data_6D00 # _model_server_result.job_id 2jDaGd8MXa2_vNMjZsPyow _model_server_result.datetime_utc '2024-11-15 10:02:01' _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 6d00 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":902}' # _entry.id 6D00 # _exptl.entry_id 6D00 _exptl.method 'ELECTRON MICROSCOPY' # _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 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,H,I,J,K,L,M,N,O,P,Q,R _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R 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 6D00 _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 G 2 ADP 1 1 901 1 ADP ADP . H 2 ADP 1 1 902 2 ADP ADP . I 2 ADP 2 1 901 1 ADP ADP . J 2 ADP 2 1 902 2 ADP ADP . K 2 ADP 3 1 901 1 ADP ADP . L 2 ADP 3 1 902 2 ADP ADP . M 2 ADP 4 1 901 1 ADP ADP . N 2 ADP 4 1 902 2 ADP ADP . O 2 ADP 5 1 901 1 ADP ADP . P 2 ADP 5 1 902 2 ADP ADP . Q 2 ADP 6 1 901 1 ADP ADP . R 2 ADP 6 1 902 2 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 . . . R 2 122.245 185.384 88.169 1 1.48 ? PB ADP 902 6 1 HETATM 2 O O1B ADP . . . R 2 123.335 185.523 87.134 1 3.44 ? O1B ADP 902 6 1 HETATM 3 O O2B ADP . . . R 2 120.852 185.641 87.645 1 2.45 ? O2B ADP 902 6 1 HETATM 4 O O3B ADP . . . R 2 122.368 184.155 89.037 1 2.12 ? O3B ADP 902 6 1 HETATM 5 P PA ADP . . . R 2 121.555 186.86 90.45 1 0.87 ? PA ADP 902 6 1 HETATM 6 O O1A ADP . . . R 2 120.221 187.359 89.95 1 1.91 ? O1A ADP 902 6 1 HETATM 7 O O2A ADP . . . R 2 121.622 185.641 91.338 1 1.54 ? O2A ADP 902 6 1 HETATM 8 O O3A ADP . . . R 2 122.512 186.61 89.178 1 1.52 ? O3A ADP 902 6 1 HETATM 9 O O5' ADP . . . R 2 122.297 188.072 91.207 1 1.43 ? O5' ADP 902 6 1 HETATM 10 C C5' ADP . . . R 2 121.958 188.402 92.553 1 1.15 ? C5' ADP 902 6 1 HETATM 11 C C4' ADP . . . R 2 122.765 189.615 92.997 1 1.08 ? C4' ADP 902 6 1 HETATM 12 O O4' ADP . . . R 2 122.389 190.764 92.234 1 1.53 ? O4' ADP 902 6 1 HETATM 13 C C3' ADP . . . R 2 122.519 189.95 94.46 1 1.29 ? C3' ADP 902 6 1 HETATM 14 O O3' ADP . . . R 2 123.678 189.636 95.237 1 1.54 ? O3' ADP 902 6 1 HETATM 15 C C2' ADP . . . R 2 122.25 191.441 94.505 1 1.55 ? C2' ADP 902 6 1 HETATM 16 O O2' ADP . . . R 2 123.241 192.096 95.302 1 1.74 ? O2' ADP 902 6 1 HETATM 17 C C1' ADP . . . R 2 122.334 191.924 93.066 1 1.54 ? C1' ADP 902 6 1 HETATM 18 N N9 ADP . . . R 2 121.13 192.728 92.738 1 1.93 ? N9 ADP 902 6 1 HETATM 19 C C8 ADP . . . R 2 119.96 192.239 92.288 1 2.81 ? C8 ADP 902 6 1 HETATM 20 N N7 ADP . . . R 2 119.058 193.232 92.085 1 3.25 ? N7 ADP 902 6 1 HETATM 21 C C5 ADP . . . R 2 119.656 194.392 92.41 1 2.59 ? C5 ADP 902 6 1 HETATM 22 C C6 ADP . . . R 2 119.27 195.823 92.429 1 2.75 ? C6 ADP 902 6 1 HETATM 23 N N6 ADP . . . R 2 118.032 196.219 92.048 1 3.58 ? N6 ADP 902 6 1 HETATM 24 N N1 ADP . . . R 2 120.196 196.718 92.839 1 2.42 ? N1 ADP 902 6 1 HETATM 25 C C2 ADP . . . R 2 121.429 196.336 93.219 1 2.31 ? C2 ADP 902 6 1 HETATM 26 N N3 ADP . . . R 2 121.846 195.057 93.228 1 1.99 ? N3 ADP 902 6 1 HETATM 27 C C4 ADP . . . R 2 121.021 194.055 92.841 1 1.92 ? C4 ADP 902 6 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #