data_6C83 # _model_server_result.job_id 1EI2TDSyFjByOnCg03562A _model_server_result.datetime_utc '2024-10-09 23:30:26' _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 6c83 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 6C83 # _exptl.entry_id 6C83 _exptl.method 'X-RAY DIFFRACTION' # _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 2 _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 6C83 _cell.length_a 63.047 _cell.length_b 69.916 _cell.length_c 173.718 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C83 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 x,y,z _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N # _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 6C83 _atom_sites.fract_transf_matrix[1][1] 0.015861 _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] 0.014303 _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] 0.005756 _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 E 3 ACP A 1 501 501 ACP ACP . F 3 ACP B 1 501 502 ACP ACP . # 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 3 7.096 12.443 15.476 0.61 121.54 ? PG ACP 501 B 1 HETATM 2 O O1G ACP . . . F 3 6.954 13.538 14.47 0.61 122.48 ? O1G ACP 501 B 1 HETATM 3 O O2G ACP . . . F 3 7.204 11.116 14.76 0.61 120.26 ? O2G ACP 501 B 1 HETATM 4 O O3G ACP . . . F 3 5.886 12.416 16.391 0.61 122.25 ? O3G ACP 501 B 1 HETATM 5 P PB ACP . . . F 3 8.435 14.283 17.512 0.61 112.78 ? PB ACP 501 B 1 HETATM 6 O O1B ACP . . . F 3 9.776 14.913 17.726 0.61 113.51 ? O1B ACP 501 B 1 HETATM 7 O O2B ACP . . . F 3 7.832 13.94 18.842 0.61 113.18 ? O2B ACP 501 B 1 HETATM 8 C C3B ACP . . . F 3 8.639 12.736 16.501 0.61 117.2 ? C3B ACP 501 B 1 HETATM 9 P PA ACP . . . F 3 5.831 15.531 16.995 0.61 99.6 ? PA ACP 501 B 1 HETATM 10 O O1A ACP . . . F 3 5.025 14.981 15.831 0.61 98.77 ? O1A ACP 501 B 1 HETATM 11 O O2A ACP . . . F 3 5.438 14.817 18.276 0.61 98.59 -1 O2A ACP 501 B 1 HETATM 12 O O3A ACP . . . F 3 7.452 15.345 16.713 0.61 106.78 ? O3A ACP 501 B 1 HETATM 13 O O5' ACP . . . F 3 5.504 17.185 17.142 0.61 92.56 ? O5' ACP 501 B 1 HETATM 14 C C5' ACP . . . F 3 5.804 17.996 16.027 0.61 84.76 ? C5' ACP 501 B 1 HETATM 15 C C4' ACP . . . F 3 4.562 18.054 15.053 0.61 78.56 ? C4' ACP 501 B 1 HETATM 16 O O4' ACP . . . F 3 3.3 18.582 15.783 0.61 73.8 ? O4' ACP 501 B 1 HETATM 17 C C3' ACP . . . F 3 4.798 18.872 14.114 0.61 78.83 ? C3' ACP 501 B 1 HETATM 18 O O3' ACP . . . F 3 4.56 18.222 12.849 0.61 81.17 ? O3' ACP 501 B 1 HETATM 19 C C2' ACP . . . F 3 3.785 20.168 14.284 0.61 75.08 ? C2' ACP 501 B 1 HETATM 20 O O2' ACP . . . F 3 2.765 20.123 13.235 0.61 72.36 ? O2' ACP 501 B 1 HETATM 21 C C1' ACP . . . F 3 3.221 20.08 15.423 0.61 71.47 ? C1' ACP 501 B 1 HETATM 22 N N9 ACP . . . F 3 3.923 20.888 16.485 0.61 62.79 ? N9 ACP 501 B 1 HETATM 23 C C8 ACP . . . F 3 4.787 20.692 17.501 0.61 62.14 ? C8 ACP 501 B 1 HETATM 24 N N7 ACP . . . F 3 5.02 21.859 18.091 0.61 62.03 ? N7 ACP 501 B 1 HETATM 25 C C5 ACP . . . F 3 4.295 22.794 17.452 0.61 62.33 ? C5 ACP 501 B 1 HETATM 26 C C6 ACP . . . F 3 4.172 24.152 17.662 0.61 59.55 ? C6 ACP 501 B 1 HETATM 27 N N6 ACP . . . F 3 4.679 25.192 18.556 0.61 61 ? N6 ACP 501 B 1 HETATM 28 N N1 ACP . . . F 3 3.38 24.875 16.884 0.61 59.4 ? N1 ACP 501 B 1 HETATM 29 C C2 ACP . . . F 3 2.688 24.275 15.878 0.61 59.5 ? C2 ACP 501 B 1 HETATM 30 N N3 ACP . . . F 3 2.807 22.941 15.672 0.61 58.79 ? N3 ACP 501 B 1 HETATM 31 C C4 ACP . . . F 3 3.615 22.198 16.463 0.61 61.39 ? C4 ACP 501 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #