data_4XHP # _model_server_result.job_id JCkhtKC8hRXiyhNHcd3O2Q _model_server_result.datetime_utc '2025-03-26 19:01:40' _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 4xhp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":903}' # _entry.id 4XHP # _exptl.entry_id 4XHP _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 98.82 _cell.angle_gamma 90 _cell.entry_id 4XHP _cell.length_a 55.306 _cell.length_b 97.275 _cell.length_c 87.898 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XHP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 C N N ? 3 E 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 covale ? covale1 A O GLY 84 A GLY 84 1_555 A CB ARG 87 A ARG 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? metalc ? metalc1 A OD1 ASP 236 A ASP 236 1_555 B MG MG . A MG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc2 A OD2 ASP 679 A ASP 679 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? metalc ? metalc3 B MG MG . A MG 900 1_555 C O2B ADP . A ADP 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc4 D MG MG . A MG 902 1_555 E O1B ADP . A ADP 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc5 D MG MG . A MG 902 1_555 E O2A ADP . A ADP 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? # _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 4XHP _atom_sites.fract_transf_matrix[1][1] 0.018081 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002805 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01028 _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] 0.011513 _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 B 2 MG A 1 900 900 MG MG . C 3 ADP A 1 901 901 ADP ADP . D 2 MG A 1 902 902 MG MG . E 3 ADP A 1 903 903 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 . . . E 3 -3.269 -30.245 -11.785 1 79.19 ? PB ADP 903 A 1 HETATM 2 O O1B ADP . . . E 3 -3.051 -31.616 -12.379 1 73.12 ? O1B ADP 903 A 1 HETATM 3 O O2B ADP . . . E 3 -2.829 -30.124 -10.346 1 63.87 ? O2B ADP 903 A 1 HETATM 4 O O3B ADP . . . E 3 -4.618 -29.633 -12.079 1 95.74 ? O3B ADP 903 A 1 HETATM 5 P PA ADP . . . E 3 -1.624 -29.677 -14.007 1 62.49 ? PA ADP 903 A 1 HETATM 6 O O1A ADP . . . E 3 -2.714 -29.649 -15.052 1 60.98 ? O1A ADP 903 A 1 HETATM 7 O O2A ADP . . . E 3 -0.77 -30.913 -13.859 1 54.92 ? O2A ADP 903 A 1 HETATM 8 O O3A ADP . . . E 3 -2.227 -29.298 -12.563 1 71.8 ? O3A ADP 903 A 1 HETATM 9 O O5' ADP . . . E 3 -0.641 -28.427 -14.248 1 57.16 ? O5' ADP 903 A 1 HETATM 10 C C5' ADP . . . E 3 0.587 -28.352 -13.526 1 56.39 ? C5' ADP 903 A 1 HETATM 11 C C4' ADP . . . E 3 1.275 -27.028 -13.827 1 54.55 ? C4' ADP 903 A 1 HETATM 12 O O4' ADP . . . E 3 1.847 -27.059 -15.135 1 50.8 ? O4' ADP 903 A 1 HETATM 13 C C3' ADP . . . E 3 0.302 -25.859 -13.786 1 56.77 ? C3' ADP 903 A 1 HETATM 14 O O3' ADP . . . E 3 0.694 -24.947 -12.758 1 55.8 ? O3' ADP 903 A 1 HETATM 15 C C2' ADP . . . E 3 0.416 -25.182 -15.138 1 55.88 ? C2' ADP 903 A 1 HETATM 16 O O2' ADP . . . E 3 0.591 -23.772 -14.98 1 59.04 ? O2' ADP 903 A 1 HETATM 17 C C1' ADP . . . E 3 1.641 -25.806 -15.784 1 51.44 ? C1' ADP 903 A 1 HETATM 18 N N9 ADP . . . E 3 1.443 -25.992 -17.243 1 51.7 ? N9 ADP 903 A 1 HETATM 19 C C8 ADP . . . E 3 0.38 -26.565 -17.839 1 55.23 ? C8 ADP 903 A 1 HETATM 20 N N7 ADP . . . E 3 0.522 -26.566 -19.191 1 55.82 ? N7 ADP 903 A 1 HETATM 21 C C5 ADP . . . E 3 1.699 -25.978 -19.475 1 51.09 ? C5 ADP 903 A 1 HETATM 22 C C6 ADP . . . E 3 2.466 -25.65 -20.7 1 49.49 ? C6 ADP 903 A 1 HETATM 23 N N6 ADP . . . E 3 1.99 -25.961 -21.93 1 52.99 ? N6 ADP 903 A 1 HETATM 24 N N1 ADP . . . E 3 3.659 -25.032 -20.549 1 44.19 ? N1 ADP 903 A 1 HETATM 25 C C2 ADP . . . E 3 4.146 -24.716 -19.335 1 41.36 ? C2 ADP 903 A 1 HETATM 26 N N3 ADP . . . E 3 3.505 -24.983 -18.184 1 40.72 ? N3 ADP 903 A 1 HETATM 27 C C4 ADP . . . E 3 2.298 -25.598 -18.187 1 46.13 ? C4 ADP 903 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 391 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #