data_8V4M # _model_server_result.job_id UjA8HzZylT2WOVNBNhLkpw _model_server_result.datetime_utc '2025-03-06 23:13:38' _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 8v4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":602}' # _entry.id 8V4M # _exptl.entry_id 8V4M _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 521.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 8V4M _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8V4M _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,N,O _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 I N N ? 6 N 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 B CD GLU 448 B GLU 503 1_555 J N GLU . B GLU 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? metalc ? metalc1 A OE2 GLU 71 A GLU 71 1_555 F MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? metalc ? metalc2 F MG MG . A MG 501 1_555 G O3G GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc3 F MG MG . A MG 501 1_555 G O2B GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc4 B OE2 GLU 69 B GLU 69 1_555 H MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc5 B OE1 GLU 448 B GLU 503 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc6 H MG MG . B MG 601 1_555 I O2G G2P . B G2P 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc7 C OE2 GLU 71 C GLU 71 1_555 K MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc8 K MG MG . C MG 501 1_555 L O2B GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc9 K MG MG . C MG 501 1_555 L O3G GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc10 K MG MG . C MG 501 1_555 L O2G GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc11 M MG MG . D MG 501 1_555 N O2B G2P . D G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc12 M MG MG . D MG 501 1_555 N O2G G2P . D G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc13 E ND1 HIS 252 E HIS 252 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc14 E OE1 GLU 255 E GLU 255 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc15 E OE2 GLU 255 E GLU 255 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc16 E ND1 HIS 434 E HIS 434 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? # _chem_comp.formula 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id G2P _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _chem_comp.type non-polymer _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 PG O1G G2P sing 83 n n PG O2G G2P doub 84 n n PG O3G G2P sing 85 n n PG O3B G2P sing 86 n n O3B PB G2P sing 87 n n PB O1B G2P sing 88 n n PB O2B G2P doub 89 n n PB C3A G2P sing 90 n n C3A PA G2P sing 91 n n C3A H3A1 G2P sing 92 n n C3A H3A2 G2P sing 93 n n PA O1A G2P sing 94 n n PA O2A G2P doub 95 n n PA O5' G2P sing 96 n n O5' C5' G2P sing 97 n n C5' C4' G2P sing 98 n n C5' "H5'1" G2P sing 99 n n C5' "H5'2" G2P sing 100 n n C4' O4' G2P sing 101 n n C4' C3' G2P sing 102 n n C4' H4' G2P sing 103 n n O4' C1' G2P sing 104 n n C3' O3' G2P sing 105 n n C3' C2' G2P sing 106 n n C3' H3' G2P sing 107 n n O3' HA G2P sing 108 n n C2' O2' G2P sing 109 n n C2' C1' G2P sing 110 n n C2' H2' G2P sing 111 n n O2' HB G2P sing 112 n n C1' N9 G2P sing 113 n n C1' H1' G2P sing 114 n n N9 C8 G2P sing 115 n y N9 C4 G2P sing 116 n y C8 N7 G2P doub 117 n y C8 H8 G2P sing 118 n n N7 C5 G2P sing 119 n y C5 C6 G2P sing 120 n