data_2HYD # _model_server_result.job_id ZDadHeieQicbLn9wIxV7HA _model_server_result.datetime_utc '2024-12-22 01:38:51' _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":"D","auth_seq_id":700}' # _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 . . . D 3 96.476 55.569 172.021 1 82.73 ? PB ADP 700 A 1 HETATM 2 O O1B ADP . . . D 3 96.673 56.787 171.206 1 83.26 ? O1B ADP 700 A 1 HETATM 3 O O2B ADP . . . D 3 94.993 55.494 172.534 1 83.24 ? O2B ADP 700 A 1 HETATM 4 O O3B ADP . . . D 3 97.404 55.599 173.314 1 80.14 ? O3B ADP 700 A 1 HETATM 5 P PA ADP . . . D 3 98.213 54.312 170.677 1 84.18 ? PA ADP 700 A 1 HETATM 6 O O1A ADP . . . D 3 98.194 55.2 169.5 1 81.66 ? O1A ADP 700 A 1 HETATM 7 O O2A ADP . . . D 3 99.214 54.98 171.746 1 85.54 ? O2A ADP 700 A 1 HETATM 8 O O3A ADP . . . D 3 96.716 54.236 171.144 1 82.89 ? O3A ADP 700 A 1 HETATM 9 O O5' ADP . . . D 3 98.638 52.847 170.093 1 84.27 ? O5' ADP 700 A 1 HETATM 10 C C5' ADP . . . D 3 100.057 52.931 170.074 1 84.35 ? C5' ADP 700 A 1 HETATM 11 C C4' ADP . . . D 3 100.686 51.63 169.684 1 83.32 ? C4' ADP 700 A 1 HETATM 12 O O4' ADP . . . D 3 100.4 51.377 168.307 1 83.46 ? O4' ADP 700 A 1 HETATM 13 C C3' ADP . . . D 3 102.189 51.767 169.863 1 83.71 ? C3' ADP 700 A 1 HETATM 14 O O3' ADP . . . D 3 102.631 50.849 170.843 1 83.59 ? O3' ADP 700 A 1 HETATM 15 C C2' ADP . . . D 3 102.824 51.556 168.509 1 84.34 ? C2' ADP 700 A 1 HETATM 16 O O2' ADP . . . D 3 103.765 50.455 168.51 1 85.26 ? O2' ADP 700 A 1 HETATM 17 C C1' ADP . . . D 3 101.648 51.328 167.553 1 83.54 ? C1' ADP 700 A 1 HETATM 18 N N9 ADP . . . D 3 101.67 52.359 166.535 1 83.05 ? N9 ADP 700 A 1 HETATM 19 C C8 ADP . . . D 3 101.08 53.589 166.574 1 83.06 ? C8 ADP 700 A 1 HETATM 20 N N7 ADP . . . D 3 101.313 54.242 165.48 1 83.04 ? N7 ADP 700 A 1 HETATM 21 C C5 ADP . . . D 3 102.061 53.472 164.679 1 83.76 ? C5 ADP 700 A 1 HETATM 22 C C6 ADP . . . D 3 102.629 53.608 163.388 1 84.71 ? C6 ADP 700 A 1 HETATM 23 N N6 ADP . . . D 3 102.448 54.76 162.653 1 84.48 ? N6 ADP 700 A 1 HETATM 24 N N1 ADP . . . D 3 103.352 52.583 162.89 1 85.05 ? N1 ADP 700 A 1 HETATM 25 C C2 ADP . . . D 3 103.538 51.444 163.59 1 84.6 ? C2 ADP 700 A 1 HETATM 26 N N3 ADP . . . D 3 103.024 51.276 164.796 1 83.23 ? N3 ADP 700 A 1 HETATM 27 C C4 ADP . . . D 3 102.29 52.249 165.361 1 83.49 ? C4 ADP 700 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #