data_2OIL # _model_server_result.job_id EPIbf9vPqlVJCna9W4ZxpA _model_server_result.datetime_utc '2024-12-26 19:54:28' _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 2oil # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 2OIL # _exptl.entry_id 2OIL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 90 _cell.angle_gamma 90 _cell.entry_id 2OIL _cell.length_a 90.25 _cell.length_b 90.25 _cell.length_c 45.598 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2OIL _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 3 _struct_asym.id C _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 metalc ? metalc1 A OG1 THR 39 A THR 26 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc2 C O3B GDP . A GDP 201 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc3 B MG MG . A MG 301 1_555 E O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc4 B MG MG . A MG 301 1_555 E O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc5 B MG MG . A MG 301 1_555 E O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc6 B MG MG . A MG 301 1_555 E O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 GDP doub 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 2OIL _atom_sites.fract_transf_matrix[1][1] 0.01108 _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] 0.01108 _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] 0.02193 _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 B 2 MG A 1 301 301 MG MG . C 3 GDP A 1 201 201 GDP GDP . D 4 UNX A 1 1001 1001 UNX UNX . E 5 HOH A 1 401 401 HOH HOH . E 5 HOH A 2 402 402 HOH HOH . E 5 HOH A 3 403 403 HOH HOH . E 5 HOH A 4 404 404 HOH HOH . E 5 HOH A 5 405 405 HOH HOH . E 5 HOH A 6 406 406 HOH HOH . E 5 HOH A 7 407 407 HOH HOH . E 5 HOH A 8 408 408 HOH HOH . E 5 HOH A 9 409 409 HOH HOH . E 5 HOH A 10 410 410 HOH HOH . E 5 HOH A 11 411 411 HOH HOH . E 5 HOH A 12 412 412 HOH HOH . E 5 HOH A 13 413 413 HOH HOH . E 5 HOH A 14 414 414 HOH HOH . E 5 HOH A 15 415 415 HOH HOH . E 5 HOH A 16 416 416 HOH HOH . E 5 HOH A 17 417 417 HOH HOH . E 5 HOH A 18 418 418 HOH HOH . # 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 GDP . . . C 3 25.39 35.936 13.548 1 27.68 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 25.043 37.059 12.597 1 28.89 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 25.184 34.61 12.842 1 28.79 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 24.536 36.035 14.785 1 25.55 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 26.951 36.118 13.843 1 29.19 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 27.813 35.632 15.112 1 26.83 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 27.325 34.267 15.581 1 30.2 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 27.807 36.692 16.167 1 26.42 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 29.255 35.573 14.389 1 31.73 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 29.585 34.51 13.5 1 34.45 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 31.084 34.233 13.502 1 33.36 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 31.766 35.449 13.199 1 30.98 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 31.658 33.775 14.845 1 34.6 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 32.896 33.108 14.55 1 34.98 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 32.014 35.081 15.485 1 33.15 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 33.01 34.944 16.476 1 39.23 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 32.598 35.814 14.304 1 32.83 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 32.571 37.275 14.467 1 32.91 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 31.506 38.019 14.855 1 34.88 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 31.818 39.346 14.876 1 35.37 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 33.096 39.445 14.498 1 31.11 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 34.018 40.544 14.31 1 32.79 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 33.669 41.737 14.519 1 33.97 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 35.26 40.231 13.907 1 34.65 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 35.679 38.973 13.654 1 34.1 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 36.965 38.805 13.257 1 34.84 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 34.878 37.894 13.813 1 33.33 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 33.592 38.084 14.228 1 32.93 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #