data_7Z6S # _model_server_result.job_id lLco3XV_J8PHhLkmbcpizA _model_server_result.datetime_utc '2024-12-26 14:47:39' _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 7z6s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 7Z6S # _exptl.entry_id 7Z6S _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 ? _pdbx_struct_assembly.oligomeric_details Hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 I N N ? 6 J 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 covale ? covale1 D N VAL 446 K VAL 440 1_555 E C ARG 259 C ARG 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.283 ? covale ? covale2 D N VAL 446 K VAL 440 1_555 E N PRO 260 C PRO 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.207 ? metalc ? metalc1 A OE2 GLU 77 A GLU 71 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc2 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? metalc ? metalc3 G O3G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc4 G O3B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc5 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc6 D OE2 GLU 77 K GLU 71 1_555 L MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc7 K O2G GTP . K GTP 501 1_555 L MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? metalc ? metalc8 K O3G GTP . K GTP 501 1_555 L MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc9 K O3B GTP . K GTP 501 1_555 L MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc10 K O1B GTP . K GTP 501 1_555 L MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc11 E NE2 HIS 280 C HIS 280 1_555 M ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc12 E NE2 HIS 285 C HIS 285 1_555 M ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc13 E OE1 GLU 316 C GLU 316 1_555 M ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc14 F NE2 HIS 280 E HIS 280 1_555 N ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc15 F NE2 HIS 285 E HIS 285 1_555 N ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc16 F OE1 GLU 316 E GLU 316 1_555 N ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? # _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 7Z6S _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 G 4 GTP A 1 501 501 GTP GTP . H 5 MG A 1 502 502 MG MG . I 6 GDP B 1 501 501 GDP GDP . J 6 GDP H 1 501 501 GDP GDP . K 4 GTP K 1 501 501 GTP GTP . L 5 MG K 1 502 502 MG MG . M 7 ZN C 1 501 1 ZN ZN . N 7 ZN E 1 501 1 ZN ZN . # 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 . . . J 6 183.494 190.122 181.64 1 88.65 ? PB GDP 501 H 1 HETATM 2 O O1B GDP . . . J 6 182.652 189.129 180.884 1 88.65 ? O1B GDP 501 H 1 HETATM 3 O O2B GDP . . . J 6 184.879 190.135 181.05 1 88.65 ? O2B GDP 501 H 1 HETATM 4 O O3B GDP . . . J 6 183.515 189.725 183.091 1 88.65 ? O3B GDP 501 H 1 HETATM 5 O O3A GDP . . . J 6 182.834 191.574 181.493 1 88.65 ? O3A GDP 501 H 1 HETATM 6 P PA GDP . . . J 6 183.097 192.737 182.568 1 88.65 ? PA GDP 501 H 1 HETATM 7 O O1A GDP . . . J 6 183.667 193.952 181.886 1 88.65 ? O1A GDP 501 H 1 HETATM 8 O O2A GDP . . . J 6 184.017 192.287 183.673 1 88.65 ? O2A GDP 501 H 1 HETATM 9 O O5' GDP . . . J 6 181.623 193.062 183.117 1 88.65 ? O5' GDP 501 H 1 HETATM 10 C C5' GDP . . . J 6 180.948 194.234 182.672 1 88.65 ? C5' GDP 501 H 1 HETATM 11 C C4' GDP . . . J 6 180.124 194.825 183.804 1 88.65 ? C4' GDP 501 H 1 HETATM 12 O O4' GDP . . . J 6 181.012 195.445 184.727 1 88.65 ? O4' GDP 501 H 1 HETATM 13 C C3' GDP . . . J 6 179.184 195.903 183.304 1 88.65 ? C3' GDP 501 H 1 HETATM 14 O O3' GDP . . . J 6 177.846 195.567 183.669 1 88.65 ? O3' GDP 501 H 1 HETATM 15 C C2' GDP . . . J 6 179.578 197.176 184.012 1 88.65 ? C2' GDP 501 H 1 HETATM 16 O O2' GDP . . . J 6 178.421 197.72 184.642 1 88.65 ? O2' GDP 501 H 1 HETATM 17 C C1' GDP . . . J 6 180.571 196.754 185.069 1 88.65 ? C1' GDP 501 H 1 HETATM 18 N N9 GDP . . . J 6 181.752 197.638 185.1 1 88.65 ? N9 GDP 501 H 1 HETATM 19 C C8 GDP . . . J 6 182.717 197.687 184.177 1 88.65 ? C8 GDP 501 H 1 HETATM 20 N N7 GDP . . . J 6 183.67 198.589 184.519 1 88.65 ? N7 GDP 501 H 1 HETATM 21 C C5 GDP . . . J 6 183.314 199.124 185.693 1 88.65 ? C5 GDP 501 H 1 HETATM 22 C C6 GDP . . . J 6 183.868 200.13 186.615 1 88.65 ? C6 GDP 501 H 1 HETATM 23 O O6 GDP . . . J 6 184.934 200.717 186.361 1 88.65 ? O6 GDP 501 H 1 HETATM 24 N N1 GDP . . . J 6 183.193 200.401 187.727 1 88.65 ? N1 GDP 501 H 1 HETATM 25 C C2 GDP . . . J 6 182.04 199.786 188.021 1 88.65 ? C2 GDP 501 H 1 HETATM 26 N N2 GDP . . . J 6 181.407 200.111 189.17 1 88.65 ? N2 GDP 501 H 1 HETATM 27 N N3 GDP . . . J 6 181.474 198.853 187.225 1 88.65 ? N3 GDP 501 H 1 HETATM 28 C C4 GDP . . . J 6 182.056 198.489 186.069 1 88.65 ? C4 GDP 501 H 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #