data_4WTE # _model_server_result.job_id fn1loh6Rx3gGrZMpEevm3A _model_server_result.datetime_utc '2024-11-25 17:06:55' _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 4wte # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":605}' # _entry.id 4WTE # _exptl.entry_id 4WTE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 120 _cell.entry_id 4WTE _cell.length_a 141.64 _cell.length_b 141.64 _cell.length_c 91.54 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WTE _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 5 _struct_asym.id H _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 B O3' U 8 P U 8 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc2 C OD1 ASP 222 A ASP 220 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc3 C OD2 ASP 222 A ASP 220 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc4 C O THR 223 A THR 221 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc5 C OE2 GLU 239 A GLU 237 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc6 C ND1 HIS 256 A HIS 254 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc7 C OD1 ASP 320 A ASP 318 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc8 C OD2 ASP 320 A ASP 318 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc9 C OD1 ASP 321 A ASP 319 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc10 D MN MN . A MN 601 1_555 H O1A GDP . A GDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc11 D MN MN . A MN 601 1_555 J O HOH . A HOH 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc12 E MN MN . A MN 602 1_555 H O1B GDP . A GDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc13 E MN MN . A MN 602 1_555 H O1A GDP . A GDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc14 E MN MN . A MN 602 1_555 J O HOH . A HOH 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? hydrog WATSON-CRICK hydrog1 A N1 A 3 T A 3 1_555 B N3 U 8 P U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N6 A 3 T A 3 1_555 B O4 U 8 P U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 A 4 T A 4 1_555 B N3 U 7 P U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N6 A 4 T A 4 1_555 B O4 U 7 P U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 A 5 T A 5 1_555 B N3 U 6 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N6 A 5 T A 5 1_555 B O4 U 6 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 U 6 T U 6 1_555 B N1 A 5 P A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 U 6 T U 6 1_555 B N6 A 5 P A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 U 7 T U 7 1_555 B N1 A 4 P A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 U 7 T U 7 1_555 B N6 A 4 P A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 158 n n PB O2B GDP sing 159 n n PB O3B GDP sing 160 n n PB O3A GDP sing 161 n n O2B HOB2 GDP sing 162 n n O3B HOB3 GDP sing 163 n n O3A PA GDP sing 164 n n PA O1A GDP doub 165 n n PA O2A GDP sing 166 n n PA O5' GDP sing 167 n n O2A HOA2 GDP sing 168 n n O5' C5' GDP sing 169 n n C5' C4' GDP sing 170 n n C5' H5' GDP sing 171 n n C5' "H5''" GDP sing 172 n n C4' O4' GDP sing 173 n n C4' C3' GDP sing 174 n n C4' H4' GDP sing 175 n n O4' C1' GDP sing 176 n n C3' O3' GDP sing 177 n n C3' C2' GDP sing 178 n n C3' H3' GDP sing 179 n n O3' HO3' GDP sing 180 n n C2' O2' GDP sing 181 n n C2' C1' GDP sing 182 n n C2' H2' GDP sing 183 n n O2' HO2' GDP sing 184 n n C1' N9 GDP sing 185 n n C1' H1' GDP sing 186 n n N9 C8 GDP sing 187 n y N9 C4 GDP sing 188 n y C8 N7 GDP doub 189 n y C8 H8 GDP sing 190 n n N7 C5 GDP sing 191 n y C5 C6 GDP sing 192 n n C5 C4 GDP doub 193 n y C6 O6 GDP doub 194 n n C6 N1 GDP sing 195 n n N1 C2 GDP sing 196 n n N1 HN1 GDP sing 197 n n C2 N2 GDP sing 198 n n C2 N3 GDP doub 199 n n N2 HN21 GDP sing 200 n n N2 HN22 GDP sing 201 n n N3 C4 GDP sing 202 n n # _atom_sites.entry_id 4WTE _atom_sites.fract_transf_matrix[1][1] 0.00706 _atom_sites.fract_transf_matrix[1][2] 0.004076 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008152 _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] 0.010924 _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 D 3 MN A 1 601 1 MN MN . E 3 MN A 1 602 2 MN MN . F 3 MN A 1 603 3 MN MN . G 4 CL A 1 604 4 CL CL . H 5 GDP A 1 605 1 GDP GDP . I 6 HOH T 1 101 19 HOH HOH . J 6 HOH A 1 701 3 HOH HOH . J 6 HOH A 2 702 14 HOH HOH . J 6 HOH A 3 703 4 HOH HOH . J 6 HOH A 4 704 1 HOH HOH . J 6 HOH A 5 705 2 HOH HOH . J 6 HOH A 6 706 5 HOH HOH . J 6 HOH A 7 707 6 HOH HOH . J 6 HOH A 8 708 7 HOH HOH . J 6 HOH A 9 709 8 HOH HOH . J 6 HOH A 10 710 9 HOH HOH . J 6 HOH A 11 711 10 HOH HOH . J 6 HOH A 12 712 11 HOH HOH . J 6 HOH A 13 713 12 HOH HOH . J 6 HOH A 14 714 13 HOH HOH . J 6 HOH A 15 715 15 HOH HOH . J 6 HOH A 16 716 16 HOH HOH . J 6 HOH A 17 717 17 HOH HOH . J 6 HOH A 18 718 18 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 . . . H 5 42.83 -43.086 2.599 1 60.52 ? PB GDP 605 A 1 HETATM 2 O O1B GDP . . . H 5 42.979 -44.064 1.44 1 47.78 ? O1B GDP 605 A 1 HETATM 3 O O2B GDP . . . H 5 43.486 -41.705 2.448 1 54.06 ? O2B GDP 605 A 1 HETATM 4 O O3B GDP . . . H 5 41.384 -42.906 3.059 1 61.34 ? O3B GDP 605 A 1 HETATM 5 O O3A GDP . . . H 5 43.552 -43.781 3.881 1 58.12 ? O3A GDP 605 A 1 HETATM 6 P PA GDP . . . H 5 44.266 -45.237 3.976 1 63.01 ? PA GDP 605 A 1 HETATM 7 O O1A GDP . . . H 5 44.86 -45.666 2.653 1 65.83 ? O1A GDP 605 A 1 HETATM 8 O O2A GDP . . . H 5 45.125 -45.242 5.211 1 69.73 ? O2A GDP 605 A 1 HETATM 9 O O5' GDP . . . H 5 43.068 -46.239 4.345 1 70.36 ? O5' GDP 605 A 1 HETATM 10 C C5' GDP . . . H 5 42.095 -46.7 3.4 1 67.92 ? C5' GDP 605 A 1 HETATM 11 C C4' GDP . . . H 5 40.725 -46.789 4.067 1 66.68 ? C4' GDP 605 A 1 HETATM 12 O O4' GDP . . . H 5 40.788 -47.56 5.273 1 67.16 ? O4' GDP 605 A 1 HETATM 13 C C3' GDP . . . H 5 40.133 -45.457 4.501 1 66.67 ? C3' GDP 605 A 1 HETATM 14 O O3' GDP . . . H 5 39.531 -44.725 3.423 1 69.36 ? O3' GDP 605 A 1 HETATM 15 C C2' GDP . . . H 5 39.137 -45.898 5.551 1 67.42 ? C2' GDP 605 A 1 HETATM 16 O O2' GDP . . . H 5 37.887 -46.324 4.977 1 71.58 ? O2' GDP 605 A 1 HETATM 17 C C1' GDP . . . H 5 39.848 -47.067 6.225 1 66.13 ? C1' GDP 605 A 1 HETATM 18 N N9 GDP . . . H 5 40.439 -46.479 7.448 1 65.7 ? N9 GDP 605 A 1 HETATM 19 C C8 GDP . . . H 5 41.647 -45.911 7.627 1 64.26 ? C8 GDP 605 A 1 HETATM 20 N N7 GDP . . . H 5 41.765 -45.467 8.915 1 66.46 ? N7 GDP 605 A 1 HETATM 21 C C5 GDP . . . H 5 40.604 -45.731 9.562 1 65.67 ? C5 GDP 605 A 1 HETATM 22 C C6 GDP . . . H 5 40.008 -45.538 10.914 1 63.45 ? C6 GDP 605 A 1 HETATM 23 O O6 GDP . . . H 5 40.624 -44.974 11.836 1 63.11 ? O6 GDP 605 A 1 HETATM 24 N N1 GDP . . . H 5 38.767 -45.976 11.145 1 63.45 ? N1 GDP 605 A 1 HETATM 25 C C2 GDP . . . H 5 38.037 -46.586 10.197 1 65.4 ? C2 GDP 605 A 1 HETATM 26 N N2 GDP . . . H 5 36.78 -47.014 10.487 1 67.45 ? N2 GDP 605 A 1 HETATM 27 N N3 GDP . . . H 5 38.51 -46.793 8.945 1 63.46 ? N3 GDP 605 A 1 HETATM 28 C C4 GDP . . . H 5 39.747 -46.394 8.578 1 65.7 ? C4 GDP 605 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #