data_5GZA # _model_server_result.job_id 8ngIRMtp_E9ALzXO17TPhQ _model_server_result.datetime_utc '2024-11-22 00:18:04' _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 5gza # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5GZA # _exptl.entry_id 5GZA _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 1 _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 120 _cell.entry_id 5GZA _cell.length_a 70.55 _cell.length_b 70.55 _cell.length_c 66.935 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GZA _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # _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,F,G _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG MAN C1 O1 . O4 HO4 . sing 2 ? 2 3 2 NGA NAG C1 O1 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B MAN 1 B 1 MAN A 401 MAN 2 n B NAG 2 B 2 NAG A 402 NAG 2 n B NGA 3 B 3 NGA A 403 NGA # 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 disulf ? disulf1 A SG CYS 1 A CYS 53 1_555 A SG CYS 14 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 20 A CYS 72 1_555 A SG CYS 87 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 149 A CYS 201 1_555 A SG CYS 189 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 G C1 ZZ1 . A ZZ1 405 1_555 B O1 MAN . B MAN 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale2 B O4 MAN . B MAN 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale3 B O3 NAG . B NAG 2 1_555 B C1 NGA . B NGA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? metalc ? metalc1 A OD1 ASP 173 A ASP 225 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc2 A OD2 ASP 173 A ASP 225 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc3 A OD2 ASP 173 A ASP 225 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc4 A OD2 ASP 175 A ASP 227 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc5 C O2B ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc6 C O1B ADP . A ADP 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc7 C O1A ADP . A ADP 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? # _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 5GZA _atom_sites.fract_transf_matrix[1][1] 0.014174 _atom_sites.fract_transf_matrix[1][2] 0.008184 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016367 _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] 0.01494 _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 3 ADP A 1 401 381 ADP ADP . D 4 MG A 1 402 391 MG MG . E 4 MG A 1 403 392 MG MG . F 5 AF3 A 1 404 395 AF3 AF3 . G 6 ZZ1 A 1 405 400 ZZ1 ZZ1 . # 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 . . . C 3 51.63 29.789 -5.053 1 45.84 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . C 3 50.656 29.913 -6.29 1 45.83 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . C 3 52.945 30.352 -5.459 1 42.89 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . C 3 51.633 28.317 -4.756 1 46.04 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . C 3 50.768 32.161 -3.59 1 42.99 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . C 3 50.141 32.69 -4.933 1 40.77 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . C 3 51.726 33.089 -3.351 1 40.46 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . C 3 50.99 30.548 -3.754 1 43.29 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . C 3 49.559 32.302 -2.558 1 41.55 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . C 3 48.443 31.445 -2.691 1 42.89 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . C 3 47.317 32 -1.868 1 42.96 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . C 3 47.656 32.119 -0.539 1 43.71 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . C 3 46.886 33.481 -2.399 1 42.17 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . C 3 46.188 33.566 -3.764 1 41.72 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . C 3 46.106 33.851 -1.391 1 42.46 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . C 3 44.68 33.318 -1.27 1 43.34 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . C 3 46.804 33.266 -0.059 1 43.36 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . C 3 47.51 34.181 0.628 1 43.05 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . C 3 48.817 34.127 0.327 1 42.62 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . C 3 49.529 35.011 1.051 1 42.11 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . C 3 48.697 35.597 1.871 1 42.14 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . C 3 48.79 36.498 2.837 1 41.59 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . C 3 49.813 37.191 3.436 1 41 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . C 3 47.666 36.85 3.556 1 41.99 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . C 3 46.479 36.297 3.371 1 42.66 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . C 3 46.27 35.428 2.341 1 43.01 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . C 3 47.446 35.034 1.683 1 42.86 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 100 _model_server_stats.create_model_time_ms 57 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #