data_7DSH # _model_server_result.job_id Lo6P93S601MAOFZK0Hrpng _model_server_result.datetime_utc '2025-02-05 06:47:36' _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 7dsh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1601}' # _entry.id 7DSH # _exptl.entry_id 7DSH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _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 7DSH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DSH _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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 3 2 BMA 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 3 n C NAG 1 C 1 NAG B 414 NAG 3 n C NAG 2 C 2 NAG B 415 NAG 3 n C BMA 3 C 3 BMA B 416 BMA # 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 B SG CYS 110 B CYS 110 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 216 B CYS 216 1_555 B SG CYS 231 B CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A NH1 ARG 909 A ARG 909 1_555 D O1B ACP . A ACP 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale2 A CD1 LEU 911 A LEU 911 1_555 D N3 ACP . A ACP 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 B ND2 ASN 240 B ASN 240 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc1 D O3G ACP . A ACP 1601 1_555 E MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? # _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" # _atom_sites.entry_id 7DSH _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 D 4 ACP A 1 1601 2002 ACP ACP . E 5 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 . . . D 4 202.406 179.057 204.498 1 80.01 ? PG ACP 1601 A 1 HETATM 2 O O1G ACP . . . D 4 202.276 180.392 203.874 1 80.01 ? O1G ACP 1601 A 1 HETATM 3 O O2G ACP . . . D 4 201.539 178.993 205.849 1 80.01 ? O2G ACP 1601 A 1 HETATM 4 O O3G ACP . . . D 4 201.895 177.93 203.466 1 80.01 ? O3G ACP 1601 A 1 HETATM 5 P PB ACP . . . D 4 204.652 180.239 205.889 1 80.01 ? PB ACP 1601 A 1 HETATM 6 O O1B ACP . . . D 4 205.802 180.999 205.333 1 80.01 ? O1B ACP 1601 A 1 HETATM 7 O O2B ACP . . . D 4 203.397 181.23 206.04 1 80.01 ? O2B ACP 1601 A 1 HETATM 8 C C3B ACP . . . D 4 204.155 178.812 204.895 1 80.01 ? C3B ACP 1601 A 1 HETATM 9 P PA ACP . . . D 4 203.801 179.136 208.227 1 80.01 ? PA ACP 1601 A 1 HETATM 10 O O1A ACP . . . D 4 203.779 177.631 208.295 1 80.01 ? O1A ACP 1601 A 1 HETATM 11 O O2A ACP . . . D 4 202.597 179.916 207.768 1 80.01 ? O2A ACP 1601 A 1 HETATM 12 O O3A ACP . . . D 4 205.028 179.604 207.307 1 80.01 ? O3A ACP 1601 A 1 HETATM 13 O O5' ACP . . . D 4 204.292 179.742 209.621 1 80.01 ? O5' ACP 1601 A 1 HETATM 14 C C5' ACP . . . D 4 203.963 181.095 209.889 1 80.01 ? C5' ACP 1601 A 1 HETATM 15 C C4' ACP . . . D 4 205.217 181.785 210.391 1 80.01 ? C4' ACP 1601 A 1 HETATM 16 O O4' ACP . . . D 4 206.148 180.802 210.834 1 80.01 ? O4' ACP 1601 A 1 HETATM 17 C C3' ACP . . . D 4 205.886 182.565 209.273 1 80.01 ? C3' ACP 1601 A 1 HETATM 18 O O3' ACP . . . D 4 205.785 183.968 209.529 1 80.01 ? O3' ACP 1601 A 1 HETATM 19 C C2' ACP . . . D 4 207.339 182.149 209.283 1 80.01 ? C2' ACP 1601 A 1 HETATM 20 O O2' ACP . . . D 4 208.168 183.295 209.481 1 80.01 ? O2' ACP 1601 A 1 HETATM 21 C C1' ACP . . . D 4 207.462 181.207 210.464 1 80.01 ? C1' ACP 1601 A 1 HETATM 22 N N9 ACP . . . D 4 208.267 180.025 210.093 1 80.01 ? N9 ACP 1601 A 1 HETATM 23 C C8 ACP . . . D 4 207.891 179.079 209.218 1 80.01 ? C8 ACP 1601 A 1 HETATM 24 N N7 ACP . . . D 4 208.845 178.125 209.095 1 80.01 ? N7 ACP 1601 A 1 HETATM 25 C C5 ACP . . . D 4 209.862 178.468 209.902 1 80.01 ? C5 ACP 1601 A 1 HETATM 26 C C6 ACP . . . D 4 211.182 177.901 210.242 1 80.01 ? C6 ACP 1601 A 1 HETATM 27 N N6 ACP . . . D 4 211.618 176.747 209.685 1 80.01 ? N6 ACP 1601 A 1 HETATM 28 N N1 ACP . . . D 4 211.943 178.571 211.129 1 80.01 ? N1 ACP 1601 A 1 HETATM 29 C C2 ACP . . . D 4 211.524 179.712 211.696 1 80.01 ? C2 ACP 1601 A 1 HETATM 30 N N3 ACP . . . D 4 210.35 180.306 211.425 1 80.01 ? N3 ACP 1601 A 1 HETATM 31 C C4 ACP . . . D 4 209.481 179.726 210.559 1 80.01 ? C4 ACP 1601 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #