data_2I5B # _model_server_result.job_id rR-rtIAm4xRfzYK8_luVDw _model_server_result.datetime_utc '2024-10-19 10:30:52' _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 2i5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 2I5B # _exptl.entry_id 2I5B _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 5 _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 2I5B _cell.length_a 102.499 _cell.length_b 102.499 _cell.length_c 251.36 _cell.Z_PDB 40 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2I5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 ? dimeric 2 author_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,F,I 1 1 B,C,G,H 2 1 E,J 3 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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -125.68 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 112 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 112 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 112 _struct_conn.ptnr2_auth_asym_id C _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 112 _struct_conn.ptnr2_symmetry 1_555 _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 2.009 _struct_conn.pdbx_value_order ? # _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 2I5B _atom_sites.fract_transf_matrix[1][1] 0.009756 _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] 0.009756 _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] 0.003978 _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 F 2 ADP A 1 301 301 ADP ADP . G 2 ADP C 1 401 401 ADP ADP . H 2 ADP D 1 501 501 ADP ADP . I 2 ADP B 1 601 601 ADP ADP . J 2 ADP E 1 701 701 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 . . . G 2 19.844 -38.724 -6.918 1 30.47 ? PB ADP 401 C 1 HETATM 2 O O1B ADP . . . G 2 20.125 -38.224 -5.531 1 30.86 ? O1B ADP 401 C 1 HETATM 3 O O2B ADP . . . G 2 21.067 -39.041 -7.765 1 30.47 ? O2B ADP 401 C 1 HETATM 4 O O3B ADP . . . G 2 18.768 -37.925 -7.622 1 33.01 ? O3B ADP 401 C 1 HETATM 5 P PA ADP . . . G 2 19.258 -41.125 -5.492 1 27.06 ? PA ADP 401 C 1 HETATM 6 O O1A ADP . . . G 2 20.69 -41.513 -5.287 1 26.94 ? O1A ADP 401 C 1 HETATM 7 O O2A ADP . . . G 2 18.425 -40.634 -4.343 1 25.8 ? O2A ADP 401 C 1 HETATM 8 O O3A ADP . . . G 2 19.089 -40.123 -6.727 1 28.66 ? O3A ADP 401 C 1 HETATM 9 O O5' ADP . . . G 2 18.515 -42.406 -6.13 1 26.28 ? O5' ADP 401 C 1 HETATM 10 C C5' ADP . . . G 2 18.979 -43.029 -7.316 1 22.57 ? C5' ADP 401 C 1 HETATM 11 C C4' ADP . . . G 2 18.639 -44.52 -7.307 1 22.72 ? C4' ADP 401 C 1 HETATM 12 O O4' ADP . . . G 2 19.849 -45.283 -7.309 1 22.65 ? O4' ADP 401 C 1 HETATM 13 C C3' ADP . . . G 2 17.866 -45.02 -6.108 1 20.56 ? C3' ADP 401 C 1 HETATM 14 O O3' ADP . . . G 2 17.186 -46.194 -6.537 1 21.02 ? O3' ADP 401 C 1 HETATM 15 C C2' ADP . . . G 2 18.96 -45.439 -5.169 1 20.06 ? C2' ADP 401 C 1 HETATM 16 O O2' ADP . . . G 2 18.516 -46.341 -4.152 1 18.23 ? O2' ADP 401 C 1 HETATM 17 C C1' ADP . . . G 2 20.001 -46.03 -6.11 1 20.91 ? C1' ADP 401 C 1 HETATM 18 N N9 ADP . . . G 2 21.372 -45.815 -5.552 1 21.56 ? N9 ADP 401 C 1 HETATM 19 C C8 ADP . . . G 2 21.924 -44.626 -5.203 1 21.08 ? C8 ADP 401 C 1 HETATM 20 N N7 ADP . . . G 2 23.175 -44.795 -4.691 1 20.87 ? N7 ADP 401 C 1 HETATM 21 C C5 ADP . . . G 2 23.436 -46.115 -4.709 1 20.81 ? C5 ADP 401 C 1 HETATM 22 C C6 ADP . . . G 2 24.565 -46.989 -4.321 1 20.34 ? C6 ADP 401 C 1 HETATM 23 N N6 ADP . . . G 2 25.686 -46.475 -3.799 1 20.92 ? N6 ADP 401 C 1 HETATM 24 N N1 ADP . . . G 2 24.444 -48.319 -4.51 1 20.87 ? N1 ADP 401 C 1 HETATM 25 C C2 ADP . . . G 2 23.325 -48.858 -5.029 1 20.93 ? C2 ADP 401 C 1 HETATM 26 N N3 ADP . . . G 2 22.254 -48.127 -5.396 1 20.88 ? N3 ADP 401 C 1 HETATM 27 C C4 ADP . . . G 2 22.249 -46.78 -5.269 1 20.25 ? C4 ADP 401 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #