data_3LJ0 # _model_server_result.job_id NPem-gfxCCotvr9uJql3QQ _model_server_result.datetime_utc '2024-10-13 14:26:25' _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 3lj0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2101}' # _entry.id 3LJ0 # _exptl.entry_id 3LJ0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 90 _cell.angle_gamma 120 _cell.entry_id 3LJ0 _cell.length_a 131.02 _cell.length_b 131.02 _cell.length_c 175.82 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LJ0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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,I,J _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 ? 4 E N N ? 4 I 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 C GLN 182 A GLN 839 1_555 A N SEP 183 A SEP 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C SEP 183 A SEP 840 1_555 A N SEP 184 A SEP 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C SEP 184 A SEP 841 1_555 A N PHE 185 A PHE 842 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 A C ARG 186 A ARG 843 1_555 A N TPO 187 A TPO 844 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 B C GLN 182 B GLN 839 1_555 B N SEP 183 B SEP 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 B C SEP 183 B SEP 840 1_555 B N SEP 184 B SEP 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 B C SEP 184 B SEP 841 1_555 B N PHE 185 B PHE 842 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 B C ARG 186 B ARG 843 1_555 B N TPO 187 B TPO 844 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A OD1 ASN 145 A ASN 802 1_555 C MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc2 A OD2 ASP 171 A ASP 828 1_555 C MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc3 A OD1 ASP 171 A ASP 828 1_555 D SR SR . A SR 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc4 E O1A ADP . A ADP 2101 1_555 C MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc5 E O3B ADP . A ADP 2101 1_555 C MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc6 E O2B ADP . A ADP 2101 1_555 D SR SR . A SR 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc7 B OD1 ASN 145 B ASN 802 1_555 G MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc8 B OD2 ASP 171 B ASP 828 1_555 G MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc9 B OD1 ASP 171 B ASP 828 1_555 H SR SR . B SR 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc10 I O1A ADP . B ADP 2101 1_555 G MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc11 I O3B ADP . B ADP 2101 1_555 G MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? metalc ? metalc12 I O2B ADP . B ADP 2101 1_555 H SR SR . B SR 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? # _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 3LJ0 _atom_sites.fract_transf_matrix[1][1] 0.007632 _atom_sites.fract_transf_matrix[1][2] 0.004407 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008813 _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] 0.005688 _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 MG A 1 2102 2102 MG MG . D 3 SR A 1 2103 2103 SR SR . E 4 ADP A 1 2101 2101 ADP ADP . F 5 QUE A 1 1 1 QUE QUE . G 2 MG B 1 2102 2102 MG MG . H 3 SR B 1 2103 2103 SR SR . I 4 ADP B 1 2101 2101 ADP ADP . J 5 QUE B 1 1 1 QUE QUE . # 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 4 47.902 -7.602 14.791 1 51.42 ? PB ADP 2101 A 1 HETATM 2 O O1B ADP . . . E 4 46.997 -6.5 14.283 1 51.42 ? O1B ADP 2101 A 1 HETATM 3 O O2B ADP . . . E 4 47.318 -8.986 14.607 1 51.42 ? O2B ADP 2101 A 1 HETATM 4 O O3B ADP . . . E 4 49.347 -7.458 14.361 1 51.42 ? O3B ADP 2101 A 1 HETATM 5 P PA ADP . . . E 4 48.708 -8.386 17.388 1 51.42 ? PA ADP 2101 A 1 HETATM 6 O O1A ADP . . . E 4 49.974 -8.899 16.745 1 51.42 ? O1A ADP 2101 A 1 HETATM 7 O O2A ADP . . . E 4 47.696 -9.362 17.923 1 51.42 ? O2A ADP 2101 A 1 HETATM 8 O O3A ADP . . . E 4 47.944 -7.38 16.391 1 51.42 ? O3A ADP 2101 A 1 HETATM 9 O O5' ADP . . . E 4 49.133 -7.415 18.588 1 51.42 ? O5' ADP 2101 A 1 HETATM 10 C C5' ADP . . . E 4 50.074 -6.379 18.333 1 51.42 ? C5' ADP 2101 A 1 HETATM 11 C C4' ADP . . . E 4 50.833 -6.042 19.606 1 51.42 ? C4' ADP 2101 A 1 HETATM 12 O O4' ADP . . . E 4 49.96 -6.053 20.74 1 51.42 ? O4' ADP 2101 A 1 HETATM 13 C C3' ADP . . . E 4 51.932 -7.045 19.906 1 51.42 ? C3' ADP 2101 A 1 HETATM 14 O O3' ADP . . . E 4 53.167 -6.625 19.326 1 51.42 ? O3' ADP 2101 A 1 HETATM 15 C C2' ADP . . . E 4 51.995 -7.068 21.421 1 51.42 ? C2' ADP 2101 A 1 HETATM 16 O O2' ADP . . . E 4 52.953 -6.134 21.925 1 51.42 ? O2' ADP 2101 A 1 HETATM 17 C C1' ADP . . . E 4 50.612 -6.632 21.874 1 51.42 ? C1' ADP 2101 A 1 HETATM 18 N N9 ADP . . . E 4 49.88 -7.835 22.334 1 51.42 ? N9 ADP 2101 A 1 HETATM 19 C C8 ADP . . . E 4 49.226 -8.709 21.546 1 51.42 ? C8 ADP 2101 A 1 HETATM 20 N N7 ADP . . . E 4 48.671 -9.709 22.272 1 51.42 ? N7 ADP 2101 A 1 HETATM 21 C C5 ADP . . . E 4 48.974 -9.473 23.564 1 51.42 ? C5 ADP 2101 A 1 HETATM 22 C C6 ADP . . . E 4 48.697 -10.138 24.853 1 51.42 ? C6 ADP 2101 A 1 HETATM 23 N N6 ADP . . . E 4 47.964 -11.277 24.889 1 51.42 ? N6 ADP 2101 A 1 HETATM 24 N N1 ADP . . . E 4 49.195 -9.571 25.976 1 51.42 ? N1 ADP 2101 A 1 HETATM 25 C C2 ADP . . . E 4 49.922 -8.438 25.936 1 51.42 ? C2 ADP 2101 A 1 HETATM 26 N N3 ADP . . . E 4 50.211 -7.782 24.798 1 51.42 ? N3 ADP 2101 A 1 HETATM 27 C C4 ADP . . . E 4 49.773 -8.241 23.602 1 51.42 ? C4 ADP 2101 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #