data_3H4M # _model_server_result.job_id YceKKLvliVDpMAiuwYsPlQ _model_server_result.datetime_utc '2025-03-05 19:21:41' _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 3h4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":439}' # _entry.id 3H4M # _exptl.entry_id 3H4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 3H4M _cell.length_a 116.425 _cell.length_b 116.425 _cell.length_c 164.169 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H4M _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D 1 1 B,E 2 1 C,F 3 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 ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3H4M _atom_sites.fract_transf_matrix[1][1] 0.008589 _atom_sites.fract_transf_matrix[1][2] 0.004959 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009918 _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] 0.006091 _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 2 ADP A 1 439 419 ADP ADP . E 2 ADP B 1 439 419 ADP ADP . F 2 ADP C 1 439 419 ADP ADP . # 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 PB ADP . . . E 2 53.637 -78.144 -2.496 1 69.06 ? PB ADP 439 B 1 HETATM 2 O O1B ADP . . . E 2 52.548 -79.069 -1.997 1 70 ? O1B ADP 439 B 1 HETATM 3 O O2B ADP . . . E 2 53.193 -77.138 -3.522 1 67.09 ? O2B ADP 439 B 1 HETATM 4 O O3B ADP . . . E 2 54.926 -78.819 -2.906 1 68.76 ? O3B ADP 439 B 1 HETATM 5 P PA ADP . . . E 2 52.882 -76.564 -0.298 1 70.12 ? PA ADP 439 B 1 HETATM 6 O O1A ADP . . . E 2 51.661 -76.363 -1.17 1 69.47 ? O1A ADP 439 B 1 HETATM 7 O O2A ADP . . . E 2 52.761 -77.141 1.09 1 68.72 ? O2A ADP 439 B 1 HETATM 8 O O3A ADP . . . E 2 54.015 -77.31 -1.175 1 66.81 ? O3A ADP 439 B 1 HETATM 9 O O5' ADP . . . E 2 53.536 -75.128 -0.001 1 71.14 ? O5' ADP 439 B 1 HETATM 10 C C5' ADP . . . E 2 54.714 -75.014 0.795 1 69.84 ? C5' ADP 439 B 1 HETATM 11 C C4' ADP . . . E 2 54.705 -73.74 1.634 1 68.26 ? C4' ADP 439 B 1 HETATM 12 O O4' ADP . . . E 2 55.357 -72.665 0.957 1 66.58 ? O4' ADP 439 B 1 HETATM 13 C C3' ADP . . . E 2 53.312 -73.249 1.956 1 66.5 ? C3' ADP 439 B 1 HETATM 14 O O3' ADP . . . E 2 52.987 -73.622 3.282 1 69.88 ? O3' ADP 439 B 1 HETATM 15 C C2' ADP . . . E 2 53.436 -71.76 1.907 1 64.15 ? C2' ADP 439 B 1 HETATM 16 O O2' ADP . . . E 2 53.871 -71.368 3.199 1 64.05 ? O2' ADP 439 B 1 HETATM 17 C C1' ADP . . . E 2 54.549 -71.496 0.918 1 63.57 ? C1' ADP 439 B 1 HETATM 18 N N9 ADP . . . E 2 53.946 -71.386 -0.427 1 61.19 ? N9 ADP 439 B 1 HETATM 19 C C8 ADP . . . E 2 54.146 -72.226 -1.453 1 62.24 ? C8 ADP 439 B 1 HETATM 20 N N7 ADP . . . E 2 53.424 -71.857 -2.536 1 61.56 ? N7 ADP 439 B 1 HETATM 21 C C5 ADP . . . E 2 52.747 -70.764 -2.194 1 60.48 ? C5 ADP 439 B 1 HETATM 22 C C6 ADP . . . E 2 51.803 -69.856 -2.854 1 62.23 ? C6 ADP 439 B 1 HETATM 23 N N6 ADP . . . E 2 51.435 -70.072 -4.121 1 65.19 ? N6 ADP 439 B 1 HETATM 24 N N1 ADP . . . E 2 51.304 -68.808 -2.176 1 64.22 ? N1 ADP 439 B 1 HETATM 25 C C2 ADP . . . E 2 51.663 -68.587 -0.902 1 64.52 ? C2 ADP 439 B 1 HETATM 26 N N3 ADP . . . E 2 52.532 -69.382 -0.244 1 63.92 ? N3 ADP 439 B 1 HETATM 27 C C4 ADP . . . E 2 53.094 -70.461 -0.817 1 60.54 ? C4 ADP 439 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #