data_4WNR # _model_server_result.job_id pBNHxgowH57xbC7L98rokg _model_server_result.datetime_utc '2024-10-28 02:38:57' _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 4wnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 4WNR # _exptl.entry_id 4WNR _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 120 _cell.entry_id 4WNR _cell.length_a 109.36 _cell.length_b 109.36 _cell.length_c 223.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 disulf ? disulf1 E S SO4 . A SO4 704 1_555 E S SO4 . A SO4 704 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc1 A OG1 THR 55 A THR 335 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc2 B O2B GDP . A GDP 701 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc3 C MG MG . A MG 702 1_555 G O HOH . A HOH 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc4 C MG MG . A MG 702 1_555 G O HOH . A HOH 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc5 C MG MG . A MG 702 1_555 G O HOH . A HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? # _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 4WNR _atom_sites.fract_transf_matrix[1][1] 0.009144 _atom_sites.fract_transf_matrix[1][2] 0.005279 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010559 _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] 0.004482 _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 1 701 1 GDP GDP . C 3 MG A 1 702 1 MG MG . D 4 GOL A 1 703 5 GOL GOL . E 5 SO4 A 1 704 1 SO4 SO4 . F 5 SO4 A 1 705 2 SO4 SO4 . G 6 HOH A 1 801 15 HOH HOH . G 6 HOH A 2 802 10 HOH HOH . G 6 HOH A 3 803 6 HOH HOH . G 6 HOH A 4 804 5 HOH HOH . G 6 HOH A 5 805 1 HOH HOH . G 6 HOH A 6 806 2 HOH HOH . G 6 HOH A 7 807 3 HOH HOH . G 6 HOH A 8 808 4 HOH HOH . G 6 HOH A 9 809 7 HOH HOH . G 6 HOH A 10 810 8 HOH HOH . G 6 HOH A 11 811 9 HOH HOH . G 6 HOH A 12 812 11 HOH HOH . G 6 HOH A 13 813 12 HOH HOH . G 6 HOH A 14 814 13 HOH HOH . G 6 HOH A 15 815 14 HOH HOH . G 6 HOH A 16 816 16 HOH HOH . G 6 HOH A 17 817 17 HOH HOH . G 6 HOH A 18 818 18 HOH HOH . G 6 HOH A 19 819 19 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 -19.358 11.72 19.01 1 66.42 ? PB GDP 701 A 1 HETATM 2 O O1B GDP . . . B 2 -19.669 10.703 17.803 1 65.45 ? O1B GDP 701 A 1 HETATM 3 O O2B GDP . . . B 2 -18.894 13.089 18.311 1 66.65 ? O2B GDP 701 A 1 HETATM 4 O O3B GDP . . . B 2 -20.548 11.93 19.867 1 68.14 ? O3B GDP 701 A 1 HETATM 5 O O3A GDP . . . B 2 -18.057 11.24 19.827 1 68.75 ? O3A GDP 701 A 1 HETATM 6 P PA GDP . . . B 2 -17.301 9.841 19.583 1 67.02 ? PA GDP 701 A 1 HETATM 7 O O1A GDP . . . B 2 -17.206 9.492 18.153 1 67.29 ? O1A GDP 701 A 1 HETATM 8 O O2A GDP . . . B 2 -15.845 10.088 20.226 1 70.33 ? O2A GDP 701 A 1 HETATM 9 O O5' GDP . . . B 2 -18.018 8.739 20.516 1 69.15 ? O5' GDP 701 A 1 HETATM 10 C C5' GDP . . . B 2 -18.211 7.443 20.042 1 68.55 ? C5' GDP 701 A 1 HETATM 11 C C4' GDP . . . B 2 -17.644 6.451 21.08 1 67.91 ? C4' GDP 701 A 1 HETATM 12 O O4' GDP . . . B 2 -17.498 5.168 20.436 1 68.6 ? O4' GDP 701 A 1 HETATM 13 C C3' GDP . . . B 2 -16.243 6.813 21.571 1 67.48 ? C3' GDP 701 A 1 HETATM 14 O O3' GDP . . . B 2 -15.999 6.195 22.843 1 67.48 ? O3' GDP 701 A 1 HETATM 15 C C2' GDP . . . B 2 -15.344 6.223 20.513 1 67.32 ? C2' GDP 701 A 1 HETATM 16 O O2' GDP . . . B 2 -14.085 5.824 21.079 1 65.95 ? O2' GDP 701 A 1 HETATM 17 C C1' GDP . . . B 2 -16.11 4.996 20.036 1 68.15 ? C1' GDP 701 A 1 HETATM 18 N N9 GDP . . . B 2 -16.031 4.809 18.555 1 69.94 ? N9 GDP 701 A 1 HETATM 19 C C8 GDP . . . B 2 -16.058 5.733 17.595 1 70.17 ? C8 GDP 701 A 1 HETATM 20 N N7 GDP . . . B 2 -15.962 5.121 16.422 1 71.01 ? N7 GDP 701 A 1 HETATM 21 C C5 GDP . . . B 2 -15.877 3.813 16.643 1 70.8 ? C5 GDP 701 A 1 HETATM 22 C C6 GDP . . . B 2 -15.764 2.785 15.799 1 70.08 ? C6 GDP 701 A 1 HETATM 23 O O6 GDP . . . B 2 -15.726 2.959 14.583 1 69.52 ? O6 GDP 701 A 1 HETATM 24 N N1 GDP . . . B 2 -15.692 1.487 16.307 1 72.11 ? N1 GDP 701 A 1 HETATM 25 C C2 GDP . . . B 2 -15.74 1.305 17.694 1 72.05 ? C2 GDP 701 A 1 HETATM 26 N N2 GDP . . . B 2 -15.672 0.083 18.212 1 72.03 ? N2 GDP 701 A 1 HETATM 27 N N3 GDP . . . B 2 -15.854 2.379 18.492 1 71.01 ? N3 GDP 701 A 1 HETATM 28 C C4 GDP . . . B 2 -15.921 3.618 17.969 1 70.85 ? C4 GDP 701 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #