data_1XCM
#
_model_server_result.job_id            W3qz3xul3jITpx0Io8dvtQ 
_model_server_result.datetime_utc      '2024-11-26 10:05:10' 
_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          1xcm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":170}' 
#
_entry.id    1XCM 
#
_exptl.entry_id    1XCM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          3 
_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            1XCM 
_cell.length_a            34.292 
_cell.length_b            81.419 
_cell.length_c            121.302 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1XCM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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                      3 
_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 A C LYS 117 A LYS 117 1_555 A N CSO 118 A CSO 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? 
covale ? covale2 A C CSO 118 A CSO 118 1_555 A N ASP 119 A ASP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
metalc ? metalc1 A OG SER 17 A SER 17 1_555 B MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc2 D O2B GNP . A GNP 170 1_555 B MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc3 D O2G GNP . A GNP 170 1_555 B MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc4 B MG MG . A MG 171 1_555 E O HOH . A HOH 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc5 B MG MG . A MG 171 1_555 E O HOH . A HOH 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc6 B MG MG . A MG 171 1_555 E O HOH . A HOH 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc7 C MG MG . A MG 172 1_555 E O HOH . A HOH 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc8 C MG MG . A MG 172 1_555 E O HOH . A HOH 253 4_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
#
_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 143 n n 
PG O2G GNP sing 144 n n 
PG O3G GNP sing 145 n n 
PG N3B GNP sing 146 n n 
O2G HOG2 GNP sing 147 n n 
O3G HOG3 GNP sing 148 n n 
N3B PB GNP sing 149 n n 
N3B HNB3 GNP sing 150 n n 
PB O1B GNP doub 151 n n 
PB O2B GNP sing 152 n n 
PB O3A GNP sing 153 n n 
O2B HOB2 GNP sing 154 n n 
O3A PA GNP sing 155 n n 
PA O1A GNP doub 156 n n 
PA O2A GNP sing 157 n n 
PA O5' GNP sing 158 n n 
O2A HOA2 GNP sing 159 n n 
O5' C5' GNP sing 160 n n 
C5' C4' GNP sing 161 n n 
C5' "H5'2" GNP sing 162 n n 
C5' "H5'1" GNP sing 163 n n 
C4' O4' GNP sing 164 n n 
C4' C3' GNP sing 165 n n 
C4' H4' GNP sing 166 n n 
O4' C1' GNP sing 167 n n 
C3' O3' GNP sing 168 n n 
C3' C2' GNP sing 169 n n 
C3' H3' GNP sing 170 n n 
O3' HO3' GNP sing 171 n n 
C2' O2' GNP sing 172 n n 
C2' C1' GNP sing 173 n n 
C2' H2' GNP sing 174 n n 
O2' HO2' GNP sing 175 n n 
C1' N9 GNP sing 176 n n 
C1' H1' GNP sing 177 n n 
N9 C8 GNP sing 178 n y 
N9 C4 GNP sing 179 n y 
C8 N7 GNP doub 180 n y 
C8 H8 GNP sing 181 n n 
N7 C5 GNP sing 182 n y 
C5 C6 GNP sing 183 n y 
C5 C4 GNP doub 184 n y 
C6 O6 GNP doub 185 n n 
C6 N1 GNP sing 186 n y 
N1 C2 GNP sing 187 n y 
N1 HN1 GNP sing 188 n n 
C2 N2 GNP sing 189 n n 
C2 N3 GNP doub 190 n y 
N2 HN21 GNP sing 191 n n 
N2 HN22 GNP sing 192 n n 
N3 C4 GNP sing 193 n y 
#
_atom_sites.entry_id                     1XCM 
_atom_sites.fract_transf_matrix[1][1]    0.029161 
_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]    0.012282 
_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]    0.008244 
_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
B 2 MG A 1 171 171 MG MG . 
C 2 MG A 1 172 172 MG MG . 
D 3 GNP A 1 170 170 GNP GNP . 
E 4 HOH A 1 173 1 HOH HOH . 
E 4 HOH A 2 174 2 HOH HOH . 
E 4 HOH A 3 175 3 HOH HOH . 
E 4 HOH A 4 176 4 HOH HOH . 
E 4 HOH A 5 177 5 HOH HOH . 
E 4 HOH A 6 178 6 HOH HOH . 
E 4 HOH A 7 179 7 HOH HOH . 
E 4 HOH A 8 180 8 HOH HOH . 
E 4 HOH A 9 181 9 HOH HOH . 
E 4 HOH A 10 182 10 HOH HOH . 
E 4 HOH A 11 183 11 HOH HOH . 
E 4 HOH A 12 184 12 HOH HOH . 
E 4 HOH A 13 185 13 HOH HOH . 
E 4 HOH A 14 186 14 HOH HOH . 
E 4 HOH A 15 187 15 HOH HOH . 
E 4 HOH A 16 188 16 HOH HOH . 
E 4 HOH A 17 189 17 HOH HOH . 
E 4 HOH A 18 190 18 HOH HOH . 
E 4 HOH A 19 191 19 HOH HOH . 
E 4 HOH A 20 192 20 HOH HOH . 
E 4 HOH A 21 193 21 HOH HOH . 
E 4 HOH A 22 194 22 HOH HOH . 
E 4 HOH A 23 195 23 HOH HOH . 
E 4 HOH A 24 196 24 HOH HOH . 
E 4 HOH A 25 197 25 HOH HOH . 
E 4 HOH A 26 198 26 HOH HOH . 
E 4 HOH A 27 199 27 HOH HOH . 
E 4 HOH A 28 200 28 HOH HOH . 
E 4 HOH A 29 201 29 HOH HOH . 
E 4 HOH A 30 202 30 HOH HOH . 
E 4 HOH A 31 203 31 HOH HOH . 
E 4 HOH A 32 204 32 HOH HOH . 
E 4 HOH A 33 205 33 HOH HOH . 
E 4 HOH A 34 206 34 HOH HOH . 
E 4 HOH A 35 207 35 HOH HOH . 
E 4 HOH A 36 208 36 HOH HOH . 
E 4 HOH A 37 209 37 HOH HOH . 
E 4 HOH A 38 210 38 HOH HOH . 
E 4 HOH A 39 211 39 HOH HOH . 
E 4 HOH A 40 212 40 HOH HOH . 
E 4 HOH A 41 213 41 HOH HOH . 
E 4 HOH A 42 214 42 HOH HOH . 
E 4 HOH A 43 215 43 HOH HOH . 
E 4 HOH A 44 216 44 HOH HOH . 
E 4 HOH A 45 217 45 HOH HOH . 
E 4 HOH A 46 218 46 HOH HOH . 
E 4 HOH A 47 219 47 HOH HOH . 
E 4 HOH A 48 220 48 HOH HOH . 
E 4 HOH A 49 221 49 HOH HOH . 
E 4 HOH A 50 222 50 HOH HOH . 
E 4 HOH A 51 223 51 HOH HOH . 
E 4 HOH A 52 224 52 HOH HOH . 
E 4 HOH A 53 225 53 HOH HOH . 
E 4 HOH A 54 226 54 HOH HOH . 
E 4 HOH A 55 227 55 HOH HOH . 
E 4 HOH A 56 228 56 HOH HOH . 
E 4 HOH A 57 229 57 HOH HOH . 
E 4 HOH A 58 230 58 HOH HOH . 
E 4 HOH A 59 231 59 HOH HOH . 
E 4 HOH A 60 232 60 HOH HOH . 
E 4 HOH A 61 233 61 HOH HOH . 
E 4 HOH A 62 234 62 HOH HOH . 
E 4 HOH A 63 235 63 HOH HOH . 
E 4 HOH A 64 236 64 HOH HOH . 
E 4 HOH A 65 237 65 HOH HOH . 
E 4 HOH A 66 238 66 HOH HOH . 
E 4 HOH A 67 239 67 HOH HOH . 
E 4 HOH A 68 240 68 HOH HOH . 
E 4 HOH A 69 241 69 HOH HOH . 
E 4 HOH A 70 242 70 HOH HOH . 
E 4 HOH A 71 243 71 HOH HOH . 
E 4 HOH A 72 244 72 HOH HOH . 
E 4 HOH A 73 245 73 HOH HOH . 
E 4 HOH A 74 246 74 HOH HOH . 
E 4 HOH A 75 247 75 HOH HOH . 
E 4 HOH A 76 248 76 HOH HOH . 
E 4 HOH A 77 249 77 HOH HOH . 
E 4 HOH A 78 250 78 HOH HOH . 
E 4 HOH A 79 251 79 HOH HOH . 
E 4 HOH A 80 252 80 HOH HOH . 
E 4 HOH A 81 253 81 HOH HOH . 
E 4 HOH A 82 254 82 HOH HOH . 
E 4 HOH A 83 255 83 HOH HOH . 
E 4 HOH A 84 256 84 HOH HOH . 
E 4 HOH A 85 257 85 HOH HOH . 
E 4 HOH A 86 258 86 HOH HOH . 
E 4 HOH A 87 259 87 HOH HOH . 
E 4 HOH A 88 260 88 HOH HOH . 
E 4 HOH A 89 261 89 HOH HOH . 
E 4 HOH A 90 262 90 HOH HOH . 
E 4 HOH A 91 263 91 HOH HOH . 
E 4 HOH A 92 264 92 HOH HOH . 
E 4 HOH A 93 265 93 HOH HOH . 
E 4 HOH A 94 266 94 HOH HOH . 
E 4 HOH A 95 267 95 HOH HOH . 
E 4 HOH A 96 268 96 HOH HOH . 
E 4 HOH A 97 269 97 HOH HOH . 
E 4 HOH A 98 270 98 HOH HOH . 
E 4 HOH A 99 271 99 HOH HOH . 
E 4 HOH A 100 272 100 HOH HOH . 
E 4 HOH A 101 273 101 HOH HOH . 
E 4 HOH A 102 274 102 HOH HOH . 
