data_7YAH # _model_server_result.job_id lyFT6oX1Ib8JwDA6TDzeBA _model_server_result.datetime_utc '2024-10-26 02:31:36' _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 7yah # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 7YAH # _exptl.entry_id 7YAH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _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 7YAH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YAH _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 22 C CYS 55 1_555 B SG CYS 95 C CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A O VAL 331 A VAL 303 1_555 D CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc2 A O ALA 332 A ALA 304 1_555 D CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc3 A O ILE 334 A ILE 306 1_555 D CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc4 A OE1 GLU 336 A GLU 308 1_555 D CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.121 ? metalc ? metalc5 A OD1 ASN 766 A ASN 738 1_555 D CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc6 A OD2 ASP 770 A ASP 742 1_555 D CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? # _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 7YAH _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 C 3 ACP A 1 1001 1001 ACP ACP . D 4 CA A 1 1002 1 CA CA . # 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 . . . C 3 99.073 88.878 63.971 1 0 ? PG ACP 1001 A 1 HETATM 2 O O1G ACP . . . C 3 99.48 87.577 63.386 1 13.91 ? O1G ACP 1001 A 1 HETATM 3 O O2G ACP . . . C 3 98.018 88.757 65.088 1 0 ? O2G ACP 1001 A 1 HETATM 4 O O3G ACP . . . C 3 100.272 89.635 64.568 1 1.59 ? O3G ACP 1001 A 1 HETATM 5 P PB ACP . . . C 3 97.349 89.152 61.478 1 0 ? PB ACP 1001 A 1 HETATM 6 O O1B ACP . . . C 3 98.097 87.98 60.896 1 9.13 ? O1B ACP 1001 A 1 HETATM 7 O O2B ACP . . . C 3 97.015 90.224 60.414 1 15.95 ? O2B ACP 1001 A 1 HETATM 8 C C3B ACP . . . C 3 98.378 89.969 62.73 1 15.77 ? C3B ACP 1001 A 1 HETATM 9 P PA ACP . . . C 3 94.825 88.625 61.214 1 0 ? PA ACP 1001 A 1 HETATM 10 O O1A ACP . . . C 3 94.231 89.955 61.095 1 9.5 ? O1A ACP 1001 A 1 HETATM 11 O O2A ACP . . . C 3 93.84 87.596 61.742 1 20.29 ? O2A ACP 1001 A 1 HETATM 12 O O3A ACP . . . C 3 96.021 88.652 62.215 1 8.54 ? O3A ACP 1001 A 1 HETATM 13 O O5' ACP . . . C 3 95.441 88.03 59.888 1 8.53 ? O5' ACP 1001 A 1 HETATM 14 C C5' ACP . . . C 3 95.04 86.734 59.396 1 11.21 ? C5' ACP 1001 A 1 HETATM 15 C C4' ACP . . . C 3 95.598 86.508 58.018 1 6.63 ? C4' ACP 1001 A 1 HETATM 16 O O4' ACP . . . C 3 95.191 87.592 57.166 1 3.19 ? O4' ACP 1001 A 1 HETATM 17 C C3' ACP . . . C 3 97.121 86.406 57.935 1 10.76 ? C3' ACP 1001 A 1 HETATM 18 O O3' ACP . . . C 3 97.559 85.184 57.355 1 16.06 ? O3' ACP 1001 A 1 HETATM 19 C C2' ACP . . . C 3 97.54 87.578 57.044 1 11.03 ? C2' ACP 1001 A 1 HETATM 20 O O2' ACP . . . C 3 98.499 87.157 56.082 1 10.32 ? O2' ACP 1001 A 1 HETATM 21 C C1' ACP . . . C 3 96.252 87.975 56.33 1 9.61 ? C1' ACP 1001 A 1 HETATM 22 N N9 ACP . . . C 3 96.156 89.411 56.132 1 15.43 ? N9 ACP 1001 A 1 HETATM 23 C C8 ACP . . . C 3 96.42 90.381 57.063 1 13.16 ? C8 ACP 1001 A 1 HETATM 24 N N7 ACP . . . C 3 96.262 91.603 56.622 1 15.22 ? N7 ACP 1001 A 1 HETATM 25 C C5 ACP . . . C 3 95.868 91.425 55.305 1 17.31 ? C5 ACP 1001 A 1 HETATM 26 C C6 ACP . . . C 3 95.543 92.334 54.284 1 16.43 ? C6 ACP 1001 A 1 HETATM 27 N N6 ACP . . . C 3 95.556 93.661 54.441 1 12.3 ? N6 ACP 1001 A 1 HETATM 28 N N1 ACP . . . C 3 95.185 91.829 53.085 1 10.38 ? N1 ACP 1001 A 1 HETATM 29 C C2 ACP . . . C 3 95.161 90.504 52.928 1 8.3 ? C2 ACP 1001 A 1 HETATM 30 N N3 ACP . . . C 3 95.449 89.551 53.814 1 9.65 ? N3 ACP 1001 A 1 HETATM 31 C C4 ACP . . . C 3 95.796 90.079 54.989 1 12.64 ? C4 ACP 1001 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #