data_6HZ7 # _model_server_result.job_id OBMe2GSuzA2UgbQ3rlUA7A _model_server_result.datetime_utc '2025-03-06 08:42:15' _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 6hz7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":1001}' # _entry.id 6HZ7 # _exptl.entry_id 6HZ7 _exptl.method 'ELECTRON MICROSCOPY' # _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 6 _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 90 _cell.entry_id 6HZ7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HZ7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetradecameric _pdbx_struct_assembly.oligomeric_count 14 _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,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA _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 ? 5 U N N ? 5 V N N ? 5 W N N ? 5 DA N N ? 5 EA N N ? 5 FA 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 A OG1 THR 47 A THR 208 1_555 P MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc2 O O3G GNP . A GNP 1001 1_555 P MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc3 O O1B GNP . A GNP 1001 1_555 P MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc4 B OG1 THR 47 B THR 208 1_555 R MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc5 Q O3G GNP . B GNP 1001 1_555 R MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc6 Q O2B GNP . B GNP 1001 1_555 R MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc7 C OG1 THR 47 C THR 208 1_555 T MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc8 S O3G GNP . C GNP 1001 1_555 T MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc9 S O2B GNP . C GNP 1001 1_555 T MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc10 S O2A GNP . C GNP 1001 1_555 T MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc11 H OG1 THR 47 G THR 208 1_555 Y MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc12 X O3G GNP . G GNP 1001 1_555 Y MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc13 X O1B GNP . G GNP 1001 1_555 Y MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc14 I OG1 THR 47 H THR 208 1_555 AA MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc15 Z O3G GNP . H GNP 1001 1_555 AA MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc16 Z O2B GNP . H GNP 1001 1_555 AA MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc17 J OG1 THR 47 I THR 208 1_555 CA MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc18 BA O3G GNP . I GNP 1001 1_555 CA MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc19 BA O2B GNP . I GNP 1001 1_555 CA MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc20 BA O2A GNP . I GNP 1001 1_555 CA MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? # _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 6HZ7 _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 O 3 GNP A 1 1001 1001 GNP GNP . P 4 MG A 1 1002 1002 MG MG . Q 3 GNP B 1 1001 1001 GNP GNP . R 4 MG B 1 1002 1002 MG MG . S 3 GNP C 1 1001 1001 GNP GNP . T 4 MG C 1 1002 1002 MG MG . U 5 GDP D 1 1001 1001 GDP GDP . V 5 GDP E 1 1001 1001 GDP GDP . W 5 GDP F 1 1001 1001 GDP GDP . X 3 GNP G 1 1001 1001 GNP GNP . Y 4 MG G 1 1002 1002 MG MG . Z 3 GNP H 1 1001 1001 GNP GNP . AA 4 MG H 1 1002 1002 MG MG . BA 3 GNP I 1 1001 1001 GNP GNP . CA 4 MG I 1 1002 1002 MG MG . DA 5 GDP J 1 1001 1001 GDP GDP . EA 5 GDP K 1 1001 1001 GDP GDP . FA 5 GDP L 1 1001 1001 GDP GDP . # 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 . . . V 5 92.759 112.105 156.57 1 153.66 ? PB GDP 1001 E 1 HETATM 2 O O1B GDP . . . V 5 93.085 110.893 155.786 1 153.66 ? O1B GDP 1001 E 1 HETATM 3 O O2B GDP . . . V 5 93.554 113.247 156.065 1 153.66 ? O2B GDP 1001 E 1 HETATM 4 O O3B GDP . . . V 5 91.317 112.404 156.435 1 153.66 ? O3B GDP 1001 E 1 HETATM 5 O O3A GDP . . . V 5 93.107 111.859 158.118 1 153.66 ? O3A GDP 1001 E 1 HETATM 6 P PA GDP . . . V 5 92.957 113.097 159.122 1 153.66 ? PA GDP 1001 E 1 HETATM 7 O O1A GDP . . . V 5 93.718 114.247 158.586 1 153.66 ? O1A GDP 1001 E 1 HETATM 8 O O2A GDP . . . V 5 91.528 113.464 159.232 1 153.66 ? O2A GDP 1001 E 1 HETATM 9 O O5' GDP . . . V 5 93.53 112.725 160.592 1 153.66 ? O5' GDP 1001 E 1 HETATM 10 C C5' GDP . . . V 5 92.763 111.972 161.541 1 153.66 ? C5' GDP 1001 E 1 HETATM 11 C C4' GDP . . . V 5 93.707 111.343 162.595 1 153.66 ? C4' GDP 1001 E 1 HETATM 12 O O4' GDP . . . V 5 94.536 112.376 163.266 1 153.66 ? O4' GDP 1001 E 1 HETATM 13 C C3' GDP . . . V 5 92.98 110.681 163.751 1 153.66 ? C3' GDP 1001 E 1 HETATM 14 O O3' GDP . . . V 5 93.881 109.774 164.429 1 153.66 ? O3' GDP 1001 E 1 HETATM 15 C C2' GDP . . . V 5 92.676 111.893 164.608 1 153.66 ? C2' GDP 1001 E 1 HETATM 16 O O2' GDP . . . V 5 92.219 111.524 165.92 1 153.66 ? O2' GDP 1001 E 1 HETATM 17 C C1' GDP . . . V 5 94.056 112.509 164.657 1 153.66 ? C1' GDP 1001 E 1 HETATM 18 N N9 GDP . . . V 5 94.015 113.892 165.173 1 153.66 ? N9 GDP 1001 E 1 HETATM 19 C C8 GDP . . . V 5 94.061 115.068 164.562 1 153.66 ? C8 GDP 1001 E 1 HETATM 20 N N7 GDP . . . V 5 93.977 116.014 165.494 1 153.66 ? N7 GDP 1001 E 1 HETATM 21 C C5 GDP . . . V 5 93.854 115.419 166.676 1 153.66 ? C5 GDP 1001 E 1 HETATM 22 C C6 GDP . . . V 5 93.729 115.905 167.907 1 153.66 ? C6 GDP 1001 E 1 HETATM 23 O O6 GDP . . . V 5 93.71 117.118 168.102 1 153.66 ? O6 GDP 1001 E 1 HETATM 24 N N1 GDP . . . V 5 93.616 115.021 168.987 1 153.66 ? N1 GDP 1001 E 1 HETATM 25 C C2 GDP . . . V 5 93.641 113.65 168.733 1 153.66 ? C2 GDP 1001 E 1 HETATM 26 N N2 GDP . . . V 5 93.54 112.754 169.71 1 153.66 ? N2 GDP 1001 E 1 HETATM 27 N N3 GDP . . . V 5 93.763 113.234 167.474 1 153.66 ? N3 GDP 1001 E 1 HETATM 28 C C4 GDP . . . V 5 93.88 114.106 166.47 1 153.66 ? C4 GDP 1001 E 1 HETATM 29 H H5' GDP . . . V 5 92.248 111.171 161.014 1 153.66 ? H5' GDP 1001 E 1 HETATM 30 H "H5''" GDP . . . V 5 92.026 112.635 161.957 1 153.66 ? "H5''" GDP 1001 E 1 HETATM 31 H H4' GDP . . . V 5 94.294 110.61 162.051 1 153.66 ? H4' GDP 1001 E 1 HETATM 32 H H3' GDP . . . V 5 92.092 110.142 163.435 1 153.66 ? H3' GDP 1001 E 1 HETATM 33 H HO3' GDP . . . V 5 94.833 110.073 164.351 1 153.66 ? HO3' GDP 1001 E 1 HETATM 34 H H2' GDP . . . V 5 91.98 112.565 164.142 1 153.66 ? H2' GDP 1001 E 1 HETATM 35 H HO2' GDP . . . V 5 92.884 110.911 166.349 1 153.66 ? HO2' GDP 1001 E 1 HETATM 36 H H1' GDP . . . V 5 94.692 111.922 165.313 1 153.66 ? H1' GDP 1001 E 1 HETATM 37 H H8 GDP . . . V 5 94.183 115.227 163.496 1 153.66 ? H8 GDP 1001 E 1 HETATM 38 H HN1 GDP . . . V 5 93.52 115.364 169.92 1 153.66 ? HN1 GDP 1001 E 1 HETATM 39 H HN21 GDP . . . V 5 93.436 113.052 170.658 1 153.66 ? HN21 GDP 1001 E 1 HETATM 40 H HN22 GDP . . . V 5 93.569 111.778 169.491 1 153.66 ? HN22 GDP 1001 E 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 67 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #