data_2F7S # _model_server_result.job_id bZnCnN0uQtKtncFrJVNIyg _model_server_result.datetime_utc '2024-11-08 16:58:37' _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 2f7s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 2F7S # _exptl.entry_id 2F7S _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 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 2F7S _cell.length_a 55.469 _cell.length_b 64.023 _cell.length_c 153.32 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2F7S _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 D N N ? 3 F 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 disulf ? disulf1 A SG CYS 139 A CYS 123 1_555 A SG CYS 204 A CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 B SG CYS 139 B CYS 123 1_555 B SG CYS 204 B CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc1 A OG1 THR 39 A THR 23 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc2 D O3B GDP . A GDP 601 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? metalc ? metalc3 C MG MG . A MG 602 1_555 H O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc4 B OG1 THR 39 B THR 23 1_555 E MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc5 F O3B GDP . B GDP 501 1_555 E MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? # _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 2F7S _atom_sites.fract_transf_matrix[1][1] 0.018028 _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] 0.015619 _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] 0.006522 _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 C 2 MG A 1 602 602 MG MG . D 3 GDP A 1 601 601 GDP GDP . E 2 MG B 1 502 502 MG MG . F 3 GDP B 1 501 501 GDP GDP . G 4 HOH A 1 603 5 HOH HOH . G 4 HOH A 2 604 6 HOH HOH . G 4 HOH A 3 605 7 HOH HOH . G 4 HOH A 4 606 9 HOH HOH . G 4 HOH A 5 607 10 HOH HOH . H 4 HOH B 1 503 1 HOH HOH . H 4 HOH B 2 504 2 HOH HOH . H 4 HOH B 3 505 3 HOH HOH . H 4 HOH B 4 506 4 HOH HOH . H 4 HOH B 5 507 8 HOH HOH . H 4 HOH B 6 508 11 HOH HOH . H 4 HOH B 7 509 12 HOH HOH . H 4 HOH B 8 510 13 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 . . . D 3 19.597 -0.231 -23.912 1 45.06 ? PB GDP 601 A 1 HETATM 2 O O1B GDP . . . D 3 20.854 0.44 -23.411 1 40.57 ? O1B GDP 601 A 1 HETATM 3 O O2B GDP . . . D 3 18.403 0.485 -23.326 1 44.27 ? O2B GDP 601 A 1 HETATM 4 O O3B GDP . . . D 3 19.548 -0.252 -25.432 1 44.55 ? O3B GDP 601 A 1 HETATM 5 O O3A GDP . . . D 3 19.482 -1.736 -23.421 1 46.27 ? O3A GDP 601 A 1 HETATM 6 P PA GDP . . . D 3 20.116 -2.913 -24.294 1 48.43 ? PA GDP 601 A 1 HETATM 7 O O1A GDP . . . D 3 19.064 -3.443 -25.214 1 49.73 ? O1A GDP 601 A 1 HETATM 8 O O2A GDP . . . D 3 21.383 -2.552 -24.998 1 46.66 ? O2A GDP 601 A 1 HETATM 9 O O5' GDP . . . D 3 20.387 -3.998 -23.141 1 51.87 ? O5' GDP 601 A 1 HETATM 10 C C5' GDP . . . D 3 21.524 -3.973 -22.277 1 52.36 ? C5' GDP 601 A 1 HETATM 11 C C4' GDP . . . D 3 21.777 -5.42 -21.867 1 53.69 ? C4' GDP 601 A 1 HETATM 12 O O4' GDP . . . D 3 20.646 -5.92 -21.148 1 53.88 ? O4' GDP 601 A 1 HETATM 13 C C3' GDP . . . D 3 21.925 -6.321 -23.092 1 53.74 ? C3' GDP 601 A 1 HETATM 14 O O3' GDP . . . D 3 23.04 -7.199 -22.935 1 52.09 ? O3' GDP 601 A 1 HETATM 15 C C2' GDP . . . D 3 20.608 -7.075 -23.178 1 53.45 ? C2' GDP 601 A 1 HETATM 16 O O2' GDP . . . D 3 20.691 -8.409 -23.655 1 55.21 ? O2' GDP 601 A 1 HETATM 17 C C1' GDP . . . D 3 20.151 -7.123 -21.748 1 53.8 ? C1' GDP 601 A 1 HETATM 18 N N9 GDP . . . D 3 18.674 -7.176 -21.736 1 54.1 ? N9 GDP 601 A 1 HETATM 19 C C8 GDP . . . D 3 17.838 -6.388 -22.441 1 54.11 ? C8 GDP 601 A 1 HETATM 20 N N7 GDP . . . D 3 16.546 -6.708 -22.196 1 53.78 ? N7 GDP 601 A 1 HETATM 21 C C5 GDP . . . D 3 16.549 -7.717 -21.314 1 53.2 ? C5 GDP 601 A 1 HETATM 22 C C6 GDP . . . D 3 15.511 -8.527 -20.638 1 53.91 ? C6 GDP 601 A 1 HETATM 23 O O6 GDP . . . D 3 14.286 -8.323 -20.839 1 53.87 ? O6 GDP 601 A 1 HETATM 24 N N1 GDP . . . D 3 15.943 -9.486 -19.81 1 54.03 ? N1 GDP 601 A 1 HETATM 25 C C2 GDP . . . D 3 17.247 -9.733 -19.585 1 53.89 ? C2 GDP 601 A 1 HETATM 26 N N2 GDP . . . D 3 17.562 -10.72 -18.72 1 54.14 ? N2 GDP 601 A 1 HETATM 27 N N3 GDP . . . D 3 18.255 -9.037 -20.165 1 53.45 ? N3 GDP 601 A 1 HETATM 28 C C4 GDP . . . D 3 17.955 -8.031 -21.02 1 53.53 ? C4 GDP 601 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #