data_3N2G # _model_server_result.job_id 28OECWavqgoaYbVPCqSY5A _model_server_result.datetime_utc '2024-10-19 01:39:16' _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 3n2g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":600}' # _entry.id 3N2G # _exptl.entry_id 3N2G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 3N2G _cell.length_a 328.553 _cell.length_b 328.553 _cell.length_c 54.745 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N2G _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,G,H,I,J,K,L,M,N _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H 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 F O3G GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc2 C OD1 ASP 98 C ASP 98 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? metalc ? metalc3 K O2B GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc4 K O3G GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? # _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 128 n n PB O2B GDP sing 129 n n PB O3B GDP sing 130 n n PB O3A GDP sing 131 n n O2B HOB2 GDP sing 132 n n O3B HOB3 GDP sing 133 n n O3A PA GDP sing 134 n n PA O1A GDP doub 135 n n PA O2A GDP sing 136 n n PA O5' GDP sing 137 n n O2A HOA2 GDP sing 138 n n O5' C5' GDP sing 139 n n C5' C4' GDP sing 140 n n C5' H5' GDP sing 141 n n C5' "H5''" GDP sing 142 n n C4' O4' GDP sing 143 n n C4' C3' GDP sing 144 n n C4' H4' GDP sing 145 n n O4' C1' GDP sing 146 n n C3' O3' GDP sing 147 n n C3' C2' GDP sing 148 n n C3' H3' GDP sing 149 n n O3' HO3' GDP sing 150 n n C2' O2' GDP sing 151 n n C2' C1' GDP sing 152 n n C2' H2' GDP sing 153 n n O2' HO2' GDP sing 154 n n C1' N9 GDP sing 155 n n C1' H1' GDP sing 156 n n N9 C8 GDP sing 157 n y N9 C4 GDP sing 158 n y C8 N7 GDP doub 159 n y C8 H8 GDP sing 160 n n N7 C5 GDP sing 161 n y C5 C6 GDP sing 162 n n C5 C4 GDP doub 163 n y C6 O6 GDP doub 164 n n C6 N1 GDP sing 165 n n N1 C2 GDP sing 166 n n N1 HN1 GDP sing 167 n n C2 N2 GDP sing 168 n n C2 N3 GDP doub 169 n n N2 HN21 GDP sing 170 n n N2 HN22 GDP sing 171 n n N3 C4 GDP sing 172 n n # _atom_sites.entry_id 3N2G _atom_sites.fract_transf_matrix[1][1] 0.003044 _atom_sites.fract_transf_matrix[1][2] 0.001757 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003515 _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] 0.018267 _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 F 4 GTP A 1 600 600 GTP GTP . G 5 MG A 1 601 601 MG MG . H 6 GDP B 1 600 600 GDP GDP . I 5 MG B 1 601 601 MG MG . J 7 G2N B 1 700 700 G2N G2N . K 4 GTP C 1 600 600 GTP GTP . L 5 MG C 1 601 601 MG MG . M 6 GDP D 1 600 600 GDP GDP . N 7 G2N D 1 700 700 G2N G2N . # 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 . . . H 6 90.833 72.428 5.223 1 80.57 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . H 6 92.089 73.089 5.7 1 79.6 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . H 6 91.038 70.914 5.174 1 80.16 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . H 6 89.554 72.601 6.092 1 79.23 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . H 6 90.569 73.076 3.761 1 81.26 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . H 6 91.219 72.552 2.379 1 81.49 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . H 6 92.442 71.844 2.803 1 81.61 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . H 6 90.189 71.763 1.506 1 79.79 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . H 6 91.741 73.859 1.62 1 80.73 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . H 6 90.928 74.364 0.597 1 81.15 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . H 6 91.777 75.194 -0.347 1 81.11 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . H 6 93.11 74.757 -0.226 1 80.74 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . H 6 91.3 74.962 -1.778 1 81.19 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . H 6 91.33 76.158 -2.532 1 80.75 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . H 6 92.3 74.019 -2.376 1 81.24 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . H 6 92.608 74.452 -3.686 1 81.35 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . H 6 93.507 74.112 -1.435 1 81.3 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . H 6 94.136 72.785 -1.19 1 80.33 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . H 6 93.507 71.611 -0.834 1 79.3 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . H 6 94.456 70.65 -0.732 1 78.65 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . H 6 95.673 71.183 -1.015 1 78.36 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . H 6 96.956 70.646 -1.058 1 77.62 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . H 6 97.172 69.633 -0.407 1 78.07 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . H 6 98.027 71.449 -1.397 1 76.83 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . H 6 97.828 72.778 -1.693 1 76.66 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . H 6 98.644 73.326 -2.554 1 76.57 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . H 6 96.564 73.313 -1.653 1 77.65 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . H 6 95.494 72.527 -1.319 1 79.16 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #