data_8DGS
#
_model_server_result.job_id            qF72YFhpS4cyE17onaLoXA 
_model_server_result.datetime_utc      '2025-02-05 04:54:50' 
_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          8dgs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":202}' 
#
_entry.id    8DGS 
#
_exptl.entry_id    8DGS 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          9 
_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            8DGS 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DGS 
_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    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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    ? 
_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                      9 
_struct_asym.id                             M 
_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 A C SER 391 A SER 364 1_555 A N SEP 392 A SEP 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 A C SEP 392 A SEP 365 1_555 A N ALA 393 A ALA 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale3 A C ALA 755 A ALA 728 1_555 A N SEP 756 A SEP 729 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale4 A C SEP 756 A SEP 729 1_555 A N GLU 757 A GLU 730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? 
metalc ? metalc1 A ND1 HIS 262 A HIS 235 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? 
metalc ? metalc2 A SG CYS 275 A CYS 248 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc3 A SG CYS 278 A CYS 251 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc4 A SG CYS 288 A CYS 261 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc5 A SG CYS 291 A CYS 264 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc6 A ND1 HIS 296 A HIS 269 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
metalc ? metalc7 A SG CYS 299 A CYS 272 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc8 A SG CYS 307 A CYS 280 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc9 I O2G AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc10 I O3B AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? 
metalc ? metalc11 I O1A AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc12 I O2A AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc13 I O3A AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? 
metalc ? metalc14 J MG MG . B MG 802 1_555 K O05 LCJ . B LCJ 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc15 E OG SER 39 E SER 17 1_555 L MG MG . E MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc16 E OG1 THR 57 E THR 35 1_555 L MG MG . E MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc17 L MG MG . E MG 201 1_555 M O2G GNP . E GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc18 L MG MG . E MG 201 1_555 M O2B GNP . E GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_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 178 n n 
PG O2G GNP sing 179 n n 
PG O3G GNP sing 180 n n 
PG N3B GNP sing 181 n n 
O2G HOG2 GNP sing 182 n n 
O3G HOG3 GNP sing 183 n n 
N3B PB GNP sing 184 n n 
N3B HNB3 GNP sing 185 n n 
PB O1B GNP doub 186 n n 
PB O2B GNP sing 187 n n 
PB O3A GNP sing 188 n n 
O2B HOB2 GNP sing 189 n n 
O3A PA GNP sing 190 n n 
PA O1A GNP doub 191 n n 
PA O2A GNP sing 192 n n 
PA O5' GNP sing 193 n n 
O2A HOA2 GNP sing 194 n n 
O5' C5' GNP sing 195 n n 
C5' C4' GNP sing 196 n n 
C5' "H5'2" GNP sing 197 n n 
C5' "H5'1" GNP sing 198 n n 
C4' O4' GNP sing 199 n n 
C4' C3' GNP sing 200 n n 
C4' H4' GNP sing 201 n n 
O4' C1' GNP sing 202 n n 
C3' O3' GNP sing 203 n n 
C3' C2' GNP sing 204 n n 
C3' H3' GNP sing 205 n n 
O3' HO3' GNP sing 206 n n 
C2' O2' GNP sing 207 n n 
C2' C1' GNP sing 208 n n 
C2' H2' GNP sing 209 n n 
O2' HO2' GNP sing 210 n n 
C1' N9 GNP sing 211 n n 
C1' H1' GNP sing 212 n n 
N9 C8 GNP sing 213 n y 
N9 C4 GNP sing 214 n y 
C8 N7 GNP doub 215 n y 
C8 H8 GNP sing 216 n n 
N7 C5 GNP sing 217 n y 
C5 C6 GNP sing 218 n y 
C5 C4 GNP doub 219 n y 
C6 O6 GNP doub 220 n n 
C6 N1 GNP sing 221 n y 
N1 C2 GNP sing 222 n y 
N1 HN1 GNP sing 223 n n 
C2 N2 GNP sing 224 n n 
C2 N3 GNP doub 225 n y 
N2 HN21 GNP sing 226 n n 
N2 HN22 GNP sing 227 n n 
N3 C4 GNP sing 228 n y 
#
_atom_sites.entry_id                     8DGS 
_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 5 AGS A 1 801 801 AGS AGS . 
G 6 ZN A 1 802 901 ZN ZN . 
H 6 ZN A 1 803 902 ZN ZN . 
I 5 AGS B 1 801 801 AGS AGS . 
J 7 MG B 1 802 802 MG MG . 
K 8 LCJ B 1 803 803 LCJ LCJ . 
L 7 MG E 1 201 201 MG MG . 
M 9 GNP E 1 202 202 GNP GNP . 
#
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 . . . M 9 127.555 84.531 150.382 1 11.41 ? PG GNP 202 E 1 
HETATM 2 O O1G GNP . . . M 9 128.477 83.369 150.548 1 12.64 ? O1G GNP 202 E 1 
HETATM 3 O O2G GNP . . . M 9 128.233 85.617 149.565 1 11.88 ? O2G GNP 202 E 1 
HETATM 4 O O3G GNP . . . M 9 127.063 85.061 151.735 1 13.41 ? O3G GNP 202 E 1 
HETATM 5 N N3B GNP . . . M 9 126.191 83.948 149.529 1 10.97 ? N3B GNP 202 E 1 
HETATM 6 P PB GNP . . . M 9 125.017 84.916 148.923 1 10.47 ? PB GNP 202 E 1 
HETATM 7 O O1B GNP . . . M 9 124.026 85.324 149.99 1 11 ? O1B GNP 202 E 1 
HETATM 8 O O2B GNP . . . M 9 125.629 86.057 148.182 1 10.23 ? O2B GNP 202 E 1 
HETATM 9 O O3A GNP . . . M 9 124.208 83.962 147.891 1 11.88 ? O3A GNP 202 E 1 
HETATM 10 P PA GNP . . . M 9 124.371 83.881 146.324 1 11.58 ? PA GNP 202 E 1 
HETATM 11 O O1A GNP . . . M 9 123.718 85.112 145.73 1 12.73 ? O1A GNP 202 E 1 
HETATM 12 O O2A GNP . . . M 9 125.786 83.501 145.994 1 13.02 ? O2A GNP 202 E 1 
HETATM 13 O O5' GNP . . . M 9 123.395 82.669 146.018 1 11.64 ? O5' GNP 202 E 1 
HETATM 14 C C5' GNP . . . M 9 123.62 81.368 146.599 1 12.6 ? C5' GNP 202 E 1 
HETATM 15 C C4' GNP . . . M 9 122.929 80.35 145.728 1 13.75 ? C4' GNP 202 E 1 
HETATM 16 O O4' GNP . . . M 9 121.497 80.557 145.782 1 12.63 ? O4' GNP 202 E 1 
HETATM 17 C C3' GNP . . . M 9 123.303 80.377 144.247 1 13.33 ? C3' GNP 202 E 1 
HETATM 18 O O3' GNP . . . M 9 123.323 79.054 143.722 1 13.89 ? O3' GNP 202 E 1 
HETATM 19 C C2' GNP . . . M 9 122.161 81.176 143.618 1 14.05 ? C2' GNP 202 E 1 
HETATM 20 O O2' GNP . . . M 9 121.916 80.836 142.26 1 14.81 ? O2' GNP 202 E 1 
HETATM 21 C C1' GNP . . . M 9 120.982 80.731 144.48 1 11.6 ? C1' GNP 202 E 1 
HETATM 22 N N9 GNP . . . M 9 119.932 81.75 144.544 1 12.37 ? N9 GNP 202 E 1 
HETATM 23 C C8 GNP . . . M 9 120.078 83.058 144.945 1 11.23 ? C8 GNP 202 E 1 
HETATM 24 N N7 GNP . . . M 9 118.953 83.732 144.9 1 11.41 ? N7 GNP 202 E 1 
HETATM 25 C C5 GNP . . . M 9 118.014 82.807 144.474 1 11.46 ? C5 GNP 202 E 1 
HETATM 26 C C6 GNP . . . M 9 116.602 82.95 144.21 1 11.22 ? C6 GNP 202 E 1 
HETATM 27 O O6 GNP . . . M 9 115.921 83.962 144.382 1 12.15 ? O6 GNP 202 E 1 
HETATM 28 N N1 GNP . . . M 9 116.033 81.763 143.777 1 11.31 ? N1 GNP 202 E 1 
HETATM 29 C C2 GNP . . . M 9 116.718 80.596 143.573 1 12.04 ? C2 GNP 202 E 1 
HETATM 30 N N2 GNP . . . M 9 116.007 79.546 143.153 1 15.24 ? N2 GNP 202 E 1 
HETATM 31 N N3 GNP . . . M 9 118.021 80.454 143.809 1 12.47 ? N3 GNP 202 E 1 
HETATM 32 C C4 GNP . . . M 9 118.602 81.589 144.239 1 11.96 ? C4 GNP 202 E 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           32 
#