E 4 HOH A 103 275 103 HOH HOH . 
E 4 HOH A 104 276 104 HOH HOH . 
E 4 HOH A 105 277 105 HOH HOH . 
E 4 HOH A 106 278 106 HOH HOH . 
E 4 HOH A 107 279 107 HOH HOH . 
E 4 HOH A 108 280 108 HOH HOH . 
E 4 HOH A 109 281 109 HOH HOH . 
E 4 HOH A 110 282 110 HOH HOH . 
E 4 HOH A 111 283 111 HOH HOH . 
E 4 HOH A 112 284 112 HOH HOH . 
E 4 HOH A 113 285 113 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 . . . D 3 12.964 9.741 38.826 1 11.69 ? PG GNP 170 A 1 
HETATM 2 O O1G GNP . . . D 3 13.649 8.588 38.199 1 8.82 ? O1G GNP 170 A 1 
HETATM 3 O O2G GNP . . . D 3 12.499 10.751 37.885 1 11.93 ? O2G GNP 170 A 1 
HETATM 4 O O3G GNP . . . D 3 13.903 10.261 39.91 1 9.97 ? O3G GNP 170 A 1 
HETATM 5 N N3B GNP . . . D 3 11.66 9.163 39.583 1 10.74 ? N3B GNP 170 A 1 
HETATM 6 P PB GNP . . . D 3 10.407 9.979 40.199 1 9.98 ? PB GNP 170 A 1 
HETATM 7 O O1B GNP . . . D 3 10.803 10.526 41.529 1 10.28 ? O1B GNP 170 A 1 
HETATM 8 O O2B GNP . . . D 3 9.924 10.924 39.165 1 9.88 ? O2B GNP 170 A 1 
HETATM 9 O O3A GNP . . . D 3 9.282 8.909 40.454 1 8.28 ? O3A GNP 170 A 1 
HETATM 10 P PA GNP . . . D 3 8.17 8.334 39.489 1 9.64 ? PA GNP 170 A 1 
HETATM 11 O O1A GNP . . . D 3 6.937 9.131 39.353 1 7.8 ? O1A GNP 170 A 1 
HETATM 12 O O2A GNP . . . D 3 8.816 7.933 38.238 1 9.22 ? O2A GNP 170 A 1 
HETATM 13 O O5' GNP . . . D 3 7.659 7.031 40.198 1 9.7 ? O5' GNP 170 A 1 
HETATM 14 C C5' GNP . . . D 3 8.585 6.01 40.542 1 10.94 ? C5' GNP 170 A 1 
HETATM 15 C C4' GNP . . . D 3 7.866 4.685 40.77 1 10.32 ? C4' GNP 170 A 1 
HETATM 16 O O4' GNP . . . D 3 7.11 4.789 42.001 1 10.38 ? O4' GNP 170 A 1 
HETATM 17 C C3' GNP . . . D 3 6.854 4.341 39.687 1 11.26 ? C3' GNP 170 A 1 
HETATM 18 O O3' GNP . . . D 3 6.709 2.939 39.585 1 8.21 ? O3' GNP 170 A 1 
HETATM 19 C C2' GNP . . . D 3 5.582 4.991 40.214 1 11.28 ? C2' GNP 170 A 1 
HETATM 20 O O2' GNP . . . D 3 4.395 4.384 39.74 1 12.07 ? O2' GNP 170 A 1 
HETATM 21 C C1' GNP . . . D 3 5.734 4.701 41.711 1 11.75 ? C1' GNP 170 A 1 
HETATM 22 N N9 GNP . . . D 3 4.998 5.613 42.567 1 8.99 ? N9 GNP 170 A 1 
HETATM 23 C C8 GNP . . . D 3 5.006 6.973 42.523 1 11 ? C8 GNP 170 A 1 
HETATM 24 N N7 GNP . . . D 3 4.23 7.515 43.41 1 9.91 ? N7 GNP 170 A 1 
HETATM 25 C C5 GNP . . . D 3 3.686 6.452 44.081 1 11.22 ? C5 GNP 170 A 1 
HETATM 26 C C6 GNP . . . D 3 2.797 6.437 45.188 1 11.49 ? C6 GNP 170 A 1 
HETATM 27 O O6 GNP . . . D 3 2.293 7.42 45.735 1 10.07 ? O6 GNP 170 A 1 
HETATM 28 N N1 GNP . . . D 3 2.469 5.138 45.588 1 10.01 ? N1 GNP 170 A 1 
HETATM 29 C C2 GNP . . . D 3 2.992 4.003 44.999 1 12.41 ? C2 GNP 170 A 1 
HETATM 30 N N2 GNP . . . D 3 2.58 2.851 45.521 1 11.21 ? N2 GNP 170 A 1 
HETATM 31 N N3 GNP . . . D 3 3.834 3.997 43.974 1 10.04 ? N3 GNP 170 A 1 
HETATM 32 C C4 GNP . . . D 3 4.154 5.265 43.588 1 10.11 ? C4 GNP 170 A 1 
#
_model_server_stats.io_time_ms              64 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#