data_6GVM # _model_server_result.job_id '_nC5paaFm4RxRwdh96bmHA' _model_server_result.datetime_utc '2024-11-29 01:30:35' _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 6gvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 6GVM # _exptl.entry_id 6GVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 121.03 _cell.angle_gamma 90 _cell.entry_id 6GVM _cell.length_a 189.267 _cell.length_b 51.721 _cell.length_c 144.137 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GVM _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 PISA _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,G _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 7 _struct_asym.id G _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 E O2G GTP . A GTP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc2 E O2B GTP . A GTP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? # _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 6GVM _atom_sites.fract_transf_matrix[1][1] 0.005284 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003178 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019335 _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] 0.008096 _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 GTP A 1 501 501 GTP GTP . F 6 MG A 1 502 502 MG MG . G 7 GDP B 1 501 501 GDP GDP . # 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 7 33.105 -41.272 13.319 1 28.19 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . G 7 33.328 -41.951 11.942 1 30.82 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . G 7 31.585 -41.006 13.538 1 27.13 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . G 7 33.722 -42.084 14.43 1 27.69 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . G 7 33.775 -39.826 13.231 1 29.34 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . G 7 33.479 -38.468 14.011 1 29.24 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . G 7 34.805 -37.852 14.484 1 30.27 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . G 7 32.627 -38.786 15.184 1 27.57 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . G 7 32.749 -37.398 13.062 1 30.21 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . G 7 33.395 -36.26 12.456 1 32.29 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . G 7 32.485 -35.06 12.572 1 32.63 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . G 7 32.329 -34.701 13.959 1 31.34 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . G 7 32.958 -33.784 11.882 1 37.32 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . G 7 31.862 -32.962 11.487 1 37.8 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . G 7 33.807 -33.124 12.967 1 38.68 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . G 7 33.884 -31.712 12.802 1 42.44 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . G 7 33.041 -33.51 14.24 1 34.52 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . G 7 33.905 -33.761 15.406 1 34.21 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . G 7 34.849 -34.751 15.547 1 33.76 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . G 7 35.442 -34.747 16.719 1 33.44 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . G 7 34.856 -33.684 17.394 1 33.81 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . G 7 35.062 -33.147 18.739 1 33.89 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . G 7 35.845 -33.551 19.598 1 33.52 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . G 7 34.245 -32.062 18.999 1 34.69 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . G 7 33.332 -31.528 18.13 1 34.91 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . G 7 32.593 -30.518 18.585 1 34.7 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . G 7 33.129 -31.99 16.895 1 34.78 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . G 7 33.908 -33.063 16.593 1 34.1 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 94 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #