data_2G83 # _model_server_result.job_id 5SUff_diTXpRxxR7nBYiCw _model_server_result.datetime_utc '2024-10-11 00:26:17' _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 2g83 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":355}' # _entry.id 2G83 # _exptl.entry_id 2G83 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 2G83 _cell.length_a 103.13 _cell.length_b 103.13 _cell.length_c 206.99 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2G83 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA dimeric 2 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,C,E,F,G,K,M 1 1 B,D,H,I,J,L 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 ? 5 G N N ? 5 J 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 OG SER 15 A SER 47 1_555 G O3B GDP . A GDP 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? covale ? covale2 J O1B GDP . B GDP 355 1_555 H F2 ALF . B ALF 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? metalc ? metalc1 A OG SER 15 A SER 47 1_555 F MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc2 A NH2 ARG 146 A ARG 178 1_555 E AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.661 ? metalc ? metalc3 A NH1 ARG 146 A ARG 178 1_555 E AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.711 ? metalc ? metalc4 A OG1 THR 149 A THR 181 1_555 F MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.687 ? metalc ? metalc5 A OE1 GLN 172 A GLN 204 1_555 E AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.505 ? metalc ? metalc6 G O3B GDP . A GDP 355 1_555 F MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.541 ? metalc ? metalc7 G O1B GDP . A GDP 355 1_555 E AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.443 ? metalc ? metalc8 G O3B GDP . A GDP 355 1_555 E AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.586 ? metalc ? metalc9 F MG MG . A MG 356 1_555 E F1 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc10 F MG MG . A MG 356 1_555 E F4 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? metalc ? metalc11 B OG SER 15 B SER 47 1_555 I MG MG . B MG 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc12 B NH2 ARG 146 B ARG 178 1_555 H AL ALF . B ALF 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.495 ? metalc ? metalc13 B OG1 THR 149 B THR 181 1_555 I MG MG . B MG 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.745 ? metalc ? metalc14 B N THR 149 B THR 181 1_555 H AL ALF . B ALF 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.709 ? metalc ? metalc15 B OE1 GLN 172 B GLN 204 1_555 H AL ALF . B ALF 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.544 ? metalc ? metalc16 J O3B GDP . B GDP 355 1_555 I MG MG . B MG 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc17 J O1B GDP . B GDP 355 1_555 I MG MG . B MG 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? metalc ? metalc18 J O1B GDP . B GDP 355 1_555 H AL ALF . B ALF 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc19 I MG MG . B MG 358 1_555 H AL ALF . B ALF 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.335 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 2G83 _atom_sites.fract_transf_matrix[1][1] 0.009696 _atom_sites.fract_transf_matrix[1][2] 0.005598 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011197 _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] 0.004831 _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 3 ALF A 1 357 357 ALF ALF . F 4 MG A 1 356 356 MG MG . G 5 GDP A 1 355 355 GDP GDP . H 3 ALF B 1 359 359 ALF ALF . I 4 MG B 1 358 358 MG MG . J 5 GDP B 1 355 355 GDP GDP . K 6 HOH A 1 2 2 HOH HOH . K 6 HOH A 2 3 3 HOH HOH . K 6 HOH A 3 4 4 HOH HOH . K 6 HOH A 4 5 5 HOH HOH . K 6 HOH A 5 6 6 HOH HOH . K 6 HOH A 6 8 8 HOH HOH . K 6 HOH A 7 10 10 HOH HOH . K 6 HOH A 8 13 13 HOH HOH . K 6 HOH A 9 14 14 HOH HOH . K 6 HOH A 10 16 16 HOH HOH . K 6 HOH A 11 19 19 HOH HOH . K 6 HOH A 12 20 20 HOH HOH . K 6 HOH A 13 23 23 HOH HOH . K 6 HOH A 14 24 24 HOH HOH . K 6 HOH A 15 25 25 HOH HOH . K 6 HOH A 16 27 27 HOH HOH . K 6 HOH A 17 29 29 HOH HOH . L 6 HOH B 1 1 1 HOH HOH . L 6 HOH B 2 7 7 HOH HOH . L 6 HOH B 3 9 9 HOH HOH . L 6 HOH B 4 11 11 HOH HOH . L 6 HOH B 5 12 12 HOH HOH . L 6 HOH B 6 15 15 HOH HOH . L 6 HOH B 7 17 17 HOH HOH . L 6 HOH B 8 18 18 HOH HOH . L 6 HOH B 9 21 21 HOH HOH . L 6 HOH B 10 26 26 HOH HOH . L 6 HOH B 11 28 28 HOH HOH . L 6 HOH B 12 30 30 HOH HOH . M 6 HOH C 1 22 22 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 . . . G 5 -47.895 27.114 35.939 1 39.38 ? PB GDP 355 A 1 HETATM 2 O O1B GDP . . . G 5 -49.22 26.893 35.956 1 39.6 ? O1B GDP 355 A 1 HETATM 3 O O2B GDP . . . G 5 -47.567 25.89 36.352 1 37.64 ? O2B GDP 355 A 1 HETATM 4 O O3B GDP . . . G 5 -47.206 27.58 34.685 1 34.73 ? O3B GDP 355 A 1 HETATM 5 O O3A GDP . . . G 5 -47.826 27.789 37.241 1 39.73 ? O3A GDP 355 A 1 HETATM 6 P PA GDP . . . G 5 -48.495 29.041 37.714 1 37.41 ? PA GDP 355 A 1 HETATM 7 O O1A GDP . . . G 5 -47.467 29.82 38.093 1 38.26 ? O1A GDP 355 A 1 HETATM 8 O O2A GDP . . . G 5 -49.185 29.808 36.863 1 40 ? O2A GDP 355 A 1 HETATM 9 O O5' GDP . . . G 5 -49.26 29.091 38.951 1 36.46 ? O5' GDP 355 A 1 HETATM 10 C C5' GDP . . . G 5 -50.499 29.59 38.736 1 34.09 ? C5' GDP 355 A 1 HETATM 11 C C4' GDP . . . G 5 -51.157 30.534 39.723 1 34.25 ? C4' GDP 355 A 1 HETATM 12 O O4' GDP . . . G 5 -51.122 30.247 41.063 1 33.31 ? O4' GDP 355 A 1 HETATM 13 C C3' GDP . . . G 5 -50.646 31.878 39.652 1 33.15 ? C3' GDP 355 A 1 HETATM 14 O O3' GDP . . . G 5 -51.669 32.731 39.818 1 32.32 ? O3' GDP 355 A 1 HETATM 15 C C2' GDP . . . G 5 -49.891 31.883 40.854 1 33.51 ? C2' GDP 355 A 1 HETATM 16 O O2' GDP . . . G 5 -49.868 33.166 41.178 1 37.89 ? O2' GDP 355 A 1 HETATM 17 C C1' GDP . . . G 5 -50.705 31.266 41.837 1 32.62 ? C1' GDP 355 A 1 HETATM 18 N N9 GDP . . . G 5 -49.873 30.584 42.785 1 31.82 ? N9 GDP 355 A 1 HETATM 19 C C8 GDP . . . G 5 -48.921 29.821 42.457 1 32.33 ? C8 GDP 355 A 1 HETATM 20 N N7 GDP . . . G 5 -48.355 29.303 43.465 1 33.2 ? N7 GDP 355 A 1 HETATM 21 C C5 GDP . . . G 5 -48.96 29.743 44.493 1 31.39 ? C5 GDP 355 A 1 HETATM 22 C C6 GDP . . . G 5 -48.877 29.57 45.882 1 32.79 ? C6 GDP 355 A 1 HETATM 23 O O6 GDP . . . G 5 -48.105 28.872 46.44 1 33.78 ? O6 GDP 355 A 1 HETATM 24 N N1 GDP . . . G 5 -49.671 30.144 46.626 1 33.27 ? N1 GDP 355 A 1 HETATM 25 C C2 GDP . . . G 5 -50.548 30.906 46.168 1 33.4 ? C2 GDP 355 A 1 HETATM 26 N N2 GDP . . . G 5 -51.292 31.439 47.076 1 30.96 ? N2 GDP 355 A 1 HETATM 27 N N3 GDP . . . G 5 -50.73 31.13 44.93 1 31.35 ? N3 GDP 355 A 1 HETATM 28 C C4 GDP . . . G 5 -49.958 30.571 44.055 1 31.43 ? C4 GDP 355 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #