data_6WVM # _model_server_result.job_id TD-lk3RxWkWYijBeRrkz8Q _model_server_result.datetime_utc '2024-11-14 06:57:12' _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 6wvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 6WVM # _exptl.entry_id 6WVM _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.entry_id 6WVM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 _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 ? _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 K 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 E O1G GTP . C GTP 501 1_555 F MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc2 E O2G GTP . C GTP 501 1_555 F MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc3 E O3B GTP . C GTP 501 1_555 F MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc4 E O2B GTP . C GTP 501 1_555 F MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc5 I O1G GTP . A GTP 501 1_555 J MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc6 I O2G GTP . A GTP 501 1_555 J MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc7 I O3B GTP . A GTP 501 1_555 J MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc8 I O2B GTP . A GTP 501 1_555 J MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 6WVM _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 GTP C 1 501 503 GTP GTP . F 4 MG C 1 502 504 MG MG . G 5 GDP D 1 501 501 GDP GDP . H 6 TA1 D 1 502 502 TA1 TA1 . I 3 GTP A 1 501 503 GTP GTP . J 4 MG A 1 502 504 MG MG . K 5 GDP B 1 501 501 GDP GDP . L 6 TA1 B 1 502 502 TA1 TA1 . # 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 . . . K 5 3.906 111.581 54.585 1 0 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . K 5 4.305 111.958 53.199 1 0 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . K 5 4.504 112.564 55.572 1 0 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . K 5 4.204 110.152 54.97 1 0 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . K 5 2.345 111.875 54.646 1 0 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . K 5 1.369 110.672 54.253 1 0 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . K 5 1.751 109.894 53.001 1 0 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . K 5 0.947 109.896 55.506 1 0 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . K 5 -0.017 111.436 53.833 1 0 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . K 5 -0.933 110.792 52.961 1 0 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . K 5 -2.403 111.101 53.217 1 0 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . K 5 -3.15 110.44 52.201 1 0 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . K 5 -2.892 110.568 54.57 1 0 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . K 5 -3.385 111.563 55.434 1 0 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . K 5 -4.028 109.615 54.195 1 0 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . K 5 -5.3 110.244 54.229 1 0 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . K 5 -3.724 109.255 52.748 1 0 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . K 5 -2.889 108.033 52.588 1 0 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . K 5 -2.063 107.407 53.492 1 0 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . K 5 -1.645 106.227 53.129 1 0 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . K 5 -2.249 106.041 51.887 1 0 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . K 5 -2.232 104.92 50.987 1 0 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . K 5 -1.702 103.819 51.113 1 0 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . K 5 -2.956 105.143 49.845 1 0 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . K 5 -3.647 106.269 49.581 1 0 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . K 5 -4.309 106.288 48.466 1 0 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . K 5 -3.74 107.303 50.406 1 0 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . K 5 -2.996 107.144 51.543 1 0 ? C4 GDP 501 B 1 HETATM 29 H H5' GDP . . . K 5 -0.715 111.065 51.929 1 0 ? H5' GDP 501 B 1 HETATM 30 H "H5''" GDP . . . K 5 -0.804 109.712 53.032 1 0 ? "H5''" GDP 501 B 1 HETATM 31 H H4' GDP . . . K 5 -2.558 112.178 53.155 1 0 ? H4' GDP 501 B 1 HETATM 32 H H3' GDP . . . K 5 -2.097 110.007 55.061 1 0 ? H3' GDP 501 B 1 HETATM 33 H HO3' GDP . . . K 5 -4.274 111.729 55.114 1 0 ? HO3' GDP 501 B 1 HETATM 34 H H2' GDP . . . K 5 -4.027 108.735 54.84 1 0 ? H2' GDP 501 B 1 HETATM 35 H HO2' GDP . . . K 5 -5.745 109.924 55.017 1 0 ? HO2' GDP 501 B 1 HETATM 36 H H1' GDP . . . K 5 -4.673 109.054 52.251 1 0 ? H1' GDP 501 B 1 HETATM 37 H H8 GDP . . . K 5 -1.782 107.855 54.434 1 0 ? H8 GDP 501 B 1 HETATM 38 H HN1 GDP . . . K 5 -2.976 104.413 49.147 1 0 ? HN1 GDP 501 B 1 HETATM 39 H HN21 GDP . . . K 5 -4.248 105.501 47.836 1 0 ? HN21 GDP 501 B 1 HETATM 40 H HN22 GDP . . . K 5 -4.908 107.085 48.308 1 0 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #