data_6MZG # _model_server_result.job_id 0HP3M8Pjd40r5FM6JTYfvw _model_server_result.datetime_utc '2025-01-03 03:32:42' _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 6mzg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":600}' # _entry.id 6MZG # _exptl.entry_id 6MZG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 90.19 _cell.angle_gamma 90 _cell.entry_id 6MZG _cell.length_a 115.13 _cell.length_b 194.99 _cell.length_c 149.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MZG _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 ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_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,E,F,M,N,O,P,Q,R,S,T 1 1 G,H,I,J,K,L,U,V,W,X,Y,Z,AA,BA 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 ? 7 O N N ? 7 S N N ? 7 W N N ? 7 AA 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 M O1G GTP . A GTP 600 1_555 N MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc2 M O1B GTP . A GTP 600 1_555 N MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc3 B OE1 GLN 11 B GLN 11 1_555 P MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc4 O O1A GDP . B GDP 600 1_555 P MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc5 Q O1G GTP . C GTP 600 1_555 R MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc6 Q O1B GTP . C GTP 600 1_555 R MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc7 S O1A GDP . D GDP 600 1_555 T MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc8 U O3G GTP . G GTP 600 1_555 V MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc9 U O2B GTP . G GTP 600 1_555 V MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc10 H OD2 ASP 177 H ASP 179 1_555 X MG MG . H MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc11 W O2A GDP . H GDP 600 1_555 X MG MG . H MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc12 Y O3G GTP . I GTP 600 1_555 Z MG MG . I MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc13 Y O2B GTP . I GTP 600 1_555 Z MG MG . I MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc14 J OE1 GLN 11 J GLN 11 1_555 BA MG MG . J MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc15 AA O2A GDP . J GDP 600 1_555 BA MG MG . J MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? # _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 6MZG _atom_sites.fract_transf_matrix[1][1] 0.008686 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000029 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005128 _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] 0.006686 _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 M 5 GTP A 1 600 600 GTP GTP . N 6 MG A 1 601 601 MG MG . O 7 GDP B 1 600 600 GDP GDP . P 6 MG B 1 601 601 MG MG . Q 5 GTP C 1 600 600 GTP GTP . R 6 MG C 1 601 601 MG MG . S 7 GDP D 1 600 600 GDP GDP . T 6 MG D 1 601 601 MG MG . U 5 GTP G 1 600 600 GTP GTP . V 6 MG G 1 601 601 MG MG . W 7 GDP H 1 600 600 GDP GDP . X 6 MG H 1 601 601 MG MG . Y 5 GTP I 1 600 600 GTP GTP . Z 6 MG I 1 601 601 MG MG . AA 7 GDP J 1 600 600 GDP GDP . BA 6 MG J 1 601 601 MG MG . # 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 . . . O 7 -3.176 -14.556 -32.701 1 48.46 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . O 7 -3.012 -13.751 -33.967 1 50.04 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . O 7 -3.039 -13.669 -31.485 1 59.31 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . O 7 -2.113 -15.626 -32.659 1 38.85 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . O 7 -4.613 -15.279 -32.715 1 53.55 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . O 7 -5.972 -14.463 -32.44 1 51.99 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . O 7 -6.966 -14.678 -33.557 1 53.02 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . O 7 -5.677 -12.994 -32.253 1 42.51 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . O 7 -6.533 -15.122 -31.084 1 62.51 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . O 7 -7.806 -15.762 -31.068 1 62.96 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . O 7 -8.647 -15.19 -29.938 1 47.84 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . O 7 -8.698 -13.776 -30.121 1 39.39 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . O 7 -10.07 -15.712 -30.014 1 33.26 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . O 7 -10.546 -16.039 -28.706 1 28.89 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . O 7 -10.886 -14.566 -30.569 1 37.56 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . O 7 -12.141 -14.475 -29.891 1 54.17 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . O 7 -10.041 -13.331 -30.308 1 35.94 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . O 7 -10.105 -12.394 -31.456 1 32.63 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . O 7 -9.49 -12.547 -32.644 1 33.3 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . O 7 -9.755 -11.501 -33.468 1 25.7 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . O 7 -10.556 -10.651 -32.797 1 36.5 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . O 7 -11.211 -9.35 -33.074 1 51.33 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . O 7 -11.068 -8.781 -34.178 1 55.07 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . O 7 -11.96 -8.804 -32.104 1 52.38 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . O 7 -12.132 -9.395 -30.906 1 48.06 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . O 7 -12.904 -8.78 -29.978 1 53.88 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . O 7 -11.562 -10.584 -30.586 1 44.78 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . O 7 -10.781 -11.245 -31.473 1 40.13 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 193 _model_server_stats.query_time_ms 415 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #