data_3IBG # _model_server_result.job_id tLHVUY6eM37E1EHV9lLK9A _model_server_result.datetime_utc '2025-02-18 20:29:49' _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 3ibg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":349}' # _entry.id 3IBG # _exptl.entry_id 3IBG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 3IBG _cell.length_a 67.76 _cell.length_b 154.78 _cell.length_c 242.88 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IBG _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H 1 1 C,D,I,J 2 1 E,F,K,L 3 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 ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L 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 283 A CYS 283 1_555 B SG CYS 283 B CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 286 A CYS 286 1_555 B SG CYS 286 B CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 C SG CYS 283 C CYS 283 1_555 D SG CYS 283 D CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 C SG CYS 286 C CYS 286 1_555 D SG CYS 286 D CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf5 E SG CYS 283 E CYS 283 1_555 F SG CYS 283 F CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf6 E SG CYS 286 E CYS 286 1_555 F SG CYS 286 F CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? # _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 3IBG _atom_sites.fract_transf_matrix[1][1] 0.014758 _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] 0.006461 _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] 0.004117 _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 G 2 ADP A 1 349 1 ADP ADP . H 2 ADP B 1 349 2 ADP ADP . I 2 ADP C 1 349 3 ADP ADP . J 2 ADP D 1 349 4 ADP ADP . K 2 ADP E 1 349 5 ADP ADP . L 2 ADP F 1 349 6 ADP ADP . # 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 2 41.389 -11.432 41.002 1 74.2 ? PB ADP 349 D 1 HETATM 2 O O1B ADP . . . J 2 42.748 -11.602 41.612 1 74.2 ? O1B ADP 349 D 1 HETATM 3 O O2B ADP . . . J 2 40.571 -12.713 41.076 1 74.2 ? O2B ADP 349 D 1 HETATM 4 O O3B ADP . . . J 2 40.647 -10.283 41.436 1 74.2 ? O3B ADP 349 D 1 HETATM 5 P PA ADP . . . J 2 42.332 -10.013 38.641 1 74.2 ? PA ADP 349 D 1 HETATM 6 O O1A ADP . . . J 2 42.458 -8.802 39.483 1 74.2 ? O1A ADP 349 D 1 HETATM 7 O O2A ADP . . . J 2 41.772 -9.87 37.264 1 74.2 ? O2A ADP 349 D 1 HETATM 8 O O3A ADP . . . J 2 41.552 -11.124 39.455 1 74.2 ? O3A ADP 349 D 1 HETATM 9 O O5' ADP . . . J 2 43.843 -10.477 38.551 1 74.2 ? O5' ADP 349 D 1 HETATM 10 C C5' ADP . . . J 2 44.264 -11.114 37.374 1 74.2 ? C5' ADP 349 D 1 HETATM 11 C C4' ADP . . . J 2 45.716 -10.888 37.045 1 74.2 ? C4' ADP 349 D 1 HETATM 12 O O4' ADP . . . J 2 45.823 -11.479 35.768 1 74.2 ? O4' ADP 349 D 1 HETATM 13 C C3' ADP . . . J 2 45.947 -9.447 36.7 1 74.2 ? C3' ADP 349 D 1 HETATM 14 O O3' ADP . . . J 2 47.303 -9.312 36.154 1 74.2 ? O3' ADP 349 D 1 HETATM 15 C C2' ADP . . . J 2 44.989 -9.32 35.545 1 74.2 ? C2' ADP 349 D 1 HETATM 16 O O2' ADP . . . J 2 45.315 -8.085 34.939 1 74.2 ? O2' ADP 349 D 1 HETATM 17 C C1' ADP . . . J 2 45.301 -10.593 34.765 1 74.2 ? C1' ADP 349 D 1 HETATM 18 N N9 ADP . . . J 2 44.22 -11.263 33.908 1 74.2 ? N9 ADP 349 D 1 HETATM 19 C C8 ADP . . . J 2 42.885 -11.357 34.17 1 74.2 ? C8 ADP 349 D 1 HETATM 20 N N7 ADP . . . J 2 42.191 -12.018 33.181 1 74.2 ? N7 ADP 349 D 1 HETATM 21 C C5 ADP . . . J 2 43.074 -12.365 32.226 1 74.2 ? C5 ADP 349 D 1 HETATM 22 C C6 ADP . . . J 2 42.994 -13.078 30.919 1 74.2 ? C6 ADP 349 D 1 HETATM 23 N N6 ADP . . . J 2 41.82 -13.567 30.433 1 74.2 ? N6 ADP 349 D 1 HETATM 24 N N1 ADP . . . J 2 44.144 -13.239 30.247 1 74.2 ? N1 ADP 349 D 1 HETATM 25 C C2 ADP . . . J 2 45.317 -12.779 30.727 1 74.2 ? C2 ADP 349 D 1 HETATM 26 N N3 ADP . . . J 2 45.45 -12.134 31.884 1 74.2 ? N3 ADP 349 D 1 HETATM 27 C C4 ADP . . . J 2 44.393 -11.88 32.7 1 74.2 ? C4 ADP 349 D 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #