data_9B4S
#
_model_server_result.job_id            c1aVaYq35dT43xW6IU8XXA 
_model_server_result.datetime_utc      '2025-01-22 13:09:19' 
_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          9b4s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    9B4S 
#
_exptl.entry_id    9B4S 
_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            9B4S 
_cell.length_a            181.488 
_cell.length_b            181.488 
_cell.length_c            96.03 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9B4S 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        94 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 42 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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
metalc ? metalc1 B OG SER 29 B SER 28 1_555 E MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc2 B OG1 THR 47 B THR 46 1_555 E MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc3 D O2G GNP . B GNP 201 1_555 E MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc4 D O2B GNP . B GNP 201 1_555 E MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
#
_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 182 n n 
PG O2G GNP sing 183 n n 
PG O3G GNP sing 184 n n 
PG N3B GNP sing 185 n n 
O2G HOG2 GNP sing 186 n n 
O3G HOG3 GNP sing 187 n n 
N3B PB GNP sing 188 n n 
N3B HNB3 GNP sing 189 n n 
PB O1B GNP doub 190 n n 
PB O2B GNP sing 191 n n 
PB O3A GNP sing 192 n n 
O2B HOB2 GNP sing 193 n n 
O3A PA GNP sing 194 n n 
PA O1A GNP doub 195 n n 
PA O2A GNP sing 196 n n 
PA O5' GNP sing 197 n n 
O2A HOA2 GNP sing 198 n n 
O5' C5' GNP sing 199 n n 
C5' C4' GNP sing 200 n n 
C5' "H5'2" GNP sing 201 n n 
C5' "H5'1" GNP sing 202 n n 
C4' O4' GNP sing 203 n n 
C4' C3' GNP sing 204 n n 
C4' H4' GNP sing 205 n n 
O4' C1' GNP sing 206 n n 
C3' O3' GNP sing 207 n n 
C3' C2' GNP sing 208 n n 
C3' H3' GNP sing 209 n n 
O3' HO3' GNP sing 210 n n 
C2' O2' GNP sing 211 n n 
C2' C1' GNP sing 212 n n 
C2' H2' GNP sing 213 n n 
O2' HO2' GNP sing 214 n n 
C1' N9 GNP sing 215 n n 
C1' H1' GNP sing 216 n n 
N9 C8 GNP sing 217 n y 
N9 C4 GNP sing 218 n y 
C8 N7 GNP doub 219 n y 
C8 H8 GNP sing 220 n n 
N7 C5 GNP sing 221 n y 
C5 C6 GNP sing 222 n y 
C5 C4 GNP doub 223 n y 
C6 O6 GNP doub 224 n n 
C6 N1 GNP sing 225 n y 
N1 C2 GNP sing 226 n y 
N1 HN1 GNP sing 227 n n 
C2 N2 GNP sing 228 n n 
C2 N3 GNP doub 229 n y 
N2 HN21 GNP sing 230 n n 
N2 HN22 GNP sing 231 n n 
N3 C4 GNP sing 232 n y 
#
_atom_sites.entry_id                     9B4S 
_atom_sites.fract_transf_matrix[1][1]    0.00551 
_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]    0.00551 
_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]    0.010413 
_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
C 3 5H5 A 1 1101 1071 5H5 GDC . 
D 4 GNP B 1 201 500 GNP GNP . 
E 5 MG B 1 202 1 MG MG . 
#
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 -15.287 15.83 -40.09 1 109.8 ? PG GNP 201 B 1 
HETATM 2 O O1G GNP . . . D 4 -15.853 15.978 -41.504 1 103.72 ? O1G GNP 201 B 1 
HETATM 3 O O2G GNP . . . D 4 -15.617 14.504 -39.407 1 112.44 ? O2G GNP 201 B 1 
HETATM 4 O O3G GNP . . . D 4 -15.527 17.049 -39.195 1 127.35 ? O3G GNP 201 B 1 
HETATM 5 N N3B GNP . . . D 4 -13.51 15.768 -40.398 1 112.37 ? N3B GNP 201 B 1 
HETATM 6 P PB GNP . . . D 4 -12.405 16.186 -39.203 1 119.42 ? PB GNP 201 B 1 
HETATM 7 O O1B GNP . . . D 4 -12.178 17.674 -39.116 1 101.05 ? O1B GNP 201 B 1 
HETATM 8 O O2B GNP . . . D 4 -12.713 15.411 -37.95 1 115.15 ? O2B GNP 201 B 1 
HETATM 9 O O3A GNP . . . D 4 -10.92 15.624 -39.784 1 136.44 ? O3A GNP 201 B 1 
HETATM 10 P PA GNP . . . D 4 -10.585 14.596 -41.002 1 116.6 ? PA GNP 201 B 1 
HETATM 11 O O1A GNP . . . D 4 -9.271 13.921 -40.768 1 103.79 ? O1A GNP 201 B 1 
HETATM 12 O O2A GNP . . . D 4 -11.798 13.825 -41.43 1 144.98 ? O2A GNP 201 B 1 
HETATM 13 O O5' GNP . . . D 4 -10.211 15.718 -42.165 1 116.66 ? O5' GNP 201 B 1 
HETATM 14 C C5' GNP . . . D 4 -10.67 15.57 -43.482 1 136.01 ? C5' GNP 201 B 1 
HETATM 15 C C4' GNP . . . D 4 -9.51 15.543 -44.457 1 140.75 ? C4' GNP 201 B 1 
HETATM 16 O O4' GNP . . . D 4 -8.457 16.425 -44.045 1 136.28 ? O4' GNP 201 B 1 
HETATM 17 C C3' GNP . . . D 4 -8.868 14.17 -44.677 1 128.78 ? C3' GNP 201 B 1 
HETATM 18 O O3' GNP . . . D 4 -8.681 14.006 -46.063 1 121.28 ? O3' GNP 201 B 1 
HETATM 19 C C2' GNP . . . D 4 -7.528 14.294 -43.957 1 131.87 ? C2' GNP 201 B 1 
HETATM 20 O O2' GNP . . . D 4 -6.566 13.442 -44.507 1 111.24 ? O2' GNP 201 B 1 
HETATM 21 C C1' GNP . . . D 4 -7.224 15.782 -44.163 1 120.7 ? C1' GNP 201 B 1 
HETATM 22 N N9 GNP . . . D 4 -6.283 16.313 -43.203 1 109.16 ? N9 GNP 201 B 1 
HETATM 23 C C8 GNP . . . D 4 -6.436 16.381 -41.84 1 125.69 ? C8 GNP 201 B 1 
HETATM 24 N N7 GNP . . . D 4 -5.409 16.907 -41.244 1 114.28 ? N7 GNP 201 B 1 
HETATM 25 C C5 GNP . . . D 4 -4.53 17.201 -42.255 1 112.25 ? C5 GNP 201 B 1 
HETATM 26 C C6 GNP . . . D 4 -3.233 17.793 -42.215 1 129.19 ? C6 GNP 201 B 1 
HETATM 27 O O6 GNP . . . D 4 -2.594 18.182 -41.252 1 118.6 ? O6 GNP 201 B 1 
HETATM 28 N N1 GNP . . . D 4 -2.701 17.901 -43.509 1 115.73 ? N1 GNP 201 B 1 
HETATM 29 C C2 GNP . . . D 4 -3.31 17.506 -44.666 1 121.58 ? C2 GNP 201 B 1 
HETATM 30 N N2 GNP . . . D 4 -2.635 17.693 -45.811 1 116.1 ? N2 GNP 201 B 1 
HETATM 31 N N3 GNP . . . D 4 -4.502 16.964 -44.694 1 115.73 ? N3 GNP 201 B 1 
HETATM 32 C C4 GNP . . . D 4 -5.057 16.836 -43.48 1 111.31 ? C4 GNP 201 B 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           32 
#