data_2OTG # _model_server_result.job_id ERdQNAFdRnkoVZMOQCNNTQ _model_server_result.datetime_utc '2025-01-09 03:05:41' _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 2otg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":999}' # _entry.id 2OTG # _exptl.entry_id 2OTG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 100.77 _cell.angle_gamma 90 _cell.entry_id 2OTG _cell.length_a 87.087 _cell.length_b 51.689 _cell.length_c 159.9 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2OTG _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OG1 THR 183 A THR 183 1_555 D MG MG . A MG 839 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc2 A OG SER 242 A SER 241 1_555 D MG MG . A MG 839 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc3 D MG MG . A MG 839 1_555 E O3B ADP . A ADP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc4 D MG MG . A MG 839 1_555 E O1B ADP . A ADP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? metalc ? metalc5 B OD1 ASP 29 B ASP 28 1_555 F MG MG . B MG 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? metalc ? metalc6 B OD1 ASN 31 B ASN 30 1_555 F MG MG . B MG 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc7 B ND2 ASN 31 B ASN 30 1_555 F MG MG . B MG 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc8 B OD1 ASP 33 B ASP 32 1_555 F MG MG . B MG 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc9 B O PHE 35 B PHE 34 1_555 F MG MG . B MG 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc10 B OD1 ASP 37 B ASP 36 1_555 F MG MG . B MG 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.005 ? metalc ? metalc11 B OD2 ASP 40 B ASP 39 1_555 F MG MG . B MG 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc12 B OD1 ASP 40 B ASP 39 1_555 F MG MG . B MG 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc13 C OD1 ASP 20 C ASP 19 1_555 G CA CA . C CA 991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.826 ? metalc ? metalc14 C O ASP 20 C ASP 19 1_555 G CA CA . C CA 991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.204 ? metalc ? metalc15 C OD1 ASP 23 C ASP 22 1_555 G CA CA . C CA 991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc16 C O ASP 23 C ASP 22 1_555 G CA CA . C CA 991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.074 ? metalc ? metalc17 C O GLY 24 C GLY 23 1_555 G CA CA . C CA 991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc18 C OD2 ASP 26 C ASP 25 1_555 G CA CA . C CA 991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc19 C O ALA 28 C ALA 27 1_555 G CA CA . C CA 991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? # _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 2OTG _atom_sites.fract_transf_matrix[1][1] 0.011483 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002184 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019346 _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] 0.006366 _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 D 4 MG A 1 839 503 MG MG . E 5 ADP A 1 999 999 ADP ADP . F 4 MG B 1 990 990 MG MG . G 6 CA C 1 991 991 CA CA . # 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 5 -10.385 -6.734 21.902 1 10.91 ? PB ADP 999 A 1 HETATM 2 O O1B ADP . . . E 5 -9.478 -7.714 21.156 1 8.58 ? O1B ADP 999 A 1 HETATM 3 O O2B ADP . . . E 5 -10.242 -6.737 23.54 1 13.16 ? O2B ADP 999 A 1 HETATM 4 O O3B ADP . . . E 5 -12.102 -6.954 21.724 1 0.02 ? O3B ADP 999 A 1 HETATM 5 P PA ADP . . . E 5 -9.98 -5.467 19.703 1 14.66 ? PA ADP 999 A 1 HETATM 6 O O1A ADP . . . E 5 -11.317 -5.501 18.968 1 15.67 ? O1A ADP 999 A 1 HETATM 7 O O2A ADP . . . E 5 -8.524 -5.301 18.876 1 6.55 ? O2A ADP 999 A 1 HETATM 8 O O3A ADP . . . E 5 -10.07 -5.273 21.329 1 12.22 ? O3A ADP 999 A 1 HETATM 9 O O5' ADP . . . E 5 -9.918 -3.802 19.871 1 10.46 ? O5' ADP 999 A 1 HETATM 10 C C5' ADP . . . E 5 -9.799 -3.049 18.659 1 12.77 ? C5' ADP 999 A 1 HETATM 11 C C4' ADP . . . E 5 -9.845 -1.531 19.031 1 14.22 ? C4' ADP 999 A 1 HETATM 12 O O4' ADP . . . E 5 -8.766 -1.13 19.99 1 11.05 ? O4' ADP 999 A 1 HETATM 13 C C3' ADP . . . E 5 -9.733 -0.606 17.725 1 14.31 ? C3' ADP 999 A 1 HETATM 14 O O3' ADP . . . E 5 -10.946 0.217 17.508 1 15.79 ? O3' ADP 999 A 1 HETATM 15 C C2' ADP . . . E 5 -8.434 0.281 17.938 1 14.43 ? C2' ADP 999 A 1 HETATM 16 O O2' ADP . . . E 5 -8.712 1.708 17.887 1 7.81 ? O2' ADP 999 A 1 HETATM 17 C C1' ADP . . . E 5 -7.828 -0.13 19.322 1 12.8 ? C1' ADP 999 A 1 HETATM 18 N N9 ADP . . . E 5 -6.418 -0.707 19.191 1 13.81 ? N9 ADP 999 A 1 HETATM 19 C C8 ADP . . . E 5 -6.002 -1.898 19.799 1 14.33 ? C8 ADP 999 A 1 HETATM 20 N N7 ADP . . . E 5 -4.771 -2.174 19.543 1 9.71 ? N7 ADP 999 A 1 HETATM 21 C C5 ADP . . . E 5 -4.275 -1.23 18.713 1 11.31 ? C5 ADP 999 A 1 HETATM 22 C C6 ADP . . . E 5 -2.978 -1.045 18.155 1 11.26 ? C6 ADP 999 A 1 HETATM 23 N N6 ADP . . . E 5 -1.991 -2.019 18.41 1 9.92 ? N6 ADP 999 A 1 HETATM 24 N N1 ADP . . . E 5 -2.749 0.064 17.324 1 10.78 ? N1 ADP 999 A 1 HETATM 25 C C2 ADP . . . E 5 -3.762 0.997 17.081 1 9.47 ? C2 ADP 999 A 1 HETATM 26 N N3 ADP . . . E 5 -5.032 0.854 17.636 1 8.66 ? N3 ADP 999 A 1 HETATM 27 C C4 ADP . . . E 5 -5.319 -0.243 18.442 1 11.07 ? C4 ADP 999 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #