data_8V4M
#
_model_server_result.job_id            gpvaKzbobA3wble0D7HyLA 
_model_server_result.datetime_utc      '2025-03-06 23:17:59' 
_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":"N","auth_seq_id":502}' 
#
_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 . . . N 6 347.392 392.982 318.752 1 108.39 ? PG G2P 502 D 1 
HETATM 2 O O1G G2P . . . N 6 346.955 393.744 319.978 1 106.83 ? O1G G2P 502 D 1 
HETATM 3 O O2G G2P . . . N 6 347.321 391.487 318.936 1 102.79 ? O2G G2P 502 D 1 
HETATM 4 O O3G G2P . . . N 6 348.726 393.44 318.232 1 106.92 ? O3G G2P 502 D 1 
HETATM 5 O O3B G2P . . . N 6 346.317 393.331 317.602 1 102.75 ? O3B G2P 502 D 1 
HETATM 6 P PB G2P . . . N 6 346.106 392.799 316.119 1 98.99 ? PB G2P 502 D 1 
HETATM 7 O O1B G2P . . . N 6 347.237 393.271 315.251 1 104.48 ? O1B G2P 502 D 1 
HETATM 8 O O2B G2P . . . N 6 345.863 391.316 316.144 1 98.66 ? O2B G2P 502 D 1 
HETATM 9 C C3A G2P . . . N 6 344.591 393.607 315.522 1 97.64 ? C3A G2P 502 D 1 
HETATM 10 P PA G2P . . . N 6 343.144 393.3 316.576 1 110.73 ? PA G2P 502 D 1 
HETATM 11 O O1A G2P . . . N 6 342.745 391.861 316.397 1 107.8 ? O1A G2P 502 D 1 
HETATM 12 O O2A G2P . . . N 6 343.484 393.723 317.979 1 111.68 ? O2A G2P 502 D 1 
HETATM 13 O O5' G2P . . . N 6 341.997 394.245 316.022 1 100.84 ? O5' G2P 502 D 1 
HETATM 14 C C5' G2P . . . N 6 341.304 393.958 314.786 1 98.9 ? C5' G2P 502 D 1 
HETATM 15 C C4' G2P . . . N 6 340.257 395.014 314.542 1 100.64 ? C4' G2P 502 D 1 
HETATM 16 O O4' G2P . . . N 6 339.31 394.51 313.57 1 102.97 ? O4' G2P 502 D 1 
HETATM 17 C C3' G2P . . . N 6 339.372 395.373 315.737 1 105.32 ? C3' G2P 502 D 1 
HETATM 18 O O3' G2P . . . N 6 338.69 396.599 315.514 1 108.53 ? O3' G2P 502 D 1 
HETATM 19 C C2' G2P . . . N 6 338.402 394.191 315.734 1 108 ? C2' G2P 502 D 1 
HETATM 20 O O2' G2P . . . N 6 337.185 394.465 316.395 1 117.74 ? O2' G2P 502 D 1 
HETATM 21 C C1' G2P . . . N 6 338.202 393.949 314.238 1 104.84 ? C1' G2P 502 D 1 
HETATM 22 N N9 G2P . . . N 6 338.13 392.536 313.891 1 100 ? N9 G2P 502 D 1 
HETATM 23 C C8 G2P . . . N 6 338.61 391.485 314.629 1 98 ? C8 G2P 502 D 1 
HETATM 24 N N7 G2P . . . N 6 338.409 390.321 314.062 1 96.74 ? N7 G2P 502 D 1 
HETATM 25 C C5 G2P . . . N 6 337.766 390.629 312.87 1 96.06 ? C5 G2P 502 D 1 
HETATM 26 C C6 G2P . . . N 6 337.305 389.776 311.839 1 95.94 ? C6 G2P 502 D 1 
HETATM 27 O O6 G2P . . . N 6 337.374 388.541 311.778 1 97.34 ? O6 G2P 502 D 1 
HETATM 28 N N1 G2P . . . N 6 336.71 390.503 310.809 1 97.79 ? N1 G2P 502 D 1 
HETATM 29 C C2 G2P . . . N 6 336.578 391.869 310.771 1 100.58 ? C2 G2P 502 D 1 
HETATM 30 N N2 G2P . . . N 6 335.978 392.386 309.691 1 103.13 ? N2 G2P 502 D 1 
HETATM 31 N N3 G2P . . . N 6 337.012 392.677 311.738 1 100.86 ? N3 G2P 502 D 1 
HETATM 32 C C4 G2P . . . N 6 337.592 391.99 312.751 1 99.05 ? C4 G2P 502 D 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           32 
#