data_3KYF
#
_model_server_result.job_id            spnT8W2xgVvqg1KoEx3AcQ 
_model_server_result.datetime_utc      '2025-03-04 21:39:50' 
_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          3kyf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":503}' 
#
_entry.id    3KYF 
#
_exptl.entry_id    3KYF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              363.221 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          92.21 
_cell.angle_gamma         90 
_cell.entry_id            3KYF 
_cell.length_a            112.7 
_cell.length_b            41.304 
_cell.length_c            61.59 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KYF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F 1 1 
A,B,C,D,E,F 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 B N N 
? 2 C N N 
? 2 D N N 
? 2 E 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
covale ? covale1 B P 5GP . A 5GP 501 1_555 C O3' 5GP . A 5GP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? 
covale ? covale2 B O3' 5GP . A 5GP 501 1_555 C P 5GP . A 5GP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? 
covale ? covale3 D P 5GP . A 5GP 503 1_555 E O3' 5GP . A 5GP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? 
covale ? covale4 D O3' 5GP . A 5GP 503 1_555 E P 5GP . A 5GP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? 
#
_chem_comp.formula           'C10 H14 N5 O8 P' 
_chem_comp.formula_weight    363.221 
_chem_comp.id                5GP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "GUANOSINE-5'-MONOPHOSPHATE" 
_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
P O1P 5GP doub 1 n n 
P O2P 5GP sing 2 n n 
P O3P 5GP sing 3 n n 
P O5' 5GP sing 4 n n 
O2P HOP2 5GP sing 5 n n 
O3P HOP3 5GP sing 6 n n 
O5' C5' 5GP sing 7 n n 
C5' C4' 5GP sing 8 n n 
C5' "H5'1" 5GP sing 9 n n 
C5' "H5'2" 5GP sing 10 n n 
C4' O4' 5GP sing 11 n n 
C4' C3' 5GP sing 12 n n 
C4' H4' 5GP sing 13 n n 
O4' C1' 5GP sing 14 n n 
C3' O3' 5GP sing 15 n n 
C3' C2' 5GP sing 16 n n 
C3' H3' 5GP sing 17 n n 
O3' HO3' 5GP sing 18 n n 
C2' O2' 5GP sing 19 n n 
C2' C1' 5GP sing 20 n n 
C2' H2' 5GP sing 21 n n 
O2' HO2' 5GP sing 22 n n 
C1' N9 5GP sing 23 n n 
C1' H1' 5GP sing 24 n n 
N9 C8 5GP sing 25 n y 
N9 C4 5GP sing 26 n y 
C8 N7 5GP doub 27 n y 
C8 H8 5GP sing 28 n n 
N7 C5 5GP sing 29 n y 
C5 C6 5GP sing 30 n n 
C5 C4 5GP doub 31 n y 
C6 O6 5GP doub 32 n n 
C6 N1 5GP sing 33 n n 
N1 C2 5GP sing 34 n n 
N1 HN1 5GP sing 35 n n 
C2 N2 5GP sing 36 n n 
C2 N3 5GP doub 37 n n 
N2 HN21 5GP sing 38 n n 
N2 HN22 5GP sing 39 n n 
N3 C4 5GP sing 40 n n 
#
_atom_sites.entry_id                     3KYF 
_atom_sites.fract_transf_matrix[1][1]    0.008873 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000342 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.024211 
_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]    0.016248 
_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 5GP A 1 501 501 5GP 5GP . 
C 2 5GP A 1 502 502 5GP 5GP . 
D 2 5GP A 1 503 503 5GP 5GP . 
E 2 5GP A 1 504 504 5GP 5GP . 
F 3 HOH A 1 1 1 HOH HOH . 
F 3 HOH A 2 2 2 HOH HOH . 
F 3 HOH A 3 3 3 HOH HOH . 
F 3 HOH A 4 4 4 HOH HOH . 
F 3 HOH A 5 5 5 HOH HOH . 
F 3 HOH A 6 6 6 HOH HOH . 
F 3 HOH A 7 7 7 HOH HOH . 
F 3 HOH A 8 239 8 HOH HOH . 
F 3 HOH A 9 240 9 HOH HOH . 
F 3 HOH A 10 241 10 HOH HOH . 
F 3 HOH A 11 242 11 HOH HOH . 
F 3 HOH A 12 243 12 HOH HOH . 
F 3 HOH A 13 244 13 HOH HOH . 
F 3 HOH A 14 245 14 HOH HOH . 
F 3 HOH A 15 246 15 HOH HOH . 
F 3 HOH A 16 247 16 HOH HOH . 
F 3 HOH A 17 248 17 HOH HOH . 
F 3 HOH A 18 249 18 HOH HOH . 
F 3 HOH A 19 250 19 HOH HOH . 
F 3 HOH A 20 251 20 HOH HOH . 
F 3 HOH A 21 252 21 HOH HOH . 
F 3 HOH A 22 253 22 HOH HOH . 
F 3 HOH A 23 254 23 HOH HOH . 
F 3 HOH A 24 255 24 HOH HOH . 
F 3 HOH A 25 256 25 HOH HOH . 
F 3 HOH A 26 257 26 HOH HOH . 
F 3 HOH A 27 258 27 HOH HOH . 
F 3 HOH A 28 259 28 HOH HOH . 
F 3 HOH A 29 260 29 HOH HOH . 
F 3 HOH A 30 261 30 HOH HOH . 
F 3 HOH A 31 262 31 HOH HOH . 
F 3 HOH A 32 263 32 HOH HOH . 
F 3 HOH A 33 264 33 HOH HOH . 
F 3 HOH A 34 265 34 HOH HOH . 
F 3 HOH A 35 266 35 HOH HOH . 
F 3 HOH A 36 267 36 HOH HOH . 
F 3 HOH A 37 268 37 HOH HOH . 
F 3 HOH A 38 269 38 HOH HOH . 
F 3 HOH A 39 270 39 HOH HOH . 
F 3 HOH A 40 271 40 HOH HOH . 
F 3 HOH A 41 272 41 HOH HOH . 
F 3 HOH A 42 273 42 HOH HOH . 
F 3 HOH A 43 274 43 HOH HOH . 
F 3 HOH A 44 275 44 HOH HOH . 
F 3 HOH A 45 276 45 HOH HOH . 
F 3 HOH A 46 277 46 HOH HOH . 
F 3 HOH A 47 278 47 HOH HOH . 
F 3 HOH A 48 279 48 HOH HOH . 
F 3 HOH A 49 280 49 HOH HOH . 
F 3 HOH A 50 281 50 HOH HOH . 
F 3 HOH A 51 282 51 HOH HOH . 
F 3 HOH A 52 283 52 HOH HOH . 
F 3 HOH A 53 284 53 HOH HOH . 
F 3 HOH A 54 285 54 HOH HOH . 
F 3 HOH A 55 286 55 HOH HOH . 
F 3 HOH A 56 287 56 HOH HOH . 
F 3 HOH A 57 288 57 HOH HOH . 
F 3 HOH A 58 289 58 HOH HOH . 
F 3 HOH A 59 290 59 HOH HOH . 
F 3 HOH A 60 291 60 HOH HOH . 
F 3 HOH A 61 292 61 HOH HOH . 
F 3 HOH A 62 293 62 HOH HOH . 
F 3 HOH A 63 294 63 HOH HOH . 
F 3 HOH A 64 295 64 HOH HOH . 
F 3 HOH A 65 296 65 HOH HOH . 
F 3 HOH A 66 297 66 HOH HOH . 
F 3 HOH A 67 298 67 HOH HOH . 
F 3 HOH A 68 299 68 HOH HOH . 
F 3 HOH A 69 300 69 HOH HOH . 
F 3 HOH A 70 301 70 HOH HOH . 
F 3 HOH A 71 302 71 HOH HOH . 
F 3 HOH A 72 303 72 HOH HOH . 
F 3 HOH A 73 304 73 HOH HOH . 
F 3 HOH A 74 305 74 HOH HOH . 
F 3 HOH A 75 306 75 HOH HOH . 
F 3 HOH A 76 307 76 HOH HOH . 
F 3 HOH A 77 308 77 HOH HOH . 
F 3 HOH A 78 309 78 HOH HOH . 
F 3 HOH A 79 310 79 HOH HOH . 
F 3 HOH A 80 311 80 HOH HOH . 
F 3 HOH A 81 312 81 HOH HOH . 
F 3 HOH A 82 313 82 HOH HOH . 
F 3 HOH A 83 314 83 HOH HOH . 
F 3 HOH A 84 315 84 HOH HOH . 
F 3 HOH A 85 316 85 HOH HOH . 
F 3 HOH A 86 317 86 HOH HOH . 
F 3 HOH A 87 318 87 HOH HOH . 
F 3 HOH A 88 319 88 HOH HOH . 
F 3 HOH A 89 320 89 HOH HOH . 
F 3 HOH A 90 321 90 HOH HOH . 
F 3 HOH A 91 322 91 HOH HOH . 
F 3 HOH A 92 323 92 HOH HOH . 
F 3 HOH A 93 324 93 HOH HOH . 
F 3 HOH A 94 325 94 HOH HOH . 
F 3 HOH A 95 326 95 HOH HOH . 
F 3 HOH A 96 327 96 HOH HOH . 
F 3 HOH A 97 328 97 HOH HOH . 
F 3 HOH A 98 329 98 HOH HOH . 
F 3 HOH A 99 330 99 HOH HOH . 
F 3 HOH A 100 331 100 HOH HOH . 
F 3 HOH A 101 332 101 HOH HOH . 
F 3 HOH A 102 333 102 HOH HOH . 
F 3 HOH A 103 334 103 HOH HOH . 
F 3 HOH A 104 335 104 HOH HOH . 
F 3 HOH A 105 336 105 HOH HOH . 
F 3 HOH A 106 337 106 HOH HOH . 
F 3 HOH A 107 338 107 HOH HOH . 
F 3 HOH A 108 339 108 HOH HOH . 
F 3 HOH A 109 340 109 HOH HOH . 
F 3 HOH A 110 341 110 HOH HOH . 
F 3 HOH A 111 342 111 HOH HOH . 
F 3 HOH A 112 343 112 HOH HOH . 
F 3 HOH A 113 344 113 HOH HOH . 
F 3 HOH A 114 345 114 HOH HOH . 
F 3 HOH A 115 346 115 HOH HOH . 
F 3 HOH A 116 347 116 HOH HOH . 
F 3 HOH A 117 348 117 HOH HOH . 
F 3 HOH A 118 349 118 HOH HOH . 
F 3 HOH A 119 350 119 HOH HOH . 
F 3 HOH A 120 351 120 HOH HOH . 
F 3 HOH A 121 352 121 HOH HOH . 
F 3 HOH A 122 353 122 HOH HOH . 
F 3 HOH A 123 354 123 HOH HOH . 
F 3 HOH A 124 355 124 HOH HOH . 
F 3 HOH A 125 356 125 HOH HOH . 
F 3 HOH A 126 357 126 HOH HOH . 
F 3 HOH A 127 358 127 HOH HOH . 
F 3 HOH A 128 359 128 HOH HOH . 
F 3 HOH A 129 360 129 HOH HOH . 
F 3 HOH A 130 361 130 HOH HOH . 
F 3 HOH A 131 362 131 HOH HOH . 
F 3 HOH A 132 363 132 HOH HOH . 
F 3 HOH A 133 364 133 HOH HOH . 
F 3 HOH A 134 365 134 HOH HOH . 
F 3 HOH A 135 366 135 HOH HOH . 
F 3 HOH A 136 367 136 HOH HOH . 
F 3 HOH A 137 368 137 HOH HOH . 
F 3 HOH A 138 369 138 HOH HOH . 
F 3 HOH A 139 370 139 HOH HOH . 
F 3 HOH A 140 371 140 HOH HOH . 
F 3 HOH A 141 372 141 HOH HOH . 
F 3 HOH A 142 373 142 HOH HOH . 
F 3 HOH A 143 374 143 HOH HOH . 
F 3 HOH A 144 375 144 HOH HOH . 
F 3 HOH A 145 376 145 HOH HOH . 
F 3 HOH A 146 377 146 HOH HOH . 
F 3 HOH A 147 378 147 HOH HOH . 
F 3 HOH A 148 379 148 HOH HOH . 
F 3 HOH A 149 380 149 HOH HOH . 
F 3 HOH A 150 381 150 HOH HOH . 
F 3 HOH A 151 382 151 HOH HOH . 
F 3 HOH A 152 383 152 HOH HOH . 
F 3 HOH A 153 384 153 HOH HOH . 
