data_6XJT
#
_model_server_result.job_id            svmH7vcYlC759k40F61aYQ 
_model_server_result.datetime_utc      '2024-10-31 18:16:23' 
_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          6xjt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    6XJT 
#
_exptl.entry_id    6XJT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          4 
_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            6XJT 
_cell.length_a            106.675 
_cell.length_b            106.675 
_cell.length_c            306.07 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XJT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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                      4 
_struct_asym.id                             D 
_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
covale ? covale1 C SG CYS 505 C CYS 539 1_555 F C3 6L8 . C 6L8 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.696 ? 
metalc ? metalc1 A OG1 THR 24 A THR 24 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc2 A OG1 THR 42 A THR 42 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc3 D O3G GNP . A GNP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc4 D O1B GNP . A GNP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.893 ? 
#
_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 173 n n 
PG O2G GNP sing 174 n n 
PG O3G GNP sing 175 n n 
PG N3B GNP sing 176 n n 
O2G HOG2 GNP sing 177 n n 
O3G HOG3 GNP sing 178 n n 
N3B PB GNP sing 179 n n 
N3B HNB3 GNP sing 180 n n 
PB O1B GNP doub 181 n n 
PB O2B GNP sing 182 n n 
PB O3A GNP sing 183 n n 
O2B HOB2 GNP sing 184 n n 
O3A PA GNP sing 185 n n 
PA O1A GNP doub 186 n n 
PA O2A GNP sing 187 n n 
PA O5' GNP sing 188 n n 
O2A HOA2 GNP sing 189 n n 
O5' C5' GNP sing 190 n n 
C5' C4' GNP sing 191 n n 
C5' "H5'2" GNP sing 192 n n 
C5' "H5'1" GNP sing 193 n n 
C4' O4' GNP sing 194 n n 
C4' C3' GNP sing 195 n n 
C4' H4' GNP sing 196 n n 
O4' C1' GNP sing 197 n n 
C3' O3' GNP sing 198 n n 
C3' C2' GNP sing 199 n n 
C3' H3' GNP sing 200 n n 
O3' HO3' GNP sing 201 n n 
C2' O2' GNP sing 202 n n 
C2' C1' GNP sing 203 n n 
C2' H2' GNP sing 204 n n 
O2' HO2' GNP sing 205 n n 
C1' N9 GNP sing 206 n n 
C1' H1' GNP sing 207 n n 
N9 C8 GNP sing 208 n y 
N9 C4 GNP sing 209 n y 
C8 N7 GNP doub 210 n y 
C8 H8 GNP sing 211 n n 
N7 C5 GNP sing 212 n y 
C5 C6 GNP sing 213 n y 
C5 C4 GNP doub 214 n y 
C6 O6 GNP doub 215 n n 
C6 N1 GNP sing 216 n y 
N1 C2 GNP sing 217 n y 
N1 HN1 GNP sing 218 n n 
C2 N2 GNP sing 219 n n 
C2 N3 GNP doub 220 n y 
N2 HN21 GNP sing 221 n n 
N2 HN22 GNP sing 222 n n 
N3 C4 GNP sing 223 n y 
#
_atom_sites.entry_id                     6XJT 
_atom_sites.fract_transf_matrix[1][1]    0.009374 
_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]    0.009374 
_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]    0.003267 
_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
D 4 GNP A 1 301 301 GNP GNP . 
E 5 MG A 1 302 302 MG MG . 
F 6 6L8 C 1 1101 1 6L8 860 . 
#
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 . . . D 4 59.958 -15.261 28.087 1 28.12 ? PG GNP 301 A 1 
HETATM 2 O O1G GNP . . . D 4 60.052 -16.639 27.453 1 28.55 ? O1G GNP 301 A 1 
HETATM 3 O O2G GNP . . . D 4 59.451 -15.412 29.535 1 27.86 ? O2G GNP 301 A 1 
HETATM 4 O O3G GNP . . . D 4 61.358 -14.596 28.094 1 28.25 ? O3G GNP 301 A 1 
HETATM 5 N N3B GNP . . . D 4 58.884 -14.308 27.189 1 27.38 ? N3B GNP 301 A 1 
HETATM 6 P PB GNP . . . D 4 58.221 -12.883 27.837 1 26.06 ? PB GNP 301 A 1 
HETATM 7 O O1B GNP . . . D 4 59.349 -11.917 28.265 1 26.04 ? O1B GNP 301 A 1 
HETATM 8 O O2B GNP . . . D 4 57.346 -13.21 29.023 1 25.28 ? O2B GNP 301 A 1 
HETATM 9 O O3A GNP . . . D 4 57.293 -12.153 26.65 1 26.17 ? O3A GNP 301 A 1 
HETATM 10 P PA GNP . . . D 4 57.907 -11.059 25.546 1 27.25 ? PA GNP 301 A 1 
HETATM 11 O O1A GNP . . . D 4 59.328 -11.43 25.214 1 27.86 ? O1A GNP 301 A 1 
HETATM 12 O O2A GNP . . . D 4 57.882 -9.658 26.154 1 26.67 ? O2A GNP 301 A 1 
HETATM 13 O O5' GNP . . . D 4 56.979 -11.086 24.137 1 28.61 ? O5' GNP 301 A 1 
HETATM 14 C C5' GNP . . . D 4 56.075 -12.137 23.936 1 28.9 ? C5' GNP 301 A 1 
HETATM 15 C C4' GNP . . . D 4 54.961 -11.706 22.998 1 29.67 ? C4' GNP 301 A 1 
HETATM 16 O O4' GNP . . . D 4 54.017 -11.075 23.682 1 29.55 ? O4' GNP 301 A 1 
HETATM 17 C C3' GNP . . . D 4 55.472 -10.708 21.942 1 31.24 ? C3' GNP 301 A 1 
HETATM 18 O O3' GNP . . . D 4 55.032 -11.063 20.712 1 32.14 ? O3' GNP 301 A 1 
HETATM 19 C C2' GNP . . . D 4 54.855 -9.348 22.36 1 31.46 ? C2' GNP 301 A 1 
HETATM 20 O O2' GNP . . . D 4 54.615 -8.475 21.136 1 32.37 ? O2' GNP 301 A 1 
HETATM 21 C C1' GNP . . . D 4 53.72 -9.685 22.92 1 30.45 ? C1' GNP 301 A 1 
HETATM 22 N N9 GNP . . . D 4 53.278 -8.702 23.872 1 29.75 ? N9 GNP 301 A 1 
HETATM 23 C C8 GNP . . . D 4 53.868 -8.226 25 1 29.36 ? C8 GNP 301 A 1 
HETATM 24 N N7 GNP . . . D 4 53.063 -7.338 25.539 1 29.28 ? N7 GNP 301 A 1 
HETATM 25 C C5 GNP . . . D 4 51.959 -7.25 24.761 1 29.5 ? C5 GNP 301 A 1 
HETATM 26 C C6 GNP . . . D 4 50.825 -6.489 24.864 1 29.68 ? C6 GNP 301 A 1 
HETATM 27 O O6 GNP . . . D 4 50.697 -5.739 25.768 1 29.17 ? O6 GNP 301 A 1 
HETATM 28 N N1 GNP . . . D 4 49.873 -6.595 23.95 1 30.48 ? N1 GNP 301 A 1 
HETATM 29 C C2 GNP . . . D 4 50.02 -7.454 22.913 1 31.62 ? C2 GNP 301 A 1 
HETATM 30 N N2 GNP . . . D 4 48.874 -7.53 21.882 1 32.59 ? N2 GNP 301 A 1 
HETATM 31 N N3 GNP . . . D 4 51.13 -8.2 22.811 1 30.95 ? N3 GNP 301 A 1 
HETATM 32 C C4 GNP . . . D 4 52.104 -8.095 23.741 1 29.84 ? C4 GNP 301 A 1 
HETATM 33 H HNB3 GNP . . . D 4 58.614 -14.587 26.422 1 32.86 ? HNB3 GNP 301 A 1 
HETATM 34 H "H5'2" GNP . . . D 4 56.544 -12.889 23.543 1 34.68 ? "H5'2" GNP 301 A 1 
HETATM 35 H "H5'1" GNP . . . D 4 55.696 -12.406 24.788 1 34.68 ? "H5'1" GNP 301 A 1 
HETATM 36 H H4' GNP . . . D 4 54.582 -12.482 22.555 1 35.6 ? H4' GNP 301 A 1 
HETATM 37 H H3' GNP . . . D 4 56.441 -10.663 21.962 1 37.49 ? H3' GNP 301 A 1 
HETATM 38 H H2' GNP . . . D 4 55.429 -8.897 22.999 1 37.75 ? H2' GNP 301 A 1 
HETATM 39 H HO2' GNP . . . D 4 55.243 -7.906 21.066 1 38.85 ? HO2' GNP 301 A 1 
HETATM 40 H H1' GNP . . . D 4 53.044 -9.82 22.237 1 36.54 ? H1' GNP 301 A 1 
HETATM 41 H H8 GNP . . . D 4 54.699 -8.48 25.33 1 35.23 ? H8 GNP 301 A 1 
HETATM 42 H HN1 GNP . . . D 4 49.161 -6.117 24.014 1 36.57 ? HN1 GNP 301 A 1 
HETATM 43 H HN21 GNP . . . D 4 48.074 -7.317 22.113 1 39.11 ? HN21 GNP 301 A 1 
HETATM 44 H HN22 GNP . . . D 4 49.035 -7.784 21.077 1 39.11 ? HN22 GNP 301 A 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           44 
#