data_5TTH # _model_server_result.job_id fFgDAbU7RZD5pQabYSEAGw _model_server_result.datetime_utc '2024-11-05 01:22:27' _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 5tth # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":901}' # _entry.id 5TTH # _exptl.entry_id 5TTH _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 134.59 _cell.angle_gamma 90 _cell.entry_id 5TTH _cell.length_a 180.086 _cell.length_b 95.711 _cell.length_c 126.558 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TTH _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 C 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 disulf ? disulf1 A SG CYS 450 A CYS 516 1_555 A SG CYS 476 A CYS 542 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.101 ? metalc ? metalc1 A OD1 ASN 68 A ASN 134 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc2 C O3B ADP . A ADP 901 1_555 D BE BEF . A BEF 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? metalc ? metalc3 C O2B ADP . A ADP 901 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc4 C O2A ADP . A ADP 901 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc5 B OD1 ASN 68 B ASN 134 1_555 H MG MG . B MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? metalc ? metalc6 F O3B ADP . B ADP 801 1_555 G BE BEF . B BEF 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.564 ? metalc ? metalc7 F O2B ADP . B ADP 801 1_555 H MG MG . B MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc8 F O2A ADP . B ADP 801 1_555 H MG MG . B MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? # _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 5TTH _atom_sites.fract_transf_matrix[1][1] 0.005553 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005474 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010448 _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] 0.011096 _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 1 901 804 ADP ADP . D 4 BEF A 1 902 805 BEF BEF . E 5 MG A 1 903 806 MG MG . F 3 ADP B 1 801 738 ADP ADP . G 4 BEF B 1 802 739 BEF BEF . H 5 MG B 1 803 740 MG MG . # 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 -46.544 10.772 -15.23 1 57.01 ? PB ADP 901 A 1 HETATM 2 O O1B ADP . . . C 3 -46.911 11.833 -16.209 1 51.96 ? O1B ADP 901 A 1 HETATM 3 O O2B ADP . . . C 3 -47.66 10.456 -14.26 1 54.39 ? O2B ADP 901 A 1 HETATM 4 O O3B ADP . . . C 3 -45.226 11.019 -14.547 1 60.79 ? O3B ADP 901 A 1 HETATM 5 P PA ADP . . . C 3 -46.967 8.055 -16.02 1 56.45 ? PA ADP 901 A 1 HETATM 6 O O1A ADP . . . C 3 -46.151 7.116 -16.902 1 53.43 ? O1A ADP 901 A 1 HETATM 7 O O2A ADP . . . C 3 -47.235 7.777 -14.561 1 50.55 ? O2A ADP 901 A 1 HETATM 8 O O3A ADP . . . C 3 -46.236 9.49 -16.154 1 53.26 ? O3A ADP 901 A 1 HETATM 9 O O5' ADP . . . C 3 -48.402 8.272 -16.729 1 56.96 ? O5' ADP 901 A 1 HETATM 10 C C5' ADP . . . C 3 -48.373 8.69 -18.098 1 57.53 ? C5' ADP 901 A 1 HETATM 11 C C4' ADP . . . C 3 -49.493 9.627 -18.498 1 54.95 ? C4' ADP 901 A 1 HETATM 12 O O4' ADP . . . C 3 -50.629 8.825 -18.666 1 52.23 ? O4' ADP 901 A 1 HETATM 13 C C3' ADP . . . C 3 -49.888 10.713 -17.516 1 59.27 ? C3' ADP 901 A 1 HETATM 14 O O3' ADP . . . C 3 -49.121 11.907 -17.724 1 63.84 ? O3' ADP 901 A 1 HETATM 15 C C2' ADP . . . C 3 -51.36 10.896 -17.784 1 57.4 ? C2' ADP 901 A 1 HETATM 16 O O2' ADP . . . C 3 -51.58 11.902 -18.769 1 57.83 ? O2' ADP 901 A 1 HETATM 17 C C1' ADP . . . C 3 -51.789 9.558 -18.332 1 56.86 ? C1' ADP 901 A 1 HETATM 18 N N9 ADP . . . C 3 -52.513 8.769 -17.328 1 59.36 ? N9 ADP 901 A 1 HETATM 19 C C8 ADP . . . C 3 -51.978 7.805 -16.565 1 61.01 ? C8 ADP 901 A 1 HETATM 20 N N7 ADP . . . C 3 -52.931 7.273 -15.774 1 63.53 ? N7 ADP 901 A 1 HETATM 21 C C5 ADP . . . C 3 -54.085 7.896 -16.028 1 61.91 ? C5 ADP 901 A 1 HETATM 22 C C6 ADP . . . C 3 -55.469 7.799 -15.53 1 66.02 ? C6 ADP 901 A 1 HETATM 23 N N6 ADP . . . C 3 -55.761 6.897 -14.561 1 70.51 ? N6 ADP 901 A 1 HETATM 24 N N1 ADP . . . C 3 -56.404 8.622 -16.07 1 66.95 ? N1 ADP 901 A 1 HETATM 25 C C2 ADP . . . C 3 -56.084 9.511 -17.036 1 66.98 ? C2 ADP 901 A 1 HETATM 26 N N3 ADP . . . C 3 -54.832 9.649 -17.521 1 65.6 ? N3 ADP 901 A 1 HETATM 27 C C4 ADP . . . C 3 -53.811 8.883 -17.064 1 62.17 ? C4 ADP 901 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #