data_7M6J # _model_server_result.job_id 440Tv4QBcLUQja5RRJXZcw _model_server_result.datetime_utc '2024-11-14 21:18:20' _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 7m6j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 7M6J # _exptl.entry_id 7M6J _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7M6J _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7M6J _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 ? _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 _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 ? 4 G N N ? 4 I N N ? 4 J N N ? 4 M 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 disulf ? disulf1 A SG CYS 78 A CYS 111 1_555 A SG CYS 81 A CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 F SG CYS 78 F CYS 111 1_555 F SG CYS 81 F CYS 114 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 E OG SER 56 E SER 56 1_555 K MG MG . E MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc2 K MG MG . E MG 501 1_555 L O1G GTP . E GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc3 K MG MG . E MG 501 1_555 L O3G GTP . E GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc4 K MG MG . E MG 501 1_555 L O1B GTP . E GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? # _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 7M6J _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 GDP A 1 401 401 GDP GDP . H 5 GTP B 1 501 431 GTP GTP . I 4 GDP C 1 501 448 GDP GDP . J 4 GDP D 1 501 449 GDP GDP . K 6 MG E 1 501 501 MG MG . L 5 GTP E 1 502 500 GTP GTP . M 4 GDP F 1 401 401 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 . . . I 4 205.86 218.469 194.163 1 127.46 ? PB GDP 501 C 1 HETATM 2 O O1B GDP . . . I 4 205.874 219.302 192.908 1 127.46 ? O1B GDP 501 C 1 HETATM 3 O O2B GDP . . . I 4 207.217 218.509 194.817 1 127.46 ? O2B GDP 501 C 1 HETATM 4 O O3B GDP . . . I 4 205.512 217.043 193.821 1 127.46 ? O3B GDP 501 C 1 HETATM 5 O O3A GDP . . . I 4 204.76 219.06 195.171 1 127.46 ? O3A GDP 501 C 1 HETATM 6 P PA GDP . . . I 4 203.258 219.325 194.661 1 127.46 ? PA GDP 501 C 1 HETATM 7 O O1A GDP . . . I 4 203.226 220.462 193.67 1 127.46 ? O1A GDP 501 C 1 HETATM 8 O O2A GDP . . . I 4 202.67 218.069 194.067 1 127.46 ? O2A GDP 501 C 1 HETATM 9 O O5' GDP . . . I 4 202.493 219.735 196.012 1 127.46 ? O5' GDP 501 C 1 HETATM 10 C C5' GDP . . . I 4 201.276 220.476 195.992 1 127.46 ? C5' GDP 501 C 1 HETATM 11 C C4' GDP . . . I 4 201.208 221.222 197.316 1 127.46 ? C4' GDP 501 C 1 HETATM 12 O O4' GDP . . . I 4 202.524 221.686 197.611 1 127.46 ? O4' GDP 501 C 1 HETATM 13 C C3' GDP . . . I 4 200.305 222.441 197.254 1 127.46 ? C3' GDP 501 C 1 HETATM 14 O O3' GDP . . . I 4 199.181 222.256 198.119 1 127.46 ? O3' GDP 501 C 1 HETATM 15 C C2' GDP . . . I 4 201.14 223.605 197.747 1 127.46 ? C2' GDP 501 C 1 HETATM 16 O O2' GDP . . . I 4 200.57 224.122 198.951 1 127.46 ? O2' GDP 501 C 1 HETATM 17 C C1' GDP . . . I 4 202.53 223.052 198.02 1 127.46 ? C1' GDP 501 C 1 HETATM 18 N N9 GDP . . . I 4 203.534 223.772 197.202 1 127.46 ? N9 GDP 501 C 1 HETATM 19 C C8 GDP . . . I 4 203.286 224.77 196.333 1 127.46 ? C8 GDP 501 C 1 HETATM 20 N N7 GDP . . . I 4 204.429 225.197 195.738 1 127.46 ? N7 GDP 501 C 1 HETATM 21 C C5 GDP . . . I 4 205.435 224.446 196.219 1 127.46 ? C5 GDP 501 C 1 HETATM 22 C C6 GDP . . . I 4 206.898 224.363 196.011 1 127.46 ? C6 GDP 501 C 1 HETATM 23 O O6 GDP . . . I 4 207.479 225.128 195.212 1 127.46 ? O6 GDP 501 C 1 HETATM 24 N N1 GDP . . . I 4 207.574 223.444 196.707 1 127.46 ? N1 GDP 501 C 1 HETATM 25 C C2 GDP . . . I 4 206.977 222.607 197.574 1 127.46 ? C2 GDP 501 C 1 HETATM 26 N N2 GDP . . . I 4 207.743 221.707 198.236 1 127.46 ? N2 GDP 501 C 1 HETATM 27 N N3 GDP . . . I 4 205.643 222.625 197.813 1 127.46 ? N3 GDP 501 C 1 HETATM 28 C C4 GDP . . . I 4 204.839 223.506 197.177 1 127.46 ? C4 GDP 501 C 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 72 _model_server_stats.create_model_time_ms 96 _model_server_stats.query_time_ms 1282 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 28 #