data_4GCY
#
_model_server_result.job_id            88RFQHHVqUEm7WNOePueqA 
_model_server_result.datetime_utc      '2025-07-10 00:30:44' 
_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          4gcy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    4GCY 
#
_exptl.entry_id    4GCY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.157 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" 
_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         120 
_cell.entry_id            4GCY 
_cell.length_a            54.94 
_cell.length_b            54.94 
_cell.length_c            83.86 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4GCY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_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    1,2,3 
#
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_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 27.47 -47.579436 0 
3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 54.94 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 O1A DUP . A DUP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc2 B O1B DUP . A DUP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc3 B O2G DUP . A DUP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc4 D MG MG . A MG 203 1_555 F O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc5 D MG MG . A MG 203 1_555 F O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc6 D MG MG . A MG 203 1_555 F O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
#
_chem_comp.formula           'C9 H16 N3 O13 P3' 
_chem_comp.formula_weight    467.157 
_chem_comp.id                DUP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" 
_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
O4 C4 DUP doub 70 n n 
C4 C5 DUP sing 71 n y 
C4 N3 DUP sing 72 n y 
C5 C6 DUP doub 73 n y 
C5 H5 DUP sing 74 n n 
C6 N1 DUP sing 75 n y 
C6 H6 DUP sing 76 n n 
N3 C2 DUP sing 77 n y 
N3 HN3 DUP sing 78 n n 
C2 O2 DUP doub 79 n n 
C2 N1 DUP sing 80 n y 
N1 C1' DUP sing 81 n n 
C1' C2' DUP sing 82 n n 
C1' O4' DUP sing 83 n n 
C1' H1' DUP sing 84 n n 
C2' C3' DUP sing 85 n n 
C2' "H2'1" DUP sing 86 n n 
C2' "H2'2" DUP sing 87 n n 
C3' O3' DUP sing 88 n n 
C3' C4' DUP sing 89 n n 
C3' H1 DUP sing 90 n n 
O3' H3' DUP sing 91 n n 
O4' C4' DUP sing 92 n n 
C4' C5' DUP sing 93 n n 
C4' H4' DUP sing 94 n n 
C5' O5' DUP sing 95 n n 
C5' "H5'1" DUP sing 96 n n 
C5' "H5'2" DUP sing 97 n n 
O5' PA DUP sing 98 n n 
PA O1A DUP doub 99 n n 
PA O2A DUP sing 100 n n 
PA N3A DUP sing 101 n n 
O2A H2A DUP sing 102 n n 
N3A PB DUP sing 103 n n 
N3A H3A DUP sing 104 n n 
PB O1B DUP doub 105 n n 
PB O2B DUP sing 106 n n 
PB O3B DUP sing 107 n n 
O2B H2B DUP sing 108 n n 
O3B PG DUP sing 109 n n 
PG O2G DUP doub 110 n n 
PG O1G DUP sing 111 n n 
PG O3G DUP sing 112 n n 
O1G H1G DUP sing 113 n n 
O3G H3G DUP sing 114 n n 
#
_atom_sites.entry_id                     4GCY 
_atom_sites.fract_transf_matrix[1][1]    0.018202 
_atom_sites.fract_transf_matrix[1][2]    0.010509 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021018 
_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]    0.011925 
_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 DUP A 1 201 2777 DUP DUP . 
C 3 TRS A 1 202 2204 TRS TRS . 
D 4 MG A 1 203 2206 MG MG . 
E 5 GOL A 1 204 2110 GOL GOL . 
F 6 HOH A 1 301 1 HOH HOH . 
F 6 HOH A 2 302 2 HOH HOH . 
F 6 HOH A 3 303 3 HOH HOH . 
F 6 HOH A 4 304 5 HOH HOH . 
F 6 HOH A 5 305 7 HOH HOH . 
F 6 HOH A 6 306 8 HOH HOH . 
F 6 HOH A 7 307 9 HOH HOH . 
F 6 HOH A 8 308 10 HOH HOH . 
F 6 HOH A 9 309 11 HOH HOH . 
F 6 HOH A 10 310 12 HOH HOH . 
F 6 HOH A 11 311 13 HOH HOH . 
F 6 HOH A 12 312 14 HOH HOH . 
F 6 HOH A 13 313 15 HOH HOH . 
F 6 HOH A 14 314 16 HOH HOH . 
F 6 HOH A 15 315 17 HOH HOH . 
F 6 HOH A 16 316 19 HOH HOH . 
F 6 HOH A 17 317 20 HOH HOH . 
F 6 HOH A 18 318 21 HOH HOH . 
F 6 HOH A 19 319 22 HOH HOH . 
F 6 HOH A 20 320 23 HOH HOH . 
F 6 HOH A 21 321 24 HOH HOH . 
F 6 HOH A 22 322 25 HOH HOH . 
F 6 HOH A 23 323 26 HOH HOH . 
F 6 HOH A 24 324 28 HOH HOH . 
F 6 HOH A 25 325 29 HOH HOH . 
F 6 HOH A 26 326 30 HOH HOH . 
F 6 HOH A 27 327 31 HOH HOH . 
F 6 HOH A 28 328 32 HOH HOH . 
F 6 HOH A 29 329 33 HOH HOH . 
F 6 HOH A 30 330 34 HOH HOH . 
F 6 HOH A 31 331 35 HOH HOH . 
F 6 HOH A 32 332 36 HOH HOH . 
F 6 HOH A 33 333 37 HOH HOH . 
F 6 HOH A 34 334 38 HOH HOH . 
F 6 HOH A 35 335 39 HOH HOH . 
F 6 HOH A 36 336 41 HOH HOH . 
F 6 HOH A 37 337 42 HOH HOH . 
F 6 HOH A 38 338 43 HOH HOH . 
F 6 HOH A 39 339 45 HOH HOH . 
F 6 HOH A 40 340 46 HOH HOH . 
F 6 HOH A 41 341 49 HOH HOH . 
F 6 HOH A 42 342 50 HOH HOH . 
F 6 HOH A 43 343 51 HOH HOH . 
F 6 HOH A 44 344 52 HOH HOH . 
F 6 HOH A 45 345 53 HOH HOH . 
F 6 HOH A 46 346 54 HOH HOH . 
F 6 HOH A 47 347 56 HOH HOH . 
F 6 HOH A 48 348 57 HOH HOH . 
F 6 HOH A 49 349 58 HOH HOH . 
F 6 HOH A 50 350 59 HOH HOH . 
F 6 HOH A 51 351 63 HOH HOH . 
F 6 HOH A 52 352 67 HOH HOH . 
F 6 HOH A 53 353 68 HOH HOH . 
F 6 HOH A 54 354 69 HOH HOH . 
F 6 HOH A 55 355 71 HOH HOH . 
F 6 HOH A 56 356 72 HOH HOH . 
F 6 HOH A 57 357 74 HOH HOH . 
F 6 HOH A 58 358 76 HOH HOH . 
F 6 HOH A 59 359 77 HOH HOH . 
F 6 HOH A 60 360 79 HOH HOH . 
F 6 HOH A 61 361 81 HOH HOH . 
F 6 HOH A 62 362 82 HOH HOH . 
F 6 HOH A 63 363 85 HOH HOH . 
F 6 HOH A 64 364 86 HOH HOH . 
F 6 HOH A 65 365 88 HOH HOH . 
F 6 HOH A 66 366 90 HOH HOH . 
F 6 HOH A 67 367 92 HOH HOH . 
F 6 HOH A 68 368 96 HOH HOH . 
F 6 HOH A 69 369 98 HOH HOH . 
F 6 HOH A 70 370 99 HOH HOH . 
F 6 HOH A 71 371 107 HOH HOH . 
F 6 HOH A 72 372 111 HOH HOH . 
F 6 HOH A 73 373 122 HOH HOH . 
F 6 HOH A 74 374 125 HOH HOH . 
F 6 HOH A 75 375 142 HOH HOH . 
F 6 HOH A 76 376 150 HOH HOH . 
F 6 HOH A 77 377 151 HOH HOH . 
F 6 HOH A 78 378 154 HOH HOH . 
F 6 HOH A 79 379 176 HOH HOH . 
F 6 HOH A 80 380 179 HOH HOH . 
F 6 HOH A 81 381 180 HOH HOH . 
F 6 HOH A 82 382 182 HOH HOH . 
F 6 HOH A 83 383 183 HOH HOH . 
F 6 HOH A 84 384 188 HOH HOH . 
F 6 HOH A 85 385 195 HOH HOH . 
F 6 HOH A 86 386 198 HOH HOH . 
F 6 HOH A 87 387 203 HOH HOH . 
F 6 HOH A 88 388 204 HOH HOH . 
F 6 HOH A 89 389 206 HOH HOH . 
F 6 HOH A 90 390 207 HOH HOH . 
F 6 HOH A 91 391 209 HOH HOH . 
F 6 HOH A 92 392 211 HOH HOH . 
F 6 HOH A 93 393 212 HOH HOH . 
F 6 HOH A 94 394 213 HOH HOH . 
F 6 HOH A 95 395 215 HOH HOH . 
F 6 HOH A 96 396 217 HOH HOH . 
F 6 HOH A 97 397 226 HOH HOH . 
F 6 HOH A 98 398 227 HOH HOH . 
F 6 HOH A 99 399 228 HOH HOH . 
F 6 HOH A 100 400 229 HOH HOH . 
F 6 HOH A 101 401 241 HOH HOH . 
F 6 HOH A 102 402 242 HOH HOH . 
F 6 HOH A 103 403 243 HOH HOH . 
F 6 HOH A 104 404 244 HOH HOH . 
F 6 HOH A 105 405 245 HOH HOH . 
F 6 HOH A 106 406 246 HOH HOH . 
F 6 HOH A 107 407 247 HOH HOH . 
F 6 HOH A 108 408 251 HOH HOH . 
F 6 HOH A 109 409 254 HOH HOH . 
F 6 HOH A 110 410 255 HOH HOH . 
F 6 HOH A 111 411 258 HOH HOH . 
F 6 HOH A 112 412 259 HOH HOH . 
F 6 HOH A 113 413 260 HOH HOH . 
F 6 HOH A 114 414 261 HOH HOH . 
F 6 HOH A 115 415 262 HOH HOH . 
F 6 HOH A 116 416 263 HOH HOH . 
F 6 HOH A 117 417 264 HOH HOH . 
F 6 HOH A 118 418 265 HOH HOH . 
F 6 HOH A 119 419 266 HOH HOH . 
F 6 HOH A 120 420 267 HOH HOH . 
F 6 HOH A 121 421 268 HOH HOH . 
F 6 HOH A 122 422 269 HOH HOH . 
F 6 HOH A 123 423 270 HOH HOH . 
F 6 HOH A 124 424 271 HOH HOH . 
F 6 HOH A 125 425 273 HOH HOH . 
F 6 HOH A 126 426 274 HOH HOH . 
F 6 HOH A 127 427 276 HOH HOH . 
F 6 HOH A 128 428 277 HOH HOH . 
F 6 HOH A 129 429 278 HOH HOH . 
F 6 HOH A 130 430 279 HOH HOH . 
F 6 HOH A 131 431 280 HOH HOH . 
F 6 HOH A 132 432 281 HOH HOH . 
F 6 HOH A 133 433 282 HOH HOH . 
F 6 HOH A 134 434 283 HOH HOH . 
F 6 HOH A 135 435 284 HOH HOH . 
F 6 HOH A 136 436 285 HOH HOH . 
F 6 HOH A 137 437 287 HOH HOH . 
F 6 HOH A 138 438 289 HOH HOH . 
F 6 HOH A 139 439 290 HOH HOH . 
F 6 HOH A 140 440 291 HOH HOH . 
F 6 HOH A 141 441 292 HOH HOH . 
F 6 HOH A 142 442 293 HOH HOH . 
F 6 HOH A 143 443 294 HOH HOH . 
F 6 HOH A 144 444 295 HOH HOH . 
F 6 HOH A 145 445 296 HOH HOH . 
F 6 HOH A 146 446 297 HOH HOH . 
F 6 HOH A 147 447 298 HOH HOH . 
F 6 HOH A 148 448 299 HOH HOH . 
F 6 HOH A 149 449 300 HOH HOH . 
F 6 HOH A 150 450 301 HOH HOH . 
F 6 HOH A 151 451 302 HOH HOH . 
F 6 HOH A 152 452 303 HOH HOH . 
F 6 HOH A 153 453 304 HOH HOH . 
F 6 HOH A 154 454 305 HOH HOH . 
F 6 HOH A 155 455 306 HOH HOH . 
F 6 HOH A 156 456 307 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 O O4 DUP . . . B 2 21.469 -7.038 0.002 1 20.98 ? O4 DUP 201 A 1 
HETATM 2 C C4 DUP . . . B 2 20.283 -6.752 -0.489 1 20.5 ? C4 DUP 201 A 1 
HETATM 3 C C5 DUP . . . B 2 19.398 -7.724 -0.963 1 20.12 ? C5 DUP 201 A 1 
HETATM 4 C C6 DUP . . . B 2 18.2 -7.254 -1.478 1 21.58 ? C6 DUP 201 A 1 
HETATM 5 N N3 DUP . . . B 2 19.979 -5.439 -0.51 1 19.91 ? N3 DUP 201 A 1 
HETATM 6 C C2 DUP . . . B 2 18.816 -5.029 -1.044 1 20.03 ? C2 DUP 201 A 1 
HETATM 7 O O2 DUP . . . B 2 18.577 -3.718 -1.052 1 21.01 ? O2 DUP 201 A 1 
HETATM 8 N N1 DUP . . . B 2 17.921 -5.924 -1.497 1 20.2 ? N1 DUP 201 A 1 
HETATM 9 C C1' DUP . . . B 2 16.646 -5.469 -2.088 1 20.36 ? C1' DUP 201 A 1 
HETATM 10 C C2' DUP . . . B 2 16.74 -5.552 -3.628 1 18.91 ? C2' DUP 201 A 1 
HETATM 11 C C3' DUP . . . B 2 16.075 -6.884 -3.958 1 19.24 ? C3' DUP 201 A 1 
HETATM 12 O O3' DUP . . . B 2 15.52 -6.905 -5.29 1 20 ? O3' DUP 201 A 1 
HETATM 13 O O4' DUP . . . B 2 15.596 -6.353 -1.704 1 20.24 ? O4' DUP 201 A 1 
HETATM 14 C C4' DUP . . . B 2 14.996 -6.936 -2.884 1 20.14 ? C4' DUP 201 A 1 
HETATM 15 C C5' DUP . . . B 2 14.513 -8.359 -2.562 1 20.87 ? C5' DUP 201 A 1 
HETATM 16 O O5' DUP . . . B 2 15.652 -9.148 -2.202 1 20.01 ? O5' DUP 201 A 1 
HETATM 17 P PA DUP . . . B 2 15.363 -10.661 -1.73 1 21.74 ? PA DUP 201 A 1 
HETATM 18 O O1A DUP . . . B 2 14.414 -11.295 -2.718 1 21.77 ? O1A DUP 201 A 1 
HETATM 19 O O2A DUP . . . B 2 16.77 -11.275 -1.667 1 23.29 ? O2A DUP 201 A 1 
HETATM 20 N N3A DUP . . . B 2 14.68 -10.571 -0.236 1 23.99 ? N3A DUP 201 A 1 
HETATM 21 P PB DUP . . . B 2 13.116 -11 0.082 1 23.92 ? PB DUP 201 A 1 
HETATM 22 O O1B DUP . . . B 2 12.642 -12.196 -0.699 1 20.97 ? O1B DUP 201 A 1 
HETATM 23 O O2B DUP . . . B 2 12.992 -11.055 1.6 1 22.92 ? O2B DUP 201 A 1 
HETATM 24 O O3B DUP . . . B 2 12.259 -9.715 -0.408 1 25.62 ? O3B DUP 201 A 1 
HETATM 25 P PG DUP . . . B 2 11.004 -9.725 -1.451 1 23.45 ? PG DUP 201 A 1 
HETATM 26 O O2G DUP . . . B 2 11.493 -10.489 -2.655 1 20.63 ? O2G DUP 201 A 1 
HETATM 27 O O1G DUP . . . B 2 9.943 -10.441 -0.711 1 26.64 ? O1G DUP 201 A 1 
HETATM 28 O O3G DUP . . . B 2 10.79 -8.243 -1.737 1 22.56 ? O3G DUP 201 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           481 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#