F 3 HOH A 154 385 154 HOH HOH . 
F 3 HOH A 155 386 155 HOH HOH . 
F 3 HOH A 156 387 156 HOH HOH . 
F 3 HOH A 157 388 157 HOH HOH . 
F 3 HOH A 158 389 158 HOH HOH . 
F 3 HOH A 159 390 159 HOH HOH . 
F 3 HOH A 160 391 160 HOH HOH . 
F 3 HOH A 161 392 161 HOH HOH . 
F 3 HOH A 162 393 162 HOH HOH . 
F 3 HOH A 163 394 163 HOH HOH . 
F 3 HOH A 164 395 164 HOH HOH . 
F 3 HOH A 165 396 165 HOH HOH . 
F 3 HOH A 166 397 166 HOH HOH . 
F 3 HOH A 167 398 167 HOH HOH . 
F 3 HOH A 168 399 168 HOH HOH . 
F 3 HOH A 169 400 169 HOH HOH . 
F 3 HOH A 170 401 170 HOH HOH . 
F 3 HOH A 171 402 171 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 P 5GP . . . D 2 -0.162 18.322 8.694 1 25.69 ? P 5GP 503 A 1 
HETATM 2 O O1P 5GP . . . D 2 -0.295 18.355 10.173 1 20.67 ? O1P 5GP 503 A 1 
HETATM 3 O O2P 5GP . . . D 2 0.71 19.409 8.182 1 25.29 ? O2P 5GP 503 A 1 
HETATM 4 O O5' 5GP . . . D 2 0.533 16.962 8.217 1 21.56 ? O5' 5GP 503 A 1 
HETATM 5 C C5' 5GP . . . D 2 0.938 16.788 6.858 1 20.55 ? C5' 5GP 503 A 1 
HETATM 6 C C4' 5GP . . . D 2 1.388 15.341 6.646 1 20.52 ? C4' 5GP 503 A 1 
HETATM 7 O O4' 5GP . . . D 2 2.346 14.932 7.637 1 22.24 ? O4' 5GP 503 A 1 
HETATM 8 C C3' 5GP . . . D 2 0.229 14.371 6.86 1 20.79 ? C3' 5GP 503 A 1 
HETATM 9 O O3' 5GP . . . D 2 -0.613 14.402 5.705 1 18.13 ? O3' 5GP 503 A 1 
HETATM 10 C C2' 5GP . . . D 2 1.069 13.095 6.864 1 19.09 ? C2' 5GP 503 A 1 
HETATM 11 O O2' 5GP . . . D 2 1.627 12.886 5.564 1 18.42 ? O2' 5GP 503 A 1 
HETATM 12 C C1' 5GP . . . D 2 2.19 13.512 7.821 1 21.8 ? C1' 5GP 503 A 1 
HETATM 13 N N9 5GP . . . D 2 1.808 13.3 9.235 1 17.89 ? N9 5GP 503 A 1 
HETATM 14 C C8 5GP . . . D 2 1.7 14.25 10.161 1 20.37 ? C8 5GP 503 A 1 
HETATM 15 N N7 5GP . . . D 2 1.423 13.693 11.338 1 15.28 ? N7 5GP 503 A 1 
HETATM 16 C C5 5GP . . . D 2 1.349 12.377 11.164 1 18.73 ? C5 5GP 503 A 1 
HETATM 17 C C6 5GP . . . D 2 1.091 11.318 12.027 1 20.55 ? C6 5GP 503 A 1 
HETATM 18 O O6 5GP . . . D 2 0.911 11.511 13.229 1 23.07 ? O6 5GP 503 A 1 
HETATM 19 N N1 5GP . . . D 2 1.066 10.019 11.506 1 22.05 ? N1 5GP 503 A 1 
HETATM 20 C C2 5GP . . . D 2 1.304 9.825 10.14 1 23.52 ? C2 5GP 503 A 1 
HETATM 21 N N2 5GP . . . D 2 1.276 8.596 9.633 1 27.4 ? N2 5GP 503 A 1 
HETATM 22 N N3 5GP . . . D 2 1.559 10.871 9.34 1 20.45 ? N3 5GP 503 A 1 
HETATM 23 C C4 5GP . . . D 2 1.586 12.124 9.818 1 18.59 ? C4 5GP 503 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           23 
#