data_5M50 # _model_server_result.job_id QCeDLdR6ywIsCoLfSAQCgQ _model_server_result.datetime_utc '2024-11-05 01:29:26' _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 5m50 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 5M50 # _exptl.entry_id 5M50 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q _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 ? _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 ? 6 H N N ? 6 L 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 F O1G GTP . D GTP 501 1_555 G MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc2 F O2B GTP . D GTP 501 1_555 G MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc3 G MG MG . D MG 502 1_555 N O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 G MG MG . D MG 502 1_555 N O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc5 G MG MG . D MG 502 1_555 N O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc6 J O1G GTP . A GTP 501 1_555 K MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc7 J O2B GTP . A GTP 501 1_555 K MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc8 J O3A GTP . A GTP 501 1_555 K MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? metalc ? metalc9 K MG MG . A MG 502 1_555 P O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc10 K MG MG . A MG 502 1_555 P O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc11 K MG MG . A MG 502 1_555 P O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? # _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 5M50 _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 F 4 GTP D 1 501 501 GTP GTP . G 5 MG D 1 502 502 MG MG . H 6 GDP E 1 501 501 GDP GDP . I 7 TA1 E 1 502 502 TA1 TA1 . J 4 GTP A 1 501 501 GTP GTP . K 5 MG A 1 502 502 MG MG . L 6 GDP B 1 501 501 GDP GDP . M 7 TA1 B 1 502 502 TA1 TA1 . N 8 HOH D 1 601 604 HOH HOH . N 8 HOH D 2 602 601 HOH HOH . N 8 HOH D 3 603 602 HOH HOH . O 8 HOH E 1 601 603 HOH HOH . P 8 HOH A 1 601 604 HOH HOH . P 8 HOH A 2 602 601 HOH HOH . P 8 HOH A 3 603 602 HOH HOH . Q 8 HOH B 1 601 603 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 6 69.444 45.847 102.857 1 121.48 ? PB GDP 501 E 1 HETATM 2 O O1B GDP . . . H 6 68.502 45.761 101.665 1 121.48 ? O1B GDP 501 E 1 HETATM 3 O O2B GDP . . . H 6 70.237 47.139 102.74 1 121.48 ? O2B GDP 501 E 1 HETATM 4 O O3B GDP . . . H 6 68.747 45.697 104.165 1 121.48 ? O3B GDP 501 E 1 HETATM 5 O O3A GDP . . . H 6 70.508 44.677 102.676 1 121.48 ? O3A GDP 501 E 1 HETATM 6 P PA GDP . . . H 6 72.036 44.701 102.229 1 121.48 ? PA GDP 501 E 1 HETATM 7 O O1A GDP . . . H 6 72.19 45.752 101.135 1 121.48 ? O1A GDP 501 E 1 HETATM 8 O O2A GDP . . . H 6 72.886 45.049 103.384 1 121.48 ? O2A GDP 501 E 1 HETATM 9 O O5' GDP . . . H 6 72.379 43.288 101.606 1 121.48 ? O5' GDP 501 E 1 HETATM 10 C C5' GDP . . . H 6 73.231 42.293 102.208 1 121.48 ? C5' GDP 501 E 1 HETATM 11 C C4' GDP . . . H 6 73.71 41.362 101.125 1 121.48 ? C4' GDP 501 E 1 HETATM 12 O O4' GDP . . . H 6 74.428 42.118 100.126 1 121.48 ? O4' GDP 501 E 1 HETATM 13 C C3' GDP . . . H 6 74.683 40.284 101.578 1 121.48 ? C3' GDP 501 E 1 HETATM 14 O O3' GDP . . . H 6 74.609 39.151 100.72 1 121.48 ? O3' GDP 501 E 1 HETATM 15 C C2' GDP . . . H 6 76.03 40.997 101.465 1 121.48 ? C2' GDP 501 E 1 HETATM 16 O O2' GDP . . . H 6 77.107 40.093 101.254 1 121.48 ? O2' GDP 501 E 1 HETATM 17 C C1' GDP . . . H 6 75.817 41.856 100.218 1 121.48 ? C1' GDP 501 E 1 HETATM 18 N N9 GDP . . . H 6 76.516 43.141 100.289 1 121.48 ? N9 GDP 501 E 1 HETATM 19 C C8 GDP . . . H 6 76.351 44.119 101.233 1 121.48 ? C8 GDP 501 E 1 HETATM 20 N N7 GDP . . . H 6 77.092 45.179 101.015 1 121.48 ? N7 GDP 501 E 1 HETATM 21 C C5 GDP . . . H 6 77.788 44.875 99.856 1 121.48 ? C5 GDP 501 E 1 HETATM 22 C C6 GDP . . . H 6 78.736 45.631 99.108 1 121.48 ? C6 GDP 501 E 1 HETATM 23 O O6 GDP . . . H 6 79.095 46.785 99.323 1 121.48 ? O6 GDP 501 E 1 HETATM 24 N N1 GDP . . . H 6 79.207 44.941 98.01 1 121.48 ? N1 GDP 501 E 1 HETATM 25 C C2 GDP . . . H 6 78.813 43.684 97.643 1 121.48 ? C2 GDP 501 E 1 HETATM 26 N N2 GDP . . . H 6 79.362 43.175 96.54 1 121.48 ? N2 GDP 501 E 1 HETATM 27 N N3 GDP . . . H 6 77.916 42.972 98.321 1 121.48 ? N3 GDP 501 E 1 HETATM 28 C C4 GDP . . . H 6 77.449 43.62 99.405 1 121.48 ? C4 GDP 501 E 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #