data_2HYD # _model_server_result.job_id ePhmEEzRwsOlgxlSoJrMPg _model_server_result.datetime_utc '2024-12-22 01:07:07' _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 2hyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":701}' # _entry.id 2HYD # _exptl.entry_id 2HYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 97.99 _cell.angle_gamma 90 _cell.entry_id 2HYD _cell.length_a 161.279 _cell.length_b 103.955 _cell.length_c 181.013 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 D N N ? 3 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A O GLY 367 A GLY 367 1_555 C NA NA . A NA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc2 A OG1 THR 369 A THR 369 1_555 C NA NA . A NA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc3 A O SER 524 A SER 524 1_555 C NA NA . A NA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc4 A O ARG 527 A ARG 527 1_555 C NA NA . A NA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc5 B O GLY 367 B GLY 367 1_555 E NA NA . B NA 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc6 B OG1 THR 369 B THR 369 1_555 E NA NA . B NA 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc7 B O SER 524 B SER 524 1_555 E NA NA . B NA 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc8 B O ARG 527 B ARG 527 1_555 E NA NA . B NA 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _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 2HYD _atom_sites.fract_transf_matrix[1][1] 0.0062 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00087 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00962 _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] 0.005579 _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 C 2 NA A 1 900 900 NA NA . D 3 ADP A 1 700 700 ADP ADP . E 2 NA B 1 910 910 NA NA . F 3 ADP B 1 701 701 ADP ADP . G 4 HOH A 1 800 800 HOH HOH . G 4 HOH A 2 801 801 HOH HOH . G 4 HOH A 3 802 802 HOH HOH . G 4 HOH A 4 804 804 HOH HOH . G 4 HOH A 5 805 805 HOH HOH . G 4 HOH A 6 806 806 HOH HOH . G 4 HOH A 7 807 807 HOH HOH . G 4 HOH A 8 813 813 HOH HOH . H 4 HOH B 1 803 803 HOH HOH . H 4 HOH B 2 810 810 HOH HOH . H 4 HOH B 3 811 811 HOH HOH . H 4 HOH B 4 812 812 HOH HOH . H 4 HOH B 5 814 814 HOH HOH . H 4 HOH B 6 815 815 HOH HOH . H 4 HOH B 7 816 816 HOH HOH . H 4 HOH B 8 817 817 HOH HOH . # 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 . . . F 3 102.211 80.57 175.563 1 80.09 ? PB ADP 701 B 1 HETATM 2 O O1B ADP . . . F 3 102.924 79.383 175.068 1 80.99 ? O1B ADP 701 B 1 HETATM 3 O O2B ADP . . . F 3 102.341 80.677 177.12 1 81.06 ? O2B ADP 701 B 1 HETATM 4 O O3B ADP . . . F 3 100.657 80.48 175.243 1 78.69 ? O3B ADP 701 B 1 HETATM 5 P PA ADP . . . F 3 102.687 81.826 173.417 1 83.2 ? PA ADP 701 B 1 HETATM 6 O O1A ADP . . . F 3 103.796 80.982 172.961 1 80.88 ? O1A ADP 701 B 1 HETATM 7 O O2A ADP . . . F 3 101.33 81.098 172.94 1 85.51 ? O2A ADP 701 B 1 HETATM 8 O O3A ADP . . . F 3 102.864 81.923 174.975 1 81.43 ? O3A ADP 701 B 1 HETATM 9 O O5' ADP . . . F 3 102.988 83.292 172.778 1 83.42 ? O5' ADP 701 B 1 HETATM 10 C C5' ADP . . . F 3 102.426 83.178 171.474 1 83.87 ? C5' ADP 701 B 1 HETATM 11 C C4' ADP . . . F 3 102.467 84.476 170.73 1 83.32 ? C4' ADP 701 B 1 HETATM 12 O O4' ADP . . . F 3 103.823 84.782 170.421 1 83.57 ? O4' ADP 701 B 1 HETATM 13 C C3' ADP . . . F 3 101.689 84.301 169.434 1 83.73 ? C3' ADP 701 B 1 HETATM 14 O O3' ADP . . . F 3 100.58 85.184 169.421 1 83.23 ? O3' ADP 701 B 1 HETATM 15 C C2' ADP . . . F 3 102.654 84.541 168.3 1 84.45 ? C2' ADP 701 B 1 HETATM 16 O O2' ADP . . . F 3 102.222 85.618 167.44 1 85.33 ? O2' ADP 701 B 1 HETATM 17 C C1' ADP . . . F 3 104.001 84.826 168.977 1 84.1 ? C1' ADP 701 B 1 HETATM 18 N N9 ADP . . . F 3 104.967 83.826 168.554 1 83.16 ? N9 ADP 701 B 1 HETATM 19 C C8 ADP . . . F 3 105.216 82.607 169.116 1 83.06 ? C8 ADP 701 B 1 HETATM 20 N N7 ADP . . . F 3 106.143 81.985 168.46 1 82.95 ? N7 ADP 701 B 1 HETATM 21 C C5 ADP . . . F 3 106.541 82.765 167.441 1 83.74 ? C5 ADP 701 B 1 HETATM 22 C C6 ADP . . . F 3 107.488 82.654 166.395 1 84.53 ? C6 ADP 701 B 1 HETATM 23 N N6 ADP . . . F 3 108.277 81.531 166.271 1 84.8 ? N6 ADP 701 B 1 HETATM 24 N N1 ADP . . . F 3 107.606 83.676 165.527 1 84.97 ? N1 ADP 701 B 1 HETATM 25 C C2 ADP . . . F 3 106.85 84.786 165.629 1 84.59 ? C2 ADP 701 B 1 HETATM 26 N N3 ADP . . . F 3 105.958 84.931 166.594 1 83.22 ? N3 ADP 701 B 1 HETATM 27 C C4 ADP . . . F 3 105.771 83.955 167.497 1 83.35 ? C4 ADP 701 B 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #