYS 777 1_555 A SG CYS 851 A CYS 851 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 B SG CYS 110 B CYS 110 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 B SG CYS 216 B CYS 216 1_555 B SG CYS 231 B CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 B ND2 ASN 240 B ASN 240 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 B ND2 ASN 256 B ASN 256 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale3 B ND2 ASN 298 B ASN 298 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale7 E O6 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A OD2 ASP 667 A ASP 667 1_555 G MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc2 A O THR 669 A THR 669 1_555 G MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 7DSI _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 F 6 ACP A 1 1601 2002 ACP ACP . G 7 MG A 1 1602 2003 MG MG . # 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 P PG ACP . . . F 6 201.612 181.715 203.381 1 46.18 ? PG ACP 1601 A 1 HETATM 2 O O1G ACP . . . F 6 200.388 181.4 204.144 1 46.18 ? O1G ACP 1601 A 1 HETATM 3 O O2G ACP . . . F 6 201.248 182.66 202.135 1 46.18 ? O2G ACP 1601 A 1 HETATM 4 O O3G ACP . . . F 6 202.236 180.334 202.843 1 46.18 ? O3G ACP 1601 A 1 HETATM 5 P PB ACP . . . F 6 203.749 181.248 205.228 1 46.18 ? PB ACP 1601 A 1 HETATM 6 O O1B ACP . . . F 6 205.125 181.244 204.688 1 46.18 ? O1B ACP 1601 A 1 HETATM 7 O O2B ACP . . . F 6 203.041 179.829 204.966 1 46.18 ? O2B ACP 1601 A 1 HETATM 8 C C3B ACP . . . F 6 202.803 182.56 204.438 1 46.18 ? C3B ACP 1601 A 1 HETATM 9 P PA ACP . . . F 6 203.481 180.324 207.816 1 46.18 ? PA ACP 1601 A 1 HETATM 10 O O1A ACP . . . F 6 204.038 179.045 207.243 1 46.18 ? O1A ACP 1601 A 1 HETATM 11 O O2A ACP . . . F 6 202.023 180.422 208.188 1 46.18 ? O2A ACP 1601 A 1 HETATM 12 O O3A ACP . . . F 6 203.795 181.523 206.8 1 46.18 ? O3A ACP 1601 A 1 HETATM 13 O O5' ACP . . . F 6 204.389 180.821 209.037 1 46.18 ? O5' ACP 1601 A 1 HETATM 14 C C5' ACP . . . F 6 203.948 181.93 209.808 1 46.18 ? C5' ACP 1601 A 1 HETATM 15 C C4' ACP . . . F 6 205.148 182.823 210.074 1 46.18 ? C4' ACP 1601 A 1 HETATM 16 O O4' ACP . . . F 6 206.264 182.003 210.405 1 46.18 ? O4' ACP 1601 A 1 HETATM 17 C C3' ACP . . . F 6 205.537 183.632 208.848 1 46.18 ? C3' ACP 1601 A 1 HETATM 18 O O3' ACP . . . F 6 205.243 185.015 209.057 1 46.18 ? O3' ACP 1601 A 1 HETATM 19 C C2' ACP . . . F 6 207.029 183.454 208.687 1 46.18 ? C2' ACP 1601 A 1 HETATM 20 O O2' ACP . . . F 6 207.687 184.712 208.846 1 46.18 ? O2' ACP 1601 A 1 HETATM 21 C C1' ACP . . . F 6 207.449 182.506 209.793 1 46.18 ? C1' ACP 1601 A 1 HETATM 22 N N9 ACP . . . F 6 208.252 181.398 209.224 1 46.18 ? N9 ACP 1601 A 1 HETATM 23 C C8 ACP . . . F 6 208.051 180.783 208.044 1 46.18 ? C8 ACP 1601 A 1 HETATM 24 N N7 ACP . . . F 6 208.984 179.819 207.835 1 46.18 ? N7 ACP 1601 A 1 HETATM 25 C C5 ACP . . . F 6 209.807 179.814 208.899 1 46.18 ? C5 ACP 1601 A 1 HETATM 26 C C6 ACP . . . F 6 211.003 179.055 209.335 1 46.18 ? C6 ACP 1601 A 1 HETATM 27 N N6 ACP . . . F 6 211.533 178.07 208.574 1 46.18 ? N6 ACP 1601 A 1 HETATM 28 N N1 ACP . . . F 6 211.555 179.374 210.522 1 46.18 ? N1 ACP 1601 A 1 HETATM 29 C C2 ACP . . . F 6 211.049 180.345 211.299 1 46.18 ? C2 ACP 1601 A 1 HETATM 30 N N3 ACP . . . F 6 209.971 181.071 210.97 1 46.18 ? N3 ACP 1601 A 1 HETATM 31 C C4 ACP . . . F 6 209.321 180.861 209.804 1 46.18 ? C4 ACP 1601 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #