data_5KHO
#
_model_server_result.job_id            YYLjjF1fjw2lPePScUamCw 
_model_server_result.datetime_utc      '2025-02-17 18:20:26' 
_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          5kho 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":201}' 
#
_entry.id    5KHO 
#
_exptl.entry_id    5KHO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC 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            5KHO 
_cell.length_a            101.54 
_cell.length_b            154.76 
_cell.length_c            38.8 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KHO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 G N N 
? 5 I 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
metalc ? metalc1 C OG SER 17 C SER 17 1_555 F MG MG . C MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc2 C OG1 THR 35 C THR 35 1_555 F MG MG . C MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc3 F MG MG . C MG 200 1_555 G O2B GNP . C GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? 
metalc ? metalc4 F MG MG . C MG 200 1_555 G O2G GNP . C GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? 
metalc ? metalc5 F MG MG . C MG 200 1_555 L O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc6 F MG MG . C MG 200 1_555 L O HOH . C HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc7 D OG SER 17 D SER 17 1_555 H MG MG . D MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc8 D OG1 THR 35 D THR 35 1_555 H MG MG . D MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc9 H MG MG . D MG 200 1_555 I O1G GNP . D GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc10 H MG MG . D MG 200 1_555 I O1B GNP . D GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc11 H MG MG . D MG 200 1_555 M O HOH . D HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc12 H MG MG . D MG 200 1_555 M O HOH . D HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? 
#
_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                     5KHO 
_atom_sites.fract_transf_matrix[1][1]    0.009848 
_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]    0.006462 
_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]    0.025773 
_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
E 3 GOL A 1 301 1 GOL GOL . 
F 4 MG C 1 200 200 MG MG . 
G 5 GNP C 1 201 201 GNP GNP . 
H 4 MG D 1 200 200 MG MG . 
I 5 GNP D 1 201 201 GNP GNP . 
J 6 HOH A 1 401 2 HOH HOH . 
J 6 HOH A 2 402 11 HOH HOH . 
K 6 HOH B 1 301 3 HOH HOH . 
L 6 HOH C 1 301 13 HOH HOH . 
L 6 HOH C 2 302 4 HOH HOH . 
L 6 HOH C 3 303 5 HOH HOH . 
L 6 HOH C 4 304 6 HOH HOH . 
M 6 HOH D 1 301 8 HOH HOH . 
M 6 HOH D 2 302 7 HOH HOH . 
M 6 HOH D 3 303 14 HOH HOH . 
M 6 HOH D 4 304 9 HOH HOH . 
M 6 HOH D 5 305 1 HOH HOH . 
M 6 HOH D 6 306 10 HOH HOH . 
M 6 HOH D 7 307 12 HOH HOH . 
#
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 . . . I 5 15.98 16.43 -7.172 1 105.77 ? PG GNP 201 D 1 
HETATM 2 O O1G GNP . . . I 5 14.971 17.435 -7.919 1 107.53 ? O1G GNP 201 D 1 
HETATM 3 O O2G GNP . . . I 5 15.957 15.1 -7.826 1 96.34 ? O2G GNP 201 D 1 
HETATM 4 O O3G GNP . . . I 5 15.524 16.305 -5.629 1 112.9 ? O3G GNP 201 D 1 
HETATM 5 N N3B GNP . . . I 5 17.598 17.08 -7.243 1 100.18 ? N3B GNP 201 D 1 
HETATM 6 P PB GNP . . . I 5 18.506 17.046 -8.732 1 98.97 ? PB GNP 201 D 1 
HETATM 7 O O1B GNP . . . I 5 17.619 17.664 -9.918 1 105.18 ? O1B GNP 201 D 1 
HETATM 8 O O2B GNP . . . I 5 18.896 15.649 -9.035 1 93.64 ? O2B GNP 201 D 1 
HETATM 9 O O3A GNP . . . I 5 19.824 17.939 -8.556 1 96.4 ? O3A GNP 201 D 1 
HETATM 10 P PA GNP . . . I 5 19.907 19.513 -8.874 1 98.51 ? PA GNP 201 D 1 
HETATM 11 O O1A GNP . . . I 5 20.081 19.69 -10.362 1 101.06 ? O1A GNP 201 D 1 
HETATM 12 O O2A GNP . . . I 5 18.828 20.294 -8.165 1 87.62 ? O2A GNP 201 D 1 
HETATM 13 O O5' GNP . . . I 5 21.324 19.789 -8.16 1 103.21 ? O5' GNP 201 D 1 
HETATM 14 C C5' GNP . . . I 5 21.413 19.951 -6.742 1 104.69 ? C5' GNP 201 D 1 
HETATM 15 C C4' GNP . . . I 5 22.394 21.072 -6.407 1 108.75 ? C4' GNP 201 D 1 
HETATM 16 O O4' GNP . . . I 5 23.696 20.679 -6.848 1 113.31 ? O4' GNP 201 D 1 
HETATM 17 C C3' GNP . . . I 5 22.064 22.403 -7.08 1 106 ? C3' GNP 201 D 1 
HETATM 18 O O3' GNP . . . I 5 22.1 23.454 -6.11 1 105.32 ? O3' GNP 201 D 1 
HETATM 19 C C2' GNP . . . I 5 23.138 22.609 -8.131 1 101.4 ? C2' GNP 201 D 1 
HETATM 20 O O2' GNP . . . I 5 23.602 23.958 -8.199 1 107.11 ? O2' GNP 201 D 1 
HETATM 21 C C1' GNP . . . I 5 24.261 21.677 -7.702 1 106.06 ? C1' GNP 201 D 1 
HETATM 22 N N9 GNP . . . I 5 24.883 21.037 -8.886 1 102.65 ? N9 GNP 201 D 1 
HETATM 23 C C8 GNP . . . I 5 24.249 20.353 -9.854 1 100.78 ? C8 GNP 201 D 1 
HETATM 24 N N7 GNP . . . I 5 25.116 19.909 -10.796 1 98.83 ? N7 GNP 201 D 1 
HETATM 25 C C5 GNP . . . I 5 26.341 20.3 -10.425 1 99.79 ? C5 GNP 201 D 1 
HETATM 26 C C6 GNP . . . I 5 27.716 20.161 -10.964 1 106 ? C6 GNP 201 D 1 
HETATM 27 O O6 GNP . . . I 5 27.945 19.543 -12.027 1 108.63 ? O6 GNP 201 D 1 
HETATM 28 N N1 GNP . . . I 5 28.712 20.72 -10.258 1 113.5 ? N1 GNP 201 D 1 
HETATM 29 C C2 GNP . . . I 5 28.507 21.392 -9.101 1 104.2 ? C2 GNP 201 D 1 
HETATM 30 N N2 GNP . . . I 5 29.572 21.925 -8.463 1 108.1 ? N2 GNP 201 D 1 
HETATM 31 N N3 GNP . . . I 5 27.279 21.556 -8.554 1 97.42 ? N3 GNP 201 D 1 
HETATM 32 C C4 GNP . . . I 5 26.184 21.042 -9.161 1 98.95 ? C4 GNP 201 D 1 
#
_model_server_stats.io_time_ms              70 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           32 
#