data_4NYM
#
_model_server_result.job_id            Wea26aDkWthsoBzcyJC5Sg 
_model_server_result.datetime_utc      '2024-11-02 04:33:08' 
_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          4nym 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":202}' 
#
_entry.id    4NYM 
#
_exptl.entry_id    4NYM 
_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    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            4NYM 
_cell.length_a            186.805 
_cell.length_b            186.805 
_cell.length_c            178.684 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NYM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_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                      5 
_struct_asym.id                             E 
_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 17 Q SER 17 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc2 A OG1 THR 35 Q THR 35 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc3 D MG MG . Q MG 201 1_555 E O2G GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc4 D MG MG . Q MG 201 1_555 E O2B GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
#
_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                     4NYM 
_atom_sites.fract_transf_matrix[1][1]    0.005353 
_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]    0.005353 
_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]    0.005596 
_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 MG Q 1 201 1002 MG MG . 
E 5 GNP Q 1 202 1001 GNP GNP . 
F 6 RND S 1 1101 401 RND RND . 
#
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 . . . E 5 15.81 51.508 70.655 1 86.05 1 PG GNP 202 Q 1 
HETATM 2 O O1G GNP . . . E 5 14.509 51.434 71.429 1 79.61 1 O1G GNP 202 Q 1 
HETATM 3 O O2G GNP . . . E 5 15.961 50.527 69.502 1 82.7 1 O2G GNP 202 Q 1 
HETATM 4 O O3G GNP . . . E 5 16.82 51.44 71.779 1 74.06 1 O3G GNP 202 Q 1 
HETATM 5 N N3B GNP . . . E 5 15.983 52.913 69.917 1 78.32 ? N3B GNP 202 Q 1 
HETATM 6 P PB GNP . . . E 5 16.364 53.082 68.367 1 73.34 1 PB GNP 202 Q 1 
HETATM 7 O O1B GNP . . . E 5 17.704 53.684 68.269 1 66.74 1 O1B GNP 202 Q 1 
HETATM 8 O O2B GNP . . . E 5 16.129 51.759 67.71 1 70.82 1 O2B GNP 202 Q 1 
HETATM 9 O O3A GNP . . . E 5 15.448 54.122 67.71 1 69.46 ? O3A GNP 202 Q 1 
HETATM 10 P PA GNP . . . E 5 14.928 53.95 66.282 1 69.87 1 PA GNP 202 Q 1 
HETATM 11 O O1A GNP . . . E 5 16.135 54.062 65.46 1 72.1 1 O1A GNP 202 Q 1 
HETATM 12 O O2A GNP . . . E 5 14.099 52.723 66.1 1 72.82 1 O2A GNP 202 Q 1 
HETATM 13 O O5' GNP . . . E 5 14.05 55.171 65.817 1 62.67 ? O5' GNP 202 Q 1 
HETATM 14 C C5' GNP . . . E 5 13.443 56.086 66.699 1 69.18 ? C5' GNP 202 Q 1 
HETATM 15 C C4' GNP . . . E 5 12.466 56.948 65.923 1 71.19 ? C4' GNP 202 Q 1 
HETATM 16 O O4' GNP . . . E 5 13.157 58.102 65.389 1 71.74 ? O4' GNP 202 Q 1 
HETATM 17 C C3' GNP . . . E 5 11.809 56.272 64.72 1 77.44 ? C3' GNP 202 Q 1 
HETATM 18 O O3' GNP . . . E 5 10.486 56.759 64.477 1 79.03 ? O3' GNP 202 Q 1 
HETATM 19 C C2' GNP . . . E 5 12.707 56.673 63.559 1 76.34 ? C2' GNP 202 Q 1 
HETATM 20 O O2' GNP . . . E 5 11.985 56.722 62.349 1 81.54 ? O2' GNP 202 Q 1 
HETATM 21 C C1' GNP . . . E 5 13.099 58.079 63.969 1 74.2 ? C1' GNP 202 Q 1 
HETATM 22 N N9 GNP . . . E 5 14.382 58.489 63.406 1 71.14 ? N9 GNP 202 Q 1 
HETATM 23 C C8 GNP . . . E 5 15.581 57.826 63.505 1 67.62 ? C8 GNP 202 Q 1 
HETATM 24 N N7 GNP . . . E 5 16.555 58.446 62.905 1 66.67 ? N7 GNP 202 Q 1 
HETATM 25 C C5 GNP . . . E 5 15.96 59.594 62.374 1 70.05 ? C5 GNP 202 Q 1 
HETATM 26 C C6 GNP . . . E 5 16.508 60.667 61.611 1 71.24 ? C6 GNP 202 Q 1 
HETATM 27 O O6 GNP . . . E 5 17.678 60.842 61.23 1 71.17 ? O6 GNP 202 Q 1 
HETATM 28 N N1 GNP . . . E 5 15.55 61.621 61.277 1 68.27 ? N1 GNP 202 Q 1 
HETATM 29 C C2 GNP . . . E 5 14.237 61.557 61.634 1 63.55 ? C2 GNP 202 Q 1 
HETATM 30 N N2 GNP . . . E 5 13.489 62.574 61.212 1 65.19 ? N2 GNP 202 Q 1 
HETATM 31 N N3 GNP . . . E 5 13.709 60.577 62.345 1 64.86 ? N3 GNP 202 Q 1 
HETATM 32 C C4 GNP . . . E 5 14.621 59.631 62.677 1 68.34 ? C4 GNP 202 Q 1 
#
_model_server_stats.io_time_ms              58 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           220 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#