data_4AII # _model_server_result.job_id FL0R6rdcdwNh_BZmml2ysg _model_server_result.datetime_utc '2024-11-05 01:25:45' _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 4aii # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1284}' # _entry.id 4AII # _exptl.entry_id 4AII _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 101.51 _cell.angle_gamma 90 _cell.entry_id 4AII _cell.length_a 50.916 _cell.length_b 59.374 _cell.length_c 57.297 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AII _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,G 1 1 B,E,F,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 ? 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 metalc ? metalc1 A OG SER 26 A SER 129 1_555 C MG MG . A MG 1283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc2 C MG MG . A MG 1283 1_555 D O1B GDP . A GDP 1284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? metalc ? metalc3 C MG MG . A MG 1283 1_555 G O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc4 C MG MG . A MG 1283 1_555 G O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc5 C MG MG . A MG 1283 1_555 G O HOH . A HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc6 C MG MG . A MG 1283 1_555 G O HOH . A HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc7 B OG SER 26 B SER 129 1_555 E MG MG . B MG 1283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc8 E MG MG . B MG 1283 1_555 F O1B GDP . B GDP 1284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc9 E MG MG . B MG 1283 1_555 H O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc10 E MG MG . B MG 1283 1_555 H O HOH . B HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc11 E MG MG . B MG 1283 1_555 H O HOH . B HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc12 E MG MG . B MG 1283 1_555 H O HOH . B HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? # _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 4AII _atom_sites.fract_transf_matrix[1][1] 0.01964 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003999 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016842 _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] 0.017811 _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 1283 1283 MG MG . D 3 GDP A 1 1284 1284 GDP GDP . E 2 MG B 1 1283 1283 MG MG . F 3 GDP B 1 1284 1284 GDP GDP . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 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 -8.555 -4.757 10.939 1 33.77 ? PB GDP 1284 A 1 HETATM 2 O O1B GDP . . . D 3 -8.381 -5.273 12.337 1 31.9 ? O1B GDP 1284 A 1 HETATM 3 O O2B GDP . . . D 3 -7.374 -3.863 10.679 1 36.45 ? O2B GDP 1284 A 1 HETATM 4 O O3B GDP . . . D 3 -9.892 -4.09 10.734 1 32.83 ? O3B GDP 1284 A 1 HETATM 5 O O3A GDP . . . D 3 -8.445 -5.908 9.811 1 35.98 ? O3A GDP 1284 A 1 HETATM 6 P PA GDP . . . D 3 -8.401 -7.493 10.111 1 33.29 ? PA GDP 1284 A 1 HETATM 7 O O1A GDP . . . D 3 -9.656 -7.729 10.935 1 31.83 ? O1A GDP 1284 A 1 HETATM 8 O O2A GDP . . . D 3 -7.095 -7.868 10.79 1 30.18 ? O2A GDP 1284 A 1 HETATM 9 O O5' GDP . . . D 3 -8.564 -8.1 8.635 1 31.35 ? O5' GDP 1284 A 1 HETATM 10 C C5' GDP . . . D 3 -9.812 -7.849 7.976 1 33.51 ? C5' GDP 1284 A 1 HETATM 11 C C4' GDP . . . D 3 -10.157 -8.896 6.908 1 35.29 ? C4' GDP 1284 A 1 HETATM 12 O O4' GDP . . . D 3 -9.228 -8.894 5.792 1 35.16 ? O4' GDP 1284 A 1 HETATM 13 C C3' GDP . . . D 3 -10.128 -10.308 7.46 1 36.37 ? C3' GDP 1284 A 1 HETATM 14 O O3' GDP . . . D 3 -11.056 -11.033 6.652 1 40.24 ? O3' GDP 1284 A 1 HETATM 15 C C2' GDP . . . D 3 -8.735 -10.791 7.112 1 36.46 ? C2' GDP 1284 A 1 HETATM 16 O O2' GDP . . . D 3 -8.571 -12.211 7.006 1 37.3 ? O2' GDP 1284 A 1 HETATM 17 C C1' GDP . . . D 3 -8.507 -10.136 5.756 1 34.12 ? C1' GDP 1284 A 1 HETATM 18 N N9 GDP . . . D 3 -7.064 -9.917 5.504 1 31.86 ? N9 GDP 1284 A 1 HETATM 19 C C8 GDP . . . D 3 -6.156 -9.368 6.339 1 30.45 ? C8 GDP 1284 A 1 HETATM 20 N N7 GDP . . . D 3 -4.934 -9.361 5.756 1 30.26 ? N7 GDP 1284 A 1 HETATM 21 C C5 GDP . . . D 3 -5.058 -9.906 4.536 1 28.17 ? C5 GDP 1284 A 1 HETATM 22 C C6 GDP . . . D 3 -4.164 -10.186 3.411 1 28.26 ? C6 GDP 1284 A 1 HETATM 23 O O6 GDP . . . D 3 -2.943 -9.896 3.467 1 27.5 ? O6 GDP 1284 A 1 HETATM 24 N N1 GDP . . . D 3 -4.691 -10.791 2.34 1 29.7 ? N1 GDP 1284 A 1 HETATM 25 C C2 GDP . . . D 3 -5.988 -11.138 2.246 1 29.64 ? C2 GDP 1284 A 1 HETATM 26 N N2 GDP . . . D 3 -6.423 -11.741 1.117 1 30.33 ? N2 GDP 1284 A 1 HETATM 27 N N3 GDP . . . D 3 -6.875 -10.905 3.232 1 29.62 ? N3 GDP 1284 A 1 HETATM 28 C C4 GDP . . . D 3 -6.457 -10.298 4.379 1 30.63 ? C4 GDP 1284 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #