data_1GM5 # _model_server_result.job_id T9kP3oan0o-sPc9MzxOGyQ _model_server_result.datetime_utc '2024-11-22 17:50:27' _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 1gm5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1756}' # _entry.id 1GM5 # _exptl.entry_id 1GM5 _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 113.82 _cell.angle_gamma 90 _cell.entry_id 1GM5 _cell.length_a 133.704 _cell.length_b 144.602 _cell.length_c 84.023 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GM5 _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 PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 disulf ? disulf1 A SG CYS 106 A CYS 106 1_555 A SG CYS 282 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc1 E O3B ADP . A ADP 1756 1_555 F MG MG . A MG 1757 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.146 ? hydrog WATSON-CRICK hydrog1 B N3 DC 1 X DC 1 1_555 C N1 DG 20 Y DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 1 X DC 1 1_555 C O6 DG 20 Y DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 1 X DC 1 1_555 C N2 DG 20 Y DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DA 2 X DA 2 1_555 C N3 DT 19 Y DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 DA 2 X DA 2 1_555 C O4 DT 19 Y DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 3 X DG 3 1_555 C N3 DC 18 Y DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 DG 3 X DG 3 1_555 C O2 DC 18 Y DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 DG 3 X DG 3 1_555 C N4 DC 18 Y DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 4 X DC 4 1_555 C N1 DG 17 Y DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 4 X DC 4 1_555 C O6 DG 17 Y DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 4 X DC 4 1_555 C N2 DG 17 Y DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog12 B N3 DT 5 X DT 5 1_555 C N3 DA 16 Y DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 DC 6 X DC 6 1_555 C N1 DG 15 Y DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N4 DC 6 X DC 6 1_555 C O6 DG 15 Y DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O2 DC 6 X DC 6 1_555 C N2 DG 15 Y DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 7 X DC 7 1_555 C N1 DG 14 Y DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 7 X DC 7 1_555 C O6 DG 14 Y DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 7 X DC 7 1_555 C N2 DG 14 Y DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DA 8 X DA 8 1_555 C N3 DT 13 Y DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N6 DA 8 X DA 8 1_555 C O4 DT 13 Y DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DT 9 X DT 9 1_555 C N1 DA 12 Y DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O4 DT 9 X DT 9 1_555 C N6 DA 12 Y DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog23 B O6 DG 10 X DG 10 1_555 C N4 DC 11 Y DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N1 DG 1 Y DG 1 1_555 D N3 DC 9 Z DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C N2 DG 1 Y DG 1 1_555 D O2 DC 9 Z DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C O6 DG 1 Y DG 1 1_555 D N4 DC 9 Z DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C N3 DC 2 Y DC 2 1_555 D N1 DG 8 Z DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C N4 DC 2 Y DC 2 1_555 D O6 DG 8 Z DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C O2 DC 2 Y DC 2 1_555 D N2 DG 8 Z DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N1 DA 3 Y DA 3 1_555 D N3 DT 7 Z DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C N6 DA 3 Y DA 3 1_555 D O4 DT 7 Z DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C N1 DG 4 Y DG 4 1_555 D N3 DC 6 Z DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N2 DG 4 Y DG 4 1_555 D O2 DC 6 Z DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C