data_3BB4
#
_model_server_result.job_id            OLqxiM9BsDOFu4TJcR5V2Q 
_model_server_result.datetime_utc      '2025-03-09 04:34:05' 
_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          3bb4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":264}' 
#
_entry.id    3BB4 
#
_exptl.entry_id    3BB4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 
_entity.pdbx_number_of_molecules    1 
_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            3BB4 
_cell.length_a            121.567 
_cell.length_b            121.567 
_cell.length_c            42.879 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3BB4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
metalc ? metalc1 A OG SER 50 A SER 50 1_555 B MG MG . A MG 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc2 B MG MG . A MG 263 1_555 C O2B GNP . A GNP 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc3 B MG MG . A MG 263 1_555 C O2G GNP . A GNP 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc4 B MG MG . A MG 263 1_555 D O HOH . A HOH 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc5 B MG MG . A MG 263 1_555 D O HOH . A HOH 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc6 B MG MG . A MG 263 1_555 D O HOH . A HOH 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
#
_chem_comp.formula           'C10 H17 N6 O13 P3' 
_chem_comp.formula_weight    522.196 
_chem_comp.id                GNP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC 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 GNP doub 129 n n 
PG O2G GNP sing 130 n n 
PG O3G GNP sing 131 n n 
PG N3B GNP sing 132 n n 
O2G HOG2 GNP sing 133 n n 
O3G HOG3 GNP sing 134 n n 
N3B PB GNP sing 135 n n 
N3B HNB3 GNP sing 136 n n 
PB O1B GNP doub 137 n n 
PB O2B GNP sing 138 n n 
PB O3A GNP sing 139 n n 
O2B HOB2 GNP sing 140 n n 
O3A PA GNP sing 141 n n 
PA O1A GNP doub 142 n n 
PA O2A GNP sing 143 n n 
PA O5' GNP sing 144 n n 
O2A HOA2 GNP sing 145 n n 
O5' C5' GNP sing 146 n n 
C5' C4' GNP sing 147 n n 
C5' "H5'2" GNP sing 148 n n 
C5' "H5'1" GNP sing 149 n n 
C4' O4' GNP sing 150 n n 
C4' C3' GNP sing 151 n n 
C4' H4' GNP sing 152 n n 
O4' C1' GNP sing 153 n n 
C3' O3' GNP sing 154 n n 
C3' C2' GNP sing 155 n n 
C3' H3' GNP sing 156 n n 
O3' HO3' GNP sing 157 n n 
C2' O2' GNP sing 158 n n 
C2' C1' GNP sing 159 n n 
C2' H2' GNP sing 160 n n 
O2' HO2' GNP sing 161 n n 
C1' N9 GNP sing 162 n n 
C1' H1' GNP sing 163 n n 
N9 C8 GNP sing 164 n y 
N9 C4 GNP sing 165 n y 
C8 N7 GNP doub 166 n y 
C8 H8 GNP sing 167 n n 
N7 C5 GNP sing 168 n y 
C5 C6 GNP sing 169 n y 
C5 C4 GNP doub 170 n y 
C6 O6 GNP doub 171 n n 
C6 N1 GNP sing 172 n y 
N1 C2 GNP sing 173 n y 
N1 HN1 GNP sing 174 n n 
C2 N2 GNP sing 175 n n 
C2 N3 GNP doub 176 n y 
N2 HN21 GNP sing 177 n n 
N2 HN22 GNP sing 178 n n 
N3 C4 GNP sing 179 n y 
#
_atom_sites.entry_id                     3BB4 
_atom_sites.fract_transf_matrix[1][1]    0.008226 
_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]    0.008226 
_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]    0.023321 
_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
B 2 MG A 1 263 261 MG MG . 
C 3 GNP A 1 264 260 GNP GNP . 
D 4 HOH A 1 265 262 HOH WAT . 
D 4 HOH A 2 266 263 HOH WAT . 
D 4 HOH A 3 267 264 HOH WAT . 
D 4 HOH A 4 268 1 HOH WAT . 
D 4 HOH A 5 269 2 HOH WAT . 
D 4 HOH A 6 270 3 HOH WAT . 
D 4 HOH A 7 271 4 HOH WAT . 
D 4 HOH A 8 272 5 HOH WAT . 
D 4 HOH A 9 273 6 HOH WAT . 
D 4 HOH A 10 274 7 HOH WAT . 
D 4 HOH A 11 275 8 HOH WAT . 
D 4 HOH A 12 276 9 HOH WAT . 
D 4 HOH A 13 277 10 HOH WAT . 
D 4 HOH A 14 278 11 HOH WAT . 
D 4 HOH A 15 279 12 HOH WAT . 
D 4 HOH A 16 280 13 HOH WAT . 
D 4 HOH A 17 281 14 HOH WAT . 
D 4 HOH A 18 282 15 HOH WAT . 
D 4 HOH A 19 283 16 HOH WAT . 
D 4 HOH A 20 284 17 HOH WAT . 
D 4 HOH A 21 285 18 HOH WAT . 
D 4 HOH A 22 286 19 HOH WAT . 
D 4 HOH A 23 287 20 HOH WAT . 
D 4 HOH A 24 288 21 HOH WAT . 
D 4 HOH A 25 289 22 HOH WAT . 
D 4 HOH A 26 290 23 HOH WAT . 
D 4 HOH A 27 291 24 HOH WAT . 
#
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 GNP . . . C 3 39.599 14.795 15.348 1 84.09 ? PG GNP 264 A 1 
HETATM 2 O O1G GNP . . . C 3 38.977 13.469 15.738 1 82.42 ? O1G GNP 264 A 1 
HETATM 3 O O2G GNP . . . C 3 39.055 16.049 15.938 1 83.8 ? O2G GNP 264 A 1 
HETATM 4 O O3G GNP . . . C 3 39.534 15.031 13.878 1 89.4 ? O3G GNP 264 A 1 
HETATM 5 N N3B GNP . . . C 3 41.218 14.847 15.88 1 83.2 ? N3B GNP 264 A 1 
HETATM 6 P PB GNP . . . C 3 42.252 15.932 15.174 1 81.11 ? PB GNP 264 A 1 
HETATM 7 O O1B GNP . . . C 3 42.6 15.385 13.838 1 77.91 ? O1B GNP 264 A 1 
HETATM 8 O O2B GNP . . . C 3 41.609 17.3 15.368 1 80.93 ? O2B GNP 264 A 1 
HETATM 9 O O3A GNP . . . C 3 43.605 15.981 16.093 1 81.1 ? O3A GNP 264 A 1 
HETATM 10 P PA GNP . . . C 3 43.801 16.84 17.485 1 77.08 ? PA GNP 264 A 1 
HETATM 11 O O1A GNP . . . C 3 44.442 18.175 17.228 1 77.38 ? O1A GNP 264 A 1 
HETATM 12 O O2A GNP . . . C 3 42.494 16.834 18.142 1 78.15 ? O2A GNP 264 A 1 
HETATM 13 O O5' GNP . . . C 3 44.885 15.981 18.249 1 75.61 ? O5' GNP 264 A 1 
HETATM 14 C C5' GNP . . . C 3 44.713 14.719 18.926 1 75.66 ? C5' GNP 264 A 1 
HETATM 15 C C4' GNP . . . C 3 45.781 14.61 20.013 1 75.9 ? C4' GNP 264 A 1 
HETATM 16 O O4' GNP . . . C 3 47.053 14.592 19.291 1 77.43 ? O4' GNP 264 A 1 
HETATM 17 C C3' GNP . . . C 3 45.95 15.735 21.062 1 76.02 ? C3' GNP 264 A 1 
HETATM 18 O O3' GNP . . . C 3 46.211 15.143 22.368 1 76.22 ? O3' GNP 264 A 1 
HETATM 19 C C2' GNP . . . C 3 47.107 16.579 20.525 1 76.04 ? C2' GNP 264 A 1 
HETATM 20 O O2' GNP . . . C 3 47.935 17.326 21.416 1 74.72 ? O2' GNP 264 A 1 
HETATM 21 C C1' GNP . . . C 3 47.999 15.542 19.795 1 76.06 ? C1' GNP 264 A 1 
HETATM 22 N N9 GNP . . . C 3 48.809 16.089 18.702 1 75.6 ? N9 GNP 264 A 1 
HETATM 23 C C8 GNP . . . C 3 48.359 16.742 17.576 1 75.24 ? C8 GNP 264 A 1 
HETATM 24 N N7 GNP . . . C 3 49.301 17.143 16.77 1 74.86 ? N7 GNP 264 A 1 
HETATM 25 C C5 GNP . . . C 3 50.441 16.709 17.423 1 74.51 ? C5 GNP 264 A 1 
HETATM 26 C C6 GNP . . . C 3 51.794 16.872 17.011 1 75.27 ? C6 GNP 264 A 1 
HETATM 27 O O6 GNP . . . C 3 52.279 17.399 16.019 1 76.08 ? O6 GNP 264 A 1 
HETATM 28 N N1 GNP . . . C 3 52.68 16.332 17.946 1 76.02 ? N1 GNP 264 A 1 
HETATM 29 C C2 GNP . . . C 3 52.352 15.708 19.096 1 74.29 ? C2 GNP 264 A 1 
HETATM 30 N N2 GNP . . . C 3 53.421 15.29 19.753 1 73.82 ? N2 GNP 264 A 1 
HETATM 31 N N3 GNP . . . C 3 51.087 15.531 19.494 1 75.06 ? N3 GNP 264 A 1 
HETATM 32 C C4 GNP . . . C 3 50.181 16.07 18.596 1 75.09 ? C4 GNP 264 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#