y C5 C4 G2P doub 121 n y C6 O6 G2P doub 122 n n C6 N1 G2P sing 123 n y N1 C2 G2P sing 124 n y N1 H1 G2P sing 125 n n C2 N2 G2P sing 126 n n C2 N3 G2P doub 127 n y N2 H2N1 G2P sing 128 n n N2 H2N2 G2P sing 129 n n N3 C4 G2P sing 130 n y HO1 O1G G2P sing 131 n n HO2 O3G G2P sing 132 n n HO3 O1A G2P sing 133 n n HO4 O1B G2P sing 134 n n # _atom_sites.entry_id 8V4M _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 MG A 1 501 502 MG MG . G 5 GTP A 1 502 503 GTP GTP . H 4 MG B 1 601 502 MG MG . I 6 G2P B 1 602 503 G2P G2P . J 7 GLU B 1 1001 3 GLU GLX . K 4 MG C 1 501 502 MG MG . L 5 GTP C 1 502 503 GTP GTP . M 4 MG D 1 501 502 MG MG . N 6 G2P D 1 502 503 G2P G2P . O 8 ZN E 1 701 701 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 PG G2P . . . I 6 387.182 357.278 327.659 1 96.5 ? PG G2P 602 B 1 HETATM 2 O O1G G2P . . . I 6 386.779 357.733 329.039 1 94.53 ? O1G G2P 602 B 1 HETATM 3 O O2G G2P . . . I 6 386.9 355.816 327.419 1 98.7 ? O2G G2P 602 B 1 HETATM 4 O O3G G2P . . . I 6 388.594 357.665 327.31 1 92.98 ? O3G G2P 602 B 1 HETATM 5 O O3B G2P . . . I 6 386.241 358.083 326.629 1 89.37 ? O3B G2P 602 B 1 HETATM 6 P PB G2P . . . I 6 386.129 358.059 325.045 1 90.91 ? PB G2P 602 B 1 HETATM 7 O O1B G2P . . . I 6 387.474 358.332 324.431 1 94.96 ? O1B G2P 602 B 1 HETATM 8 O O2B G2P . . . I 6 385.447 356.79 324.616 1 86.17 ? O2B G2P 602 B 1 HETATM 9 C C3A G2P . . . I 6 385.04 359.455 324.63 1 87.82 ? C3A G2P 602 B 1 HETATM 10 P PA G2P . . . I 6 383.269 359.136 324.883 1 95.63 ? PA G2P 602 B 1 HETATM 11 O O1A G2P . . . I 6 382.794 358.275 323.747 1 92.65 ? O1A G2P 602 B 1 HETATM 12 O O2A G2P . . . I 6 383.095 358.562 326.262 1 97.39 ? O2A G2P 602 B 1 HETATM 13 O O5' G2P . . . I 6 382.566 360.558 324.813 1 87.24 ? O5' G2P 602 B 1 HETATM 14 C C5' G2P . . . I 6 383.061 361.619 323.961 1 83.91 ? C5' G2P 602 B 1 HETATM 15 C C4' G2P . . . I 6 381.951 362.599 323.67 1 87.73 ? C4' G2P 602 B 1 HETATM 16 O O4' G2P . . . I 6 380.978 361.957 322.805 1 88.04 ? O4' G2P 602 B 1 HETATM 17 C C3' G2P . . . I 6 381.155 363.108 324.882 1 96.91 ? C3' G2P 602 B 1 HETATM 18 O O3' G2P . . . I 6 380.865 364.493 324.746 1 100.65 ? O3' G2P 602 B 1 HETATM 19 C C2' G2P . . . I 6 379.873 362.275 324.818 1 95.27 ? C2' G2P 602 B 1 HETATM 20 O O2' G2P . . . I 6 378.772 362.881 325.459 1 101.89 ? O2' G2P 602 B 1 HETATM 21 C C1' G2P . . . I 6 379.684 362.178 323.31 1 87.32 ? C1' G2P 602 B 1 HETATM 22 N N9 G2P . . . I 6 378.838 361.067 322.898 1 83.17 ? N9 G2P 602 B 1 HETATM 23 C C8 G2P . . . I 6 378.581 359.925 323.613 1 83.63 ? C8 G2P 602 B 1 HETATM 24 N N7 G2P . . . I 6 377.787 359.092 322.988 1 83.45 ? N7 G2P 602 B 1 HETATM 25 C C5 G2P . . . I 6 377.511 359.722 321.781 1 81.02 ? C5 G2P 602 B 1 HETATM 26 C C6 G2P . . . I 6 376.709 359.296 320.695 1 81.13 ? C6 G2P 602 B 1 HETATM 27 O O6 G2P . . . I 6 376.062 358.246 320.585 1 82.37 ? O6 G2P 602 B 1 HETATM 28 N N1 G2P . . . I 6 376.7 360.241 319.669 1 81.63 ? N1 G2P 602 B 1 HETATM 29 C C2 G2P . . . I 6 377.376 361.436 319.683 1 83.3 ? C2 G2P 602 B 1 HETATM 30 N N2 G2P . . . I 6 377.245 362.21 318.598 1 85.91 ? N2 G2P 602 B 1 HETATM 31 N N3 G2P . . . I 6 378.134 361.841 320.702 1 85.16 ? N3 G2P 602 B 1 HETATM 32 C C4 G2P . . . I 6 378.155 360.938 321.712 1 83.14 ? C4 G2P 602 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #