data_6ASA # _model_server_result.job_id A_55zchHVv2QgmcicxlsaA _model_server_result.datetime_utc '2025-07-30 22:21:32' _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 6asa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6ASA # _exptl.entry_id 6ASA _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 6ASA _cell.length_a 34.527 _cell.length_b 47.075 _cell.length_c 90.765 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ASA _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 A OG SER 17 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc3 C MG MG . A MG 202 1_555 D O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc4 C MG MG . A MG 202 1_555 D O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? # _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 6ASA _atom_sites.fract_transf_matrix[1][1] 0.028963 _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] 0.021243 _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] 0.011017 _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 1 201 1 GDP GDP . C 3 MG A 1 202 1 MG MG . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 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 -5.723 12.83 -14.12 1 42.83 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -5.517 11.325 -14.31 1 45.23 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -4.554 13.698 -14.55 1 51.54 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -6.066 13.14 -12.686 1 45.95 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -6.904 13.357 -15.085 1 42.87 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -7.883 14.623 -14.805 1 49.51 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -9.141 14.133 -14.132 1 52.07 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -7.16 15.687 -14.004 1 43.67 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -8.291 15.171 -16.276 1 50.67 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -7.479 16.144 -16.954 1 52.91 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -8.299 16.836 -18.026 1 45.72 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -9.035 15.892 -18.814 1 52.28 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -9.317 17.754 -17.37 1 48.43 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -9.311 19.047 -17.987 1 51.24 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -10.646 17.078 -17.619 1 53.02 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -11.687 18.037 -17.814 1 61.51 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -10.399 16.281 -18.882 1 52.42 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -11.228 15.068 -18.901 1 50.18 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -11.212 14.148 -17.922 1 49.36 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -12.046 13.158 -18.238 1 54.26 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -12.593 13.476 -19.435 1 55.67 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -13.527 12.817 -20.24 1 56.85 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -13.993 11.727 -19.862 1 55.37 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -13.929 13.315 -21.397 1 56.87 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -13.384 14.49 -21.75 1 55.16 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -13.809 14.985 -22.945 1 63.68 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -12.47 15.227 -21.055 1 48.93 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -12.072 14.701 -19.859 1 52.17 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 505 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 28 #