O6 DG 4 Y DG 4 1_555 D N4 DC 6 Z DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C N3 DT 5 Y DT 5 1_555 D N1 DA 5 Z DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C O4 DT 5 Y DT 5 1_555 D N6 DA 5 Z DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C N1 DG 6 Y DG 6 1_555 D N3 DC 4 Z DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C N2 DG 6 Y DG 6 1_555 D O2 DC 4 Z DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C O6 DG 6 Y DG 6 1_555 D N4 DC 4 Z DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N3 DC 7 Y DC 7 1_555 D N1 DG 3 Z DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C N4 DC 7 Y DC 7 1_555 D O6 DG 3 Z DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 C O2 DC 7 Y DC 7 1_555 D N2 DG 3 Z DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 C N3 DT 8 Y DT 8 1_555 D N1 DA 2 Z DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 C O4 DT 8 Y DT 8 1_555 D N6 DA 2 Z DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 C N3 DC 9 Y DC 9 1_555 D N1 DG 1 Z DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 C N4 DC 9 Y DC 9 1_555 D O6 DG 1 Z DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 C O2 DC 9 Y DC 9 1_555 D N2 DG 1 Z DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 1GM5 _atom_sites.fract_transf_matrix[1][1] 0.007479 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003302 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006915 _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] 0.01301 _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 E 5 ADP A 1 1756 1756 ADP ADP . F 6 MG A 1 1757 1757 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 . . . E 5 3.367 11.297 22.975 1 79.53 ? PB ADP 1756 A 1 HETATM 2 O O1B ADP . . . E 5 3.187 10.016 22.137 1 73.87 ? O1B ADP 1756 A 1 HETATM 3 O O2B ADP . . . E 5 2.225 11.446 23.971 1 99.69 ? O2B ADP 1756 A 1 HETATM 4 O O3B ADP . . . E 5 4.641 11.157 23.702 1 95.49 ? O3B ADP 1756 A 1 HETATM 5 P PA ADP . . . E 5 2.752 12.9 20.658 1 81.13 ? PA ADP 1756 A 1 HETATM 6 O O1A ADP . . . E 5 2.306 14.315 20.582 1 85.24 ? O1A ADP 1756 A 1 HETATM 7 O O2A ADP . . . E 5 3.725 12.507 19.514 1 85.19 ? O2A ADP 1756 A 1 HETATM 8 O O3A ADP . . . E 5 3.383 12.67 22.131 1 76.53 ? O3A ADP 1756 A 1 HETATM 9 O O5' ADP . . . E 5 1.494 11.98 20.457 1 50.52 ? O5' ADP 1756 A 1 HETATM 10 C C5' ADP . . . E 5 0.299 12.596 20.074 1 69.64 ? C5' ADP 1756 A 1 HETATM 11 C C4' ADP . . . E 5 -0.064 12.389 18.613 1 68.7 ? C4' ADP 1756 A 1 HETATM 12 O O4' ADP . . . E 5 -1.165 13.228 18.371 1 93.9 ? O4' ADP 1756 A 1 HETATM 13 C C3' ADP . . . E 5 0.965 13.01 17.715 1 85.73 ? C3' ADP 1756 A 1 HETATM 14 O O3' ADP . . . E 5 0.551 12.705 16.409 1 60.65 ? O3' ADP 1756 A 1 HETATM 15 C C2' ADP . . . E 5 0.76 14.48 17.914 1 74.33 ? C2' ADP 1756 A 1 HETATM 16 O O2' ADP . . . E 5 1.234 15.138 16.777 1 82.75 ? O2' ADP 1756 A 1 HETATM 17 C C1' ADP . . . E 5 -0.747 14.527 17.964 1 80.33 ? C1' ADP 1756 A 1 HETATM 18 N N9 ADP . . . E 5 -1.252 15.561 18.882 1 83.76 ? N9 ADP 1756 A 1 HETATM 19 C C8 ADP . . . E 5 -0.547 16.266 19.816 1 103.64 ? C8 ADP 1756 A 1 HETATM 20 N N7 ADP . . . E 5 -1.394 17.115 20.442 1 95.73 ? N7 ADP 1756 A 1 HETATM 21 C C5 ADP . . . E 5 -2.613 16.969 19.91 1 88.56 ? C5 ADP 1756 A 1 HETATM 22 C C6 ADP . . . E 5 -3.808 17.577 20.186 1 87.22 ? C6 ADP 1756 A 1 HETATM 23 N N6 ADP . . . E 5 -3.864 18.564 21.066 1 83.17 ? N6 ADP 1756 A 1 HETATM 24 N N1 ADP . . . E 5 -4.917 17.211 19.478 1 103.05 ? N1 ADP 1756 A 1 HETATM 25 C C2 ADP . . . E 5 -4.826 16.249 18.509 1 100.82 ? C2 ADP 1756 A 1 HETATM 26 N N3 ADP . . . E 5 -3.627 15.643 18.243 1 94.38 ? N3 ADP 1756 A 1 HETATM 27 C C4 ADP . . . E 5 -2.539 16.002 18.933 1 87.96 ? C4 ADP 1756 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #