data_4M8N # _model_server_result.job_id joE2yk0_P5UxZ81FLyLifA _model_server_result.datetime_utc '2024-11-05 00:40:58' _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 4m8n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":201}' # _entry.id 4M8N # _exptl.entry_id 4M8N _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 91.09 _cell.angle_beta 95.15 _cell.angle_gamma 90.32 _cell.entry_id 4M8N _cell.length_a 76.276 _cell.length_b 84.734 _cell.length_c 138.752 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M8N _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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,D,E,H,I,J,K,R,S,T,U,X,Y 1 1 B,C,F,G,L,M,N,O,P,Q,V,W 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 J N N ? 4 M N N ? 4 P N N ? 4 S 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 E OG SER 20 E SER 17 1_555 I MG MG . E MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc2 E OG1 THR 38 E THR 35 1_555 I MG MG . E MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc3 I MG MG . E MG 200 1_555 J O2B GDP . E GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc4 F OG SER 20 F SER 17 1_555 L MG MG . F MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc5 F OG1 THR 38 F THR 35 1_555 L MG MG . F MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc6 L MG MG . F MG 200 1_555 M O2B GDP . F GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc7 L MG MG . F MG 200 1_555 M O1B GDP . F GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? metalc ? metalc8 G OG SER 20 G SER 17 1_555 O MG MG . G MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc9 G OG1 THR 38 G THR 35 1_555 O MG MG . G MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc10 O MG MG . G MG 200 1_555 P O2B GDP . G GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc11 H OG SER 20 H SER 17 1_555 R MG MG . H MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc12 H OG1 THR 38 H THR 35 1_555 R MG MG . H MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc13 H OD2 ASP 60 H ASP 57 1_555 R MG MG . H MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc14 R MG MG . H MG 200 1_555 S O2B GDP . H GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? # _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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 4M8N _atom_sites.fract_transf_matrix[1][1] 0.01311 _atom_sites.fract_transf_matrix[1][2] 0.000073 _atom_sites.fract_transf_matrix[1][3] 0.001183 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011802 _atom_sites.fract_transf_matrix[2][3] 0.000231 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007238 _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 MG E 1 200 200 MG MG . J 4 GDP E 1 201 201 GDP GDP . K 5 AF3 E 1 202 202 AF3 AF3 . L 3 MG F 1 200 200 MG MG . M 4 GDP F 1 201 201 GDP GDP . N 5 AF3 F 1 202 202 AF3 AF3 . O 3 MG G 1 200 200 MG MG . P 4 GDP G 1 201 201 GDP GDP . Q 5 AF3 G 1 202 202 AF3 AF3 . R 3 MG H 1 200 200 MG MG . S 4 GDP H 1 201 201 GDP GDP . T 5 AF3 H 1 202 202 AF3 AF3 . U 6 HOH A 1 1201 1 HOH HOH . U 6 HOH A 2 1202 5 HOH HOH . U 6 HOH A 3 1203 7 HOH HOH . U 6 HOH A 4 1204 10 HOH HOH . V 6 HOH B 1 1201 2 HOH HOH . W 6 HOH C 1 1201 3 HOH HOH . W 6 HOH C 2 1202 6 HOH HOH . W 6 HOH C 3 1203 8 HOH HOH . X 6 HOH D 1 1201 4 HOH HOH . Y 6 HOH H 1 301 9 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 . . . M 4 49.205 178.83 -152.127 1 109.63 ? PB GDP 201 F 1 HETATM 2 O O1B GDP . . . M 4 50.323 179.632 -151.514 1 111.61 ? O1B GDP 201 F 1 HETATM 3 O O2B GDP . . . M 4 48.606 177.896 -151.101 1 105.7 ? O2B GDP 201 F 1 HETATM 4 O O3B GDP . . . M 4 48.143 179.781 -152.632 1 107.59 ? O3B GDP 201 F 1 HETATM 5 O O3A GDP . . . M 4 49.828 178.009 -153.364 1 100.36 ? O3A GDP 201 F 1 HETATM 6 P PA GDP . . . M 4 49.693 176.418 -153.504 1 98.83 ? PA GDP 201 F 1 HETATM 7 O O1A GDP . . . M 4 50.519 175.744 -152.433 1 97.65 ? O1A GDP 201 F 1 HETATM 8 O O2A GDP . . . M 4 48.252 175.963 -153.437 1 107.78 ? O2A GDP 201 F 1 HETATM 9 O O5' GDP . . . M 4 50.303 176.15 -154.97 1 103.1 ? O5' GDP 201 F 1 HETATM 10 C C5' GDP . . . M 4 49.439 176.033 -156.098 1 110.93 ? C5' GDP 201 F 1 HETATM 11 C C4' GDP . . . M 4 49.941 174.956 -157.054 1 117.01 ? C4' GDP 201 F 1 HETATM 12 O O4' GDP . . . M 4 51.335 175.121 -157.329 1 120.48 ? O4' GDP 201 F 1 HETATM 13 C C3' GDP . . . M 4 49.77 173.571 -156.457 1 118.79 ? C3' GDP 201 F 1 HETATM 14 O O3' GDP . . . M 4 48.841 172.812 -157.235 1 123.13 ? O3' GDP 201 F 1 HETATM 15 C C2' GDP . . . M 4 51.123 172.912 -156.556 1 121.92 ? C2' GDP 201 F 1 HETATM 16 O O2' GDP . . . M 4 50.972 171.634 -157.176 1 128.21 ? O2' GDP 201 F 1 HETATM 17 C C1' GDP . . . M 4 51.963 173.841 -157.416 1 122.83 ? C1' GDP 201 F 1 HETATM 18 N N9 GDP . . . M 4 53.344 173.865 -156.877 1 123.07 ? N9 GDP 201 F 1 HETATM 19 C C8 GDP . . . M 4 53.703 174.309 -155.657 1 120.45 ? C8 GDP 201 F 1 HETATM 20 N N7 GDP . . . M 4 55.042 174.19 -155.471 1 121.83 ? N7 GDP 201 F 1 HETATM 21 C C5 GDP . . . M 4 55.561 173.661 -156.596 1 125.31 ? C5 GDP 201 F 1 HETATM 22 C C6 GDP . . . M 4 56.91 173.274 -157.071 1 130.88 ? C6 GDP 201 F 1 HETATM 23 O O6 GDP . . . M 4 57.912 173.426 -156.341 1 132.66 ? O6 GDP 201 F 1 HETATM 24 N N1 GDP . . . M 4 57.024 172.759 -158.302 1 134.74 ? N1 GDP 201 F 1 HETATM 25 C C2 GDP . . . M 4 55.96 172.585 -159.108 1 134.54 ? C2 GDP 201 F 1 HETATM 26 N N2 GDP . . . M 4 56.161 172.055 -160.34 1 138.25 ? N2 GDP 201 F 1 HETATM 27 N N3 GDP . . . M 4 54.694 172.918 -158.738 1 130.12 ? N3 GDP 201 F 1 HETATM 28 C C4 GDP . . . M 4 54.438 173.449 -157.519 1 125.24 ? C4 GDP 201 F 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #