data_8GJU # _model_server_result.job_id NdY7GHqWRwClnYtb_EGjLg _model_server_result.datetime_utc '2024-11-08 12:41:41' _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 8gju # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 8GJU # _exptl.entry_id 8GJU _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.53 _cell.angle_gamma 90 _cell.entry_id 8GJU _cell.length_a 95.806 _cell.length_b 221.872 _cell.length_c 121.824 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GJU _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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,C,D,I,J,K,L,M,N,U,V 1 1 E,F,G,H,O,P,Q,R,S,T,W,X,Y 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 I N N ? 3 K N N ? 3 P N N ? 3 R 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 88 D SER 157 1_555 J MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc2 A OD1 ASP 124 D ASP 193 1_555 J MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc3 A OE2 GLU 173 D GLU 242 1_555 J MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc4 I O1B GDP . D GDP 501 1_555 J MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc5 J MG MG . D MG 502 1_555 U O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc6 J MG MG . D MG 502 1_555 U O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc7 B OG SER 88 F SER 157 1_555 L MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc8 B OD1 ASP 124 F ASP 193 1_555 L MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc9 B OE2 GLU 173 F GLU 242 1_555 L MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc10 K O1B GDP . F GDP 601 1_555 L MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc11 L MG MG . F MG 602 1_555 V O HOH . F HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc12 F OG SER 88 A SER 157 1_555 Q MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc13 F OD1 ASP 124 A ASP 193 1_555 Q MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc14 F OE2 GLU 173 A GLU 242 1_555 Q MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc15 P O2B GDP . A GDP 501 1_555 Q MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc16 Q MG MG . A MG 502 1_555 W O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc17 G OG SER 88 B SER 157 1_555 S MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc18 G OD1 ASP 124 B ASP 193 1_555 S MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc19 G OE2 GLU 173 B GLU 242 1_555 S MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc20 R O2B GDP . B GDP 501 1_555 S MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc21 S MG MG . B MG 502 1_555 X O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc22 S MG MG . B MG 502 1_555 X O HOH . B HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _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 169 n n PB O2B GDP sing 170 n n PB O3B GDP sing 171 n n PB O3A GDP sing 172 n n O2B HOB2 GDP sing 173 n n O3B HOB3 GDP sing 174 n n O3A PA GDP sing 175 n n PA O1A GDP doub 176 n n PA O2A GDP sing 177 n n PA O5' GDP sing 178 n n O2A HOA2 GDP sing 179 n n O5' C5' GDP sing 180 n n C5' C4' GDP sing 181 n n C5' H5' GDP sing 182 n n C5' "H5''" GDP sing 183 n n C4' O4' GDP sing 184 n n C4' C3' GDP sing 185 n n C4' H4' GDP sing 186 n n O4' C1' GDP sing 187 n n C3' O3' GDP sing 188 n n C3' C2' GDP sing 189 n n C3' H3' GDP sing 190 n n O3' HO3' GDP sing 191 n n C2' O2' GDP sing 192 n n C2' C1' GDP sing 193 n n C2' H2' GDP sing 194 n n O2' HO2' GDP sing 195 n n C1' N9 GDP sing 196 n n C1' H1' GDP sing 197 n n N9 C8 GDP sing 198 n y N9 C4 GDP sing 199 n y C8 N7 GDP doub 200 n y C8 H8 GDP sing 201 n n N7 C5 GDP sing 202 n y C5 C6 GDP sing 203 n n C5 C4 GDP doub 204 n y C6 O6 GDP doub 205 n n C6 N1 GDP sing 206 n n N1 C2 GDP sing 207 n n N1 HN1 GDP sing 208 n n C2 N2 GDP sing 209 n n C2 N3 GDP doub 210 n n N2 HN21 GDP sing 211 n n N2 HN22 GDP sing 212 n n N3 C4 GDP sing 213 n n # _atom_sites.entry_id 8GJU _atom_sites.fract_transf_matrix[1][1] 0.010438 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002901 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004507 _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] 0.00852 _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 I 3 GDP D 1 501 600 GDP GDP . J 4 MG D 1 502 2 MG MG . K 3 GDP F 1 601 601 GDP GDP . L 4 MG F 1 602 9 MG MG . M 5 COA J 1 801 1002 COA COA . N 5 COA K 1 801 1003 COA COA . O 5 COA L 1 801 1004 COA COA . P 3 GDP A 1 501 602 GDP GDP . Q 4 MG A 1 502 10 MG MG . R 3 GDP B 1 501 603 GDP GDP . S 4 MG B 1 502 1 MG MG . T 5 COA H 1 1001 1001 COA COA . U 6 HOH D 1 601 1 HOH HOH . U 6 HOH D 2 602 5 HOH HOH . U 6 HOH D 3 603 12 HOH HOH . V 6 HOH F 1 701 7 HOH HOH . V 6 HOH F 2 702 2 HOH HOH . W 6 HOH A 1 601 11 HOH HOH . W 6 HOH A 2 602 3 HOH HOH . W 6 HOH A 3 603 9 HOH HOH . X 6 HOH B 1 601 6 HOH HOH . X 6 HOH B 2 602 4 HOH HOH . X 6 HOH B 3 603 8 HOH HOH . X 6 HOH B 4 604 14 HOH HOH . Y 6 HOH H 1 1101 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 . . . I 3 60.569 -111.504 53.367 1 55.38 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . I 3 61.755 -110.958 52.609 1 52.91 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . I 3 59.641 -110.507 54.043 1 48.43 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . I 3 59.917 -112.688 52.674 1 52.88 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . I 3 61.233 -112.127 54.827 1 39.32 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . I 3 62.203 -111.729 55.949 1 53.54 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . I 3 63.357 -112.675 56.039 1 52.15 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . I 3 62.413 -110.298 56.384 1 64.15 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . I 3 61.26 -112.303 57.313 1 57.5 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . I 3 61.249 -113.628 57.646 1 51.28 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . I 3 60.737 -113.649 59.113 1 60.39 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . I 3 60.76 -115 59.59 1 71.35 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . I 3 61.683 -112.873 60.076 1 63.16 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . I 3 60.956 -112.513 61.197 1 68.86 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . I 3 62.77 -113.934 60.428 1 65.81 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . I 3 63.08 -113.773 61.781 1 60.16 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . I 3 61.966 -115.259 60.229 1 67.01 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . I 3 62.764 -116.166 59.372 1 57.71 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . I 3 63.521 -115.949 58.196 1 58.57 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . I 3 64.091 -117.089 57.755 1 64.28 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . I 3 63.695 -118.068 58.67 1 62.12 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . I 3 64.016 -119.451 58.679 1 60.52 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . I 3 64.693 -120.151 57.931 1 58.45 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . I 3 63.411 -120.124 59.795 1 57.18 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . I 3 62.606 -119.451 60.738 1 58.14 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . I 3 62.093 -120.237 61.758 1 61.01 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . I 3 62.287 -118.15 60.756 1 54.88 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . I 3 62.874 -117.502 59.677 1 55.09 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #