data_7F1B # _model_server_result.job_id J-xe_cG-bFGdV0DDNGd2TQ _model_server_result.datetime_utc '2025-01-31 02:53:37' _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 7f1b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7F1B # _exptl.entry_id 7F1B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 90 _cell.angle_gamma 90 _cell.entry_id 7F1B _cell.length_a 40.883 _cell.length_b 94.428 _cell.length_c 100.846 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7F1B _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2 _struct_asym.id B _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 C MG MG . A MG 502 1_555 D O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc2 C MG MG . A MG 502 1_555 D O HOH . A HOH 611 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc3 C MG MG . A MG 502 1_555 D O HOH . A HOH 616 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc4 C MG MG . A MG 502 1_555 D O HOH . A HOH 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc5 C MG MG . A MG 502 1_555 D O HOH . A HOH 632 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _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 7F1B _atom_sites.fract_transf_matrix[1][1] 0.02446 _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] 0.01059 _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] 0.009916 _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 B 2 GDP A 1 501 501 GDP GDP . C 3 MG A 1 502 1 MG MG . D 4 HOH A 1 601 19 HOH HOH . D 4 HOH A 2 602 22 HOH HOH . D 4 HOH A 3 603 24 HOH HOH . D 4 HOH A 4 604 25 HOH HOH . D 4 HOH A 5 605 14 HOH HOH . D 4 HOH A 6 606 6 HOH HOH . D 4 HOH A 7 607 29 HOH HOH . D 4 HOH A 8 608 21 HOH HOH . D 4 HOH A 9 609 9 HOH HOH . D 4 HOH A 10 610 18 HOH HOH . D 4 HOH A 11 611 30 HOH HOH . D 4 HOH A 12 612 20 HOH HOH . D 4 HOH A 13 613 16 HOH HOH . D 4 HOH A 14 614 2 HOH HOH . D 4 HOH A 15 615 5 HOH HOH . D 4 HOH A 16 616 31 HOH HOH . D 4 HOH A 17 617 17 HOH HOH . D 4 HOH A 18 618 8 HOH HOH . D 4 HOH A 19 619 1 HOH HOH . D 4 HOH A 20 620 27 HOH HOH . D 4 HOH A 21 621 11 HOH HOH . D 4 HOH A 22 622 28 HOH HOH . D 4 HOH A 23 623 7 HOH HOH . D 4 HOH A 24 624 13 HOH HOH . D 4 HOH A 25 625 10 HOH HOH . D 4 HOH A 26 626 12 HOH HOH . D 4 HOH A 27 627 3 HOH HOH . D 4 HOH A 28 628 15 HOH HOH . D 4 HOH A 29 629 4 HOH HOH . D 4 HOH A 30 630 26 HOH HOH . D 4 HOH A 31 631 23 HOH HOH . D 4 HOH A 32 632 32 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 . . . B 2 38.301 52.654 33.91 1 79.41 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . B 2 38.887 51.588 33.016 1 83.16 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . B 2 38.582 52.286 35.347 1 87.5 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . B 2 36.813 52.733 33.669 1 77.48 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . B 2 39.027 54.051 33.569 1 85.55 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . B 2 38.244 55.449 33.402 1 84.42 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . B 2 36.848 55.398 33.979 1 87.97 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . B 2 39.03 56.565 34.048 1 85.99 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . B 2 38.208 55.657 31.809 1 87.38 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . B 2 38.868 56.778 31.232 1 83.93 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . B 2 37.907 57.506 30.31 1 79.02 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . B 2 36.733 57.821 31.056 1 72.1 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . B 2 38.52 58.807 29.831 1 80.76 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . B 2 38.498 58.831 28.403 1 86.11 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . B 2 37.654 59.918 30.389 1 74.59 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . B 2 37.151 60.719 29.316 1 65 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . B 2 36.509 59.231 31.117 1 74.61 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . B 2 36.463 59.621 32.55 1 74.74 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . B 2 37.227 59.095 33.526 1 67.47 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . B 2 36.941 59.65 34.73 1 63.06 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . B 2 35.964 60.553 34.533 1 65.44 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . B 2 35.195 61.494 35.382 1 64.62 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . B 2 35.404 61.573 36.612 1 60.02 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . B 2 34.27 62.256 34.786 1 68.95 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . B 2 34.024 62.19 33.464 1 68.89 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . B 2 33.073 62.997 32.942 1 58.95 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . B 2 34.688 61.354 32.627 1 75.17 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . B 2 35.651 60.527 33.096 1 72.35 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #