data_1CC0 # _model_server_result.job_id lRikXbsAoc_93_2TknzpmQ _model_server_result.datetime_utc '2025-02-05 10:49:32' _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 1cc0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":202}' # _entry.id 1CC0 # _exptl.entry_id 1CC0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 120 _cell.entry_id 1CC0 _cell.length_a 139.3 _cell.length_b 139.3 _cell.length_c 253.1 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CC0 _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F 1 1 C,D,G,H 2 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 ? 4 F N N ? 4 H 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 A OG1 THR 19 A THR 19 1_555 E MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc2 A O THR 37 A THR 37 1_555 E MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc3 F O2B GDP . A GDP 201 1_555 E MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc4 C OG1 THR 19 C THR 19 1_555 G MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc5 C O THR 37 C THR 37 1_555 G MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc6 H O2B GDP . C GDP 202 1_555 G MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? # _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 1CC0 _atom_sites.fract_transf_matrix[1][1] 0.007179 _atom_sites.fract_transf_matrix[1][2] 0.004145 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008289 _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] 0.003951 _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 MG A 1 301 301 MG MG . F 4 GDP A 1 201 201 GDP GDP . G 3 MG C 1 302 302 MG MG . H 4 GDP C 1 202 202 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 . . . H 4 50.963 50.287 62.779 1 35 ? PB GDP 202 C 1 HETATM 2 O O1B GDP . . . H 4 50.184 51.538 62.416 1 35 ? O1B GDP 202 C 1 HETATM 3 O O2B GDP . . . H 4 50.632 49.212 61.805 1 35 ? O2B GDP 202 C 1 HETATM 4 O O3B GDP . . . H 4 52.461 50.634 63.168 1 35 ? O3B GDP 202 C 1 HETATM 5 O O3A GDP . . . H 4 50.088 49.917 64.11 1 35 ? O3A GDP 202 C 1 HETATM 6 P PA GDP . . . H 4 49.771 48.419 64.659 1 35 ? PA GDP 202 C 1 HETATM 7 O O1A GDP . . . H 4 48.57 47.981 63.927 1 35 ? O1A GDP 202 C 1 HETATM 8 O O2A GDP . . . H 4 51.031 47.676 64.6 1 35 ? O2A GDP 202 C 1 HETATM 9 O O5' GDP . . . H 4 49.42 48.618 66.234 1 35 ? O5' GDP 202 C 1 HETATM 10 C C5' GDP . . . H 4 50.175 49.354 67.159 1 35 ? C5' GDP 202 C 1 HETATM 11 C C4' GDP . . . H 4 49.833 49.127 68.591 1 35 ? C4' GDP 202 C 1 HETATM 12 O O4' GDP . . . H 4 48.499 49.56 68.84 1 35 ? O4' GDP 202 C 1 HETATM 13 C C3' GDP . . . H 4 49.852 47.637 68.888 1 35 ? C3' GDP 202 C 1 HETATM 14 O O3' GDP . . . H 4 50.319 47.47 70.187 1 35 ? O3' GDP 202 C 1 HETATM 15 C C2' GDP . . . H 4 48.367 47.256 68.672 1 35 ? C2' GDP 202 C 1 HETATM 16 O O2' GDP . . . H 4 47.828 46.255 69.563 1 35 ? O2' GDP 202 C 1 HETATM 17 C C1' GDP . . . H 4 47.646 48.505 69.25 1 35 ? C1' GDP 202 C 1 HETATM 18 N N9 GDP . . . H 4 46.291 48.738 68.697 1 35 ? N9 GDP 202 C 1 HETATM 19 C C8 GDP . . . H 4 45.98 48.624 67.336 1 35 ? C8 GDP 202 C 1 HETATM 20 N N7 GDP . . . H 4 44.702 48.911 67.12 1 35 ? N7 GDP 202 C 1 HETATM 21 C C5 GDP . . . H 4 44.231 49.212 68.409 1 35 ? C5 GDP 202 C 1 HETATM 22 C C6 GDP . . . H 4 42.909 49.581 68.761 1 35 ? C6 GDP 202 C 1 HETATM 23 O O6 GDP . . . H 4 41.988 49.676 67.987 1 35 ? O6 GDP 202 C 1 HETATM 24 N N1 GDP . . . H 4 42.75 49.829 70.096 1 35 ? N1 GDP 202 C 1 HETATM 25 C C2 GDP . . . H 4 43.802 49.701 71.004 1 35 ? C2 GDP 202 C 1 HETATM 26 N N2 GDP . . . H 4 43.524 49.977 72.258 1 35 ? N2 GDP 202 C 1 HETATM 27 N N3 GDP . . . H 4 45.032 49.376 70.599 1 35 ? N3 GDP 202 C 1 HETATM 28 C C4 GDP . . . H 4 45.137 49.093 69.328 1 35 ? C4 GDP 202 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #