data_8V4L
#
_model_server_result.job_id            o2F_lIc4P4difb2IZMjEDA 
_model_server_result.datetime_utc      '2024-11-22 13:36:51' 
_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          8v4l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":502}' 
#
_entry.id    8V4L 
#
_exptl.entry_id    8V4L 
_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            8V4L 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8V4L 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? 
metalc ? metalc1 F MG MG . A MG 501 1_555 G O3G GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc2 F MG MG . A MG 501 1_555 G O2B GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc3 B OE1 GLU 448 B GLU 503 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
metalc ? metalc4 H MG MG . B MG 601 1_555 I O2G G2P . B G2P 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc5 H MG MG . B MG 601 1_555 I O3B G2P . B G2P 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? 
metalc ? metalc6 C OE2 GLU 71 C GLU 71 1_555 K MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? 
metalc ? metalc7 K MG MG . C MG 501 1_555 L O2B GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc8 K MG MG . C MG 501 1_555 L O3G GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc9 K MG MG . C MG 501 1_555 L O2G GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
metalc ? metalc10 M MG MG . D MG 501 1_555 N O2B G2P . D G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? 
metalc ? metalc11 M MG MG . D MG 501 1_555 N O2G G2P . D G2P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc12 E ND1 HIS 252 E HIS 252 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc13 E OE2 GLU 255 E GLU 255 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? 
metalc ? metalc14 E ND1 HIS 434 E HIS 434 1_555 O ZN ZN . E ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
#
_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                     8V4L 
_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 6 347.278 393.018 318.725 1 121.26 ? PG G2P 502 D 1 
HETATM 2 O O1G G2P . . . N 6 346.797 393.705 319.979 1 117.14 ? O1G G2P 502 D 1 
HETATM 3 O O2G G2P . . . N 6 347.239 391.514 318.833 1 113.14 ? O2G G2P 502 D 1 
HETATM 4 O O3G G2P . . . N 6 348.614 393.531 318.26 1 114.17 ? O3G G2P 502 D 1 
HETATM 5 O O3B G2P . . . N 6 346.221 393.401 317.569 1 118.98 ? O3B G2P 502 D 1 
HETATM 6 P PB G2P . . . N 6 346.157 393.021 316.027 1 112.61 ? PB G2P 502 D 1 
HETATM 7 O O1B G2P . . . N 6 347.25 393.75 315.296 1 115.29 ? O1B G2P 502 D 1 
HETATM 8 O O2B G2P . . . N 6 346.154 391.525 315.889 1 105.88 ? O2B G2P 502 D 1 
HETATM 9 C C3A G2P . . . N 6 344.566 393.645 315.401 1 107.59 ? C3A G2P 502 D 1 
HETATM 10 P PA G2P . . . N 6 343.129 393.098 316.37 1 113.57 ? PA G2P 502 D 1 
HETATM 11 O O1A G2P . . . N 6 343.129 391.596 316.384 1 110.04 ? O1A G2P 502 D 1 
HETATM 12 O O2A G2P . . . N 6 343.191 393.773 317.713 1 122.55 ? O2A G2P 502 D 1 
HETATM 13 O O5' G2P . . . N 6 341.845 393.608 315.587 1 110.97 ? O5' G2P 502 D 1 
HETATM 14 C C5' G2P . . . N 6 341.678 394.994 315.202 1 108.34 ? C5' G2P 502 D 1 
HETATM 15 C C4' G2P . . . N 6 340.229 395.256 314.871 1 110.4 ? C4' G2P 502 D 1 
HETATM 16 O O4' G2P . . . N 6 339.737 394.186 314.022 1 108.79 ? O4' G2P 502 D 1 
HETATM 17 C C3' G2P . . . N 6 339.262 395.319 316.063 1 118.96 ? C3' G2P 502 D 1 
HETATM 18 O O3' G2P . . . N 6 338.288 396.335 315.866 1 123.06 ? O3' G2P 502 D 1 
HETATM 19 C C2' G2P . . . N 6 338.613 393.934 316.036 1 118.35 ? C2' G2P 502 D 1 
HETATM 20 O O2' G2P . . . N 6 337.356 393.889 316.675 1 125.36 ? O2' G2P 502 D 1 
HETATM 21 C C1' G2P . . . N 6 338.511 393.718 314.532 1 111.5 ? C1' G2P 502 D 1 
HETATM 22 N N9 G2P . . . N 6 338.353 392.323 314.148 1 108.08 ? N9 G2P 502 D 1 
HETATM 23 C C8 G2P . . . N 6 338.763 391.224 314.86 1 108.75 ? C8 G2P 502 D 1 
HETATM 24 N N7 G2P . . . N 6 338.486 390.09 314.265 1 108.25 ? N7 G2P 502 D 1 
HETATM 25 C C5 G2P . . . N 6 337.855 390.467 313.086 1 106.74 ? C5 G2P 502 D 1 
HETATM 26 C C6 G2P . . . N 6 337.332 389.67 312.039 1 106.66 ? C6 G2P 502 D 1 
HETATM 27 O O6 G2P . . . N 6 337.321 388.435 311.948 1 107.25 ? O6 G2P 502 D 1 
HETATM 28 N N1 G2P . . . N 6 336.777 390.458 311.03 1 107.18 ? N1 G2P 502 D 1 
HETATM 29 C C2 G2P . . . N 6 336.733 391.831 311.028 1 109.27 ? C2 G2P 502 D 1 
HETATM 30 N N2 G2P . . . N 6 336.157 392.411 309.966 1 107.03 ? N2 G2P 502 D 1 
HETATM 31 N N3 G2P . . . N 6 337.224 392.585 312.01 1 111.85 ? N3 G2P 502 D 1 
HETATM 32 C C4 G2P . . . N 6 337.767 391.839 313.002 1 108.71 ? C4 G2P 502 D 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#