data_3CF3 # _model_server_result.job_id 8RUxKZ7MAX5fzca219FMog _model_server_result.datetime_utc '2024-11-08 07:23:35' _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 3cf3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":900}' # _entry.id 3CF3 # _exptl.entry_id 3CF3 _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 6 _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 3CF3 _cell.length_a 163.97 _cell.length_b 178.93 _cell.length_c 320.64 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 163.97 178.93 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 ? 2 G N N ? 2 H N N ? 2 I 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 3CF3 _atom_sites.fract_transf_matrix[1][1] 0.006099 _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] 0.005589 _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] 0.003119 _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 1 807 807 ADP ADP . E 2 ADP A 1 900 900 ADP ADP . F 2 ADP B 1 807 807 ADP ADP . G 2 ADP B 1 900 900 ADP ADP . H 2 ADP C 1 807 807 ADP ADP . I 2 ADP C 1 900 900 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 . . . I 2 108.066 66.337 301.574 1 174.44 ? PB ADP 900 C 1 HETATM 2 O O1B ADP . . . I 2 107.335 65.578 300.572 1 206.72 ? O1B ADP 900 C 1 HETATM 3 O O2B ADP . . . I 2 107.849 65.637 303.018 1 157.75 ? O2B ADP 900 C 1 HETATM 4 O O3B ADP . . . I 2 107.568 67.733 301.631 1 142.08 ? O3B ADP 900 C 1 HETATM 5 P PA ADP . . . I 2 110.323 65.841 299.903 1 150.54 ? PA ADP 900 C 1 HETATM 6 O O1A ADP . . . I 2 110.054 64.417 299.644 1 144.4 ? O1A ADP 900 C 1 HETATM 7 O O2A ADP . . . I 2 109.872 66.636 298.755 1 146.24 ? O2A ADP 900 C 1 HETATM 8 O O3A ADP . . . I 2 109.606 66.344 301.203 1 118.88 ? O3A ADP 900 C 1 HETATM 9 O O5' ADP . . . I 2 111.86 66.215 299.985 1 133.9 ? O5' ADP 900 C 1 HETATM 10 C C5' ADP . . . I 2 112.487 66.938 301.01 1 173.11 ? C5' ADP 900 C 1 HETATM 11 C C4' ADP . . . I 2 113.988 66.997 300.55 1 166.99 ? C4' ADP 900 C 1 HETATM 12 O O4' ADP . . . I 2 114.715 66.667 301.735 1 141.97 ? O4' ADP 900 C 1 HETATM 13 C C3' ADP . . . I 2 114.462 65.927 299.534 1 167.13 ? C3' ADP 900 C 1 HETATM 14 O O3' ADP . . . I 2 114.537 66.397 298.172 1 200.43 ? O3' ADP 900 C 1 HETATM 15 C C2' ADP . . . I 2 115.817 65.452 300.063 1 165.15 ? C2' ADP 900 C 1 HETATM 16 O O2' ADP . . . I 2 116.953 66.202 299.577 1 155.57 ? O2' ADP 900 C 1 HETATM 17 C C1' ADP . . . I 2 115.606 65.514 301.549 1 146.6 ? C1' ADP 900 C 1 HETATM 18 N N9 ADP . . . I 2 114.927 64.253 302.179 1 153.69 ? N9 ADP 900 C 1 HETATM 19 C C8 ADP . . . I 2 113.713 64.229 302.796 1 187.57 ? C8 ADP 900 C 1 HETATM 20 N N7 ADP . . . I 2 113.423 63.011 303.211 1 183.02 ? N7 ADP 900 C 1 HETATM 21 C C5 ADP . . . I 2 114.405 62.24 302.881 1 151.23 ? C5 ADP 900 C 1 HETATM 22 C C6 ADP . . . I 2 114.652 60.885 303.038 1 165.05 ? C6 ADP 900 C 1 HETATM 23 N N6 ADP . . . I 2 113.751 60.133 303.638 1 185.95 ? N6 ADP 900 C 1 HETATM 24 N N1 ADP . . . I 2 115.846 60.328 302.549 1 171.19 ? N1 ADP 900 C 1 HETATM 25 C C2 ADP . . . I 2 116.8 61.076 301.92 1 177.54 ? C2 ADP 900 C 1 HETATM 26 N N3 ADP . . . I 2 116.55 62.41 301.771 1 163.26 ? N3 ADP 900 C 1 HETATM 27 C C4 ADP . . . I 2 115.398 63.017 302.221 1 143.15 ? C4 ADP 900 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #