data_3DIN # _model_server_result.job_id W6p70uerZWMEcEOXidgkvQ _model_server_result.datetime_utc '2024-11-21 13:39:56' _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 3din # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":873}' # _entry.id 3DIN # _exptl.entry_id 3DIN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 90 _cell.entry_id 3DIN _cell.length_a 101.616 _cell.length_b 156.003 _cell.length_c 358.155 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DIN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,K 1 1 E,F,G,H,L,M,N 2 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 ? 6 J N N ? 6 M 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 metalc ? metalc1 J O2B ADP . A ADP 873 1_555 K BE BEF . A BEF 874 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? metalc ? metalc2 M O2B ADP . B ADP 873 1_555 N BE BEF . B BEF 874 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? # _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 3DIN _atom_sites.fract_transf_matrix[1][1] 0.009841 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00641 _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] 0.002792 _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 I 5 MG A 1 872 1 MG MG . J 6 ADP A 1 873 1 ADP ADP . K 7 BEF A 1 874 1 BEF BEF . L 5 MG B 1 872 2 MG MG . M 6 ADP B 1 873 2 ADP ADP . N 7 BEF B 1 874 2 BEF BEF . # 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 . . . J 6 -35.766 14.801 61.642 1 183.45 ? PB ADP 873 A 1 HETATM 2 O O1B ADP . . . J 6 -36.776 15.489 60.65 1 181.45 ? O1B ADP 873 A 1 HETATM 3 O O2B ADP . . . J 6 -34.994 13.581 61.038 1 184.42 ? O2B ADP 873 A 1 HETATM 4 O O3B ADP . . . J 6 -36.247 14.679 63.122 1 184.5 ? O3B ADP 873 A 1 HETATM 5 P PA ADP . . . J 6 -34.015 16.915 60.528 1 186.82 ? PA ADP 873 A 1 HETATM 6 O O1A ADP . . . J 6 -32.593 17.449 60.934 1 183.51 ? O1A ADP 873 A 1 HETATM 7 O O2A ADP . . . J 6 -34.163 16.159 59.131 1 180.06 ? O2A ADP 873 A 1 HETATM 8 O O3A ADP . . . J 6 -34.644 15.991 61.741 1 186.76 ? O3A ADP 873 A 1 HETATM 9 O O5' ADP . . . J 6 -34.991 18.21 60.543 1 186.46 ? O5' ADP 873 A 1 HETATM 10 C C5' ADP . . . J 6 -36.345 18.096 60.115 1 186.67 ? C5' ADP 873 A 1 HETATM 11 C C4' ADP . . . J 6 -36.819 19.417 59.527 1 188.35 ? C4' ADP 873 A 1 HETATM 12 O O4' ADP . . . J 6 -36.866 20.414 60.558 1 190.54 ? O4' ADP 873 A 1 HETATM 13 C C3' ADP . . . J 6 -35.928 20.01 58.447 1 192.89 ? C3' ADP 873 A 1 HETATM 14 O O3' ADP . . . J 6 -36.166 19.434 57.158 1 191.77 ? O3' ADP 873 A 1 HETATM 15 C C2' ADP . . . J 6 -36.28 21.478 58.567 1 195.28 ? C2' ADP 873 A 1 HETATM 16 O O2' ADP . . . J 6 -37.488 21.758 57.857 1 188.67 ? O2' ADP 873 A 1 HETATM 17 C C1' ADP . . . J 6 -36.445 21.69 60.07 1 187.81 ? C1' ADP 873 A 1 HETATM 18 N N9 ADP . . . J 6 -35.112 22.046 60.589 1 189.05 ? N9 ADP 873 A 1 HETATM 19 C C8 ADP . . . J 6 -34.431 21.295 61.656 1 185.94 ? C8 ADP 873 A 1 HETATM 20 N N7 ADP . . . J 6 -33.379 22.183 62.085 1 188.99 ? N7 ADP 873 A 1 HETATM 21 C C5 ADP . . . J 6 -33.61 23.437 61.511 1 191.78 ? C5 ADP 873 A 1 HETATM 22 C C6 ADP . . . J 6 -32.947 24.624 61.754 1 181.73 ? C6 ADP 873 A 1 HETATM 23 N N6 ADP . . . J 6 -31.867 24.707 62.647 1 186.4 ? N6 ADP 873 A 1 HETATM 24 N N1 ADP . . . J 6 -33.372 25.697 61.07 1 185.82 ? N1 ADP 873 A 1 HETATM 25 C C2 ADP . . . J 6 -34.416 25.621 60.208 1 187.47 ? C2 ADP 873 A 1 HETATM 26 N N3 ADP . . . J 6 -35.079 24.465 59.982 1 134.73 ? N3 ADP 873 A 1 HETATM 27 C C4 ADP . . . J 6 -34.665 23.377 60.64 1 399.04 ? C4 ADP 873 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #