data_2OYN
#
_model_server_result.job_id            cbjwfPG6PSHZJ1Aw-lEZRg 
_model_server_result.datetime_utc      '2024-11-06 12:29:07' 
_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          2oyn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    2OYN 
#
_exptl.entry_id    2OYN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-DIPHOSPHATE" 
_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            2OYN 
_cell.length_a            63.48 
_cell.length_b            63.48 
_cell.length_c            73.117 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2OYN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 63.48 63.48 36.5585 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 A O THR 45 A THR 43 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc2 A OG1 THR 45 A THR 43 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc3 A OD1 ASN 47 A ASN 45 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc4 B NA NA . A NA 201 1_555 C O1A CDP . A CDP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? 
metalc ? metalc5 B NA NA . A NA 201 1_555 C O3A CDP . A CDP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? 
metalc ? metalc6 B NA NA . A NA 201 1_555 D O HOH . A HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
#
_chem_comp.formula           'C9 H15 N3 O11 P2' 
_chem_comp.formula_weight    403.176 
_chem_comp.id                CDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-DIPHOSPHATE" 
_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
O3B PB CDP sing 70 n n 
PB O1B CDP doub 71 n n 
PB O2B CDP sing 72 n n 
PB O3A CDP sing 73 n n 
O3A PA CDP sing 74 n n 
PA O1A CDP doub 75 n n 
PA O2A CDP sing 76 n n 
PA O5' CDP sing 77 n n 
O5' C5' CDP sing 78 n n 
C5' C4' CDP sing 79 n n 
C5' "H5'1" CDP sing 80 n n 
C5' "H5'2" CDP sing 81 n n 
C4' O4' CDP sing 82 n n 
C4' C3' CDP sing 83 n n 
C4' H4' CDP sing 84 n n 
O4' C1' CDP sing 85 n n 
C3' O3' CDP sing 86 n n 
C3' C2' CDP sing 87 n n 
C3' H3' CDP sing 88 n n 
O3' HA CDP sing 89 n n 
C2' O2' CDP sing 90 n n 
C2' C1' CDP sing 91 n n 
C2' H2' CDP sing 92 n n 
O2' HB CDP sing 93 n n 
C1' N1 CDP sing 94 n n 
C1' H1' CDP sing 95 n n 
N1 C2 CDP sing 96 n n 
N1 C6 CDP sing 97 n n 
C2 O2 CDP doub 98 n n 
C2 N3 CDP sing 99 n n 
N3 C4 CDP doub 100 n n 
C4 N4 CDP sing 101 n n 
C4 C5 CDP sing 102 n n 
N4 H4N1 CDP sing 103 n n 
N4 H4N2 CDP sing 104 n n 
C5 C6 CDP doub 105 n n 
C5 H5 CDP sing 106 n n 
C6 H6 CDP sing 107 n n 
HO1 O2A CDP sing 108 n n 
HO2 O2B CDP sing 109 n n 
HO3 O3B CDP sing 110 n n 
#
_atom_sites.entry_id                     2OYN 
_atom_sites.fract_transf_matrix[1][1]    0.015753 
_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]    0.015753 
_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]    0.013677 
_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 NA A 1 201 201 NA NA . 
C 3 CDP A 1 301 301 CDP CDP . 
D 4 HOH A 1 302 6 HOH HOH . 
D 4 HOH A 2 303 7 HOH HOH . 
D 4 HOH A 3 304 9 HOH HOH . 
D 4 HOH A 4 305 10 HOH HOH . 
D 4 HOH A 5 306 11 HOH HOH . 
D 4 HOH A 6 307 12 HOH HOH . 
D 4 HOH A 7 308 13 HOH HOH . 
D 4 HOH A 8 309 14 HOH HOH . 
D 4 HOH A 9 310 15 HOH HOH . 
D 4 HOH A 10 311 16 HOH HOH . 
D 4 HOH A 11 312 17 HOH HOH . 
D 4 HOH A 12 313 18 HOH HOH . 
D 4 HOH A 13 314 20 HOH HOH . 
D 4 HOH A 14 315 21 HOH HOH . 
D 4 HOH A 15 316 22 HOH HOH . 
D 4 HOH A 16 317 23 HOH HOH . 
D 4 HOH A 17 318 24 HOH HOH . 
D 4 HOH A 18 319 25 HOH HOH . 
D 4 HOH A 19 320 26 HOH HOH . 
D 4 HOH A 20 321 27 HOH HOH . 
D 4 HOH A 21 322 28 HOH HOH . 
D 4 HOH A 22 323 29 HOH HOH . 
D 4 HOH A 23 324 31 HOH HOH . 
D 4 HOH A 24 325 33 HOH HOH . 
D 4 HOH A 25 326 34 HOH HOH . 
D 4 HOH A 26 327 35 HOH HOH . 
D 4 HOH A 27 328 36 HOH HOH . 
D 4 HOH A 28 329 37 HOH HOH . 
D 4 HOH A 29 330 38 HOH HOH . 
D 4 HOH A 30 331 39 HOH HOH . 
D 4 HOH A 31 332 40 HOH HOH . 
D 4 HOH A 32 333 41 HOH HOH . 
D 4 HOH A 33 334 42 HOH HOH . 
D 4 HOH A 34 335 43 HOH HOH . 
D 4 HOH A 35 336 45 HOH HOH . 
D 4 HOH A 36 337 46 HOH HOH . 
D 4 HOH A 37 338 47 HOH HOH . 
D 4 HOH A 38 339 49 HOH HOH . 
D 4 HOH A 39 340 50 HOH HOH . 
D 4 HOH A 40 341 51 HOH HOH . 
D 4 HOH A 41 342 53 HOH HOH . 
D 4 HOH A 42 343 54 HOH HOH . 
D 4 HOH A 43 344 55 HOH HOH . 
D 4 HOH A 44 345 56 HOH HOH . 
D 4 HOH A 45 346 57 HOH HOH . 
D 4 HOH A 46 347 58 HOH HOH . 
D 4 HOH A 47 348 59 HOH HOH . 
D 4 HOH A 48 349 60 HOH HOH . 
D 4 HOH A 49 350 61 HOH HOH . 
D 4 HOH A 50 351 62 HOH HOH . 
D 4 HOH A 51 352 63 HOH HOH . 
D 4 HOH A 52 353 66 HOH HOH . 
D 4 HOH A 53 354 67 HOH HOH . 
D 4 HOH A 54 355 68 HOH HOH . 
D 4 HOH A 55 356 69 HOH HOH . 
D 4 HOH A 56 357 70 HOH HOH . 
D 4 HOH A 57 358 71 HOH HOH . 
D 4 HOH A 58 359 73 HOH HOH . 
D 4 HOH A 59 360 75 HOH HOH . 
D 4 HOH A 60 361 77 HOH HOH . 
D 4 HOH A 61 362 78 HOH HOH . 
D 4 HOH A 62 363 79 HOH HOH . 
D 4 HOH A 63 364 80 HOH HOH . 
D 4 HOH A 64 365 81 HOH HOH . 
D 4 HOH A 65 366 82 HOH HOH . 
D 4 HOH A 66 367 83 HOH HOH . 
D 4 HOH A 67 368 85 HOH HOH . 
D 4 HOH A 68 369 87 HOH HOH . 
D 4 HOH A 69 370 88 HOH HOH . 
D 4 HOH A 70 371 89 HOH HOH . 
D 4 HOH A 71 372 90 HOH HOH . 
D 4 HOH A 72 373 91 HOH HOH . 
D 4 HOH A 73 374 92 HOH HOH . 
D 4 HOH A 74 375 94 HOH HOH . 
D 4 HOH A 75 376 95 HOH HOH . 
D 4 HOH A 76 377 96 HOH HOH . 
D 4 HOH A 77 378 97 HOH HOH . 
D 4 HOH A 78 379 98 HOH HOH . 
D 4 HOH A 79 380 99 HOH HOH . 
D 4 HOH A 80 381 100 HOH HOH . 
D 4 HOH A 81 382 107 HOH HOH . 
D 4 HOH A 82 383 108 HOH HOH . 
D 4 HOH A 83 384 112 HOH HOH . 
D 4 HOH A 84 385 113 HOH HOH . 
D 4 HOH A 85 386 115 HOH HOH . 
D 4 HOH A 86 387 116 HOH HOH . 
D 4 HOH A 87 388 117 HOH HOH . 
D 4 HOH A 88 389 118 HOH HOH . 
D 4 HOH A 89 390 120 HOH HOH . 
D 4 HOH A 90 391 121 HOH HOH . 
D 4 HOH A 91 392 122 HOH HOH . 
D 4 HOH A 92 393 130 HOH HOH . 
D 4 HOH A 93 394 132 HOH HOH . 
D 4 HOH A 94 395 137 HOH HOH . 
D 4 HOH A 95 396 138 HOH HOH . 
D 4 HOH A 96 397 139 HOH HOH . 
D 4 HOH A 97 398 141 HOH HOH . 
D 4 HOH A 98 399 145 HOH HOH . 
D 4 HOH A 99 400 147 HOH HOH . 
D 4 HOH A 100 401 149 HOH HOH . 
D 4 HOH A 101 402 167 HOH HOH . 
D 4 HOH A 102 403 187 HOH HOH . 
D 4 HOH A 103 404 193 HOH HOH . 
D 4 HOH A 104 405 194 HOH HOH . 
D 4 HOH A 105 406 195 HOH HOH . 
D 4 HOH A 106 407 196 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 O3B CDP . . . C 3 17.094 6.761 28.349 1 17.53 ? O3B CDP 301 A 1 
HETATM 2 P PB CDP . . . C 3 18.415 6.048 28.452 1 18.69 ? PB CDP 301 A 1 
HETATM 3 O O1B CDP . . . C 3 19.464 6.824 29.195 1 18.81 ? O1B CDP 301 A 1 
HETATM 4 O O2B CDP . . . C 3 18.415 4.582 28.808 1 19.51 ? O2B CDP 301 A 1 
HETATM 5 O O3A CDP . . . C 3 18.995 6.012 26.926 1 17.66 ? O3A CDP 301 A 1 
HETATM 6 P PA CDP . . . C 3 18.635 5.201 25.566 1 17.52 ? PA CDP 301 A 1 
HETATM 7 O O1A CDP . . . C 3 18.397 6.186 24.45 1 17.13 ? O1A CDP 301 A 1 
HETATM 8 O O2A CDP . . . C 3 17.478 4.227 25.821 1 19.27 ? O2A CDP 301 A 1 
HETATM 9 O O5' CDP . . . C 3 19.913 4.355 25.159 1 19.09 ? O5' CDP 301 A 1 
HETATM 10 C C5' CDP . . . C 3 20.205 3.067 25.694 1 19.23 ? C5' CDP 301 A 1 
HETATM 11 C C4' CDP . . . C 3 21.528 3.068 26.433 1 18.21 ? C4' CDP 301 A 1 
HETATM 12 O O4' CDP . . . C 3 22.64 3.271 25.539 1 18.1 ? O4' CDP 301 A 1 
HETATM 13 C C3' CDP . . . C 3 21.608 4.153 27.501 1 16.81 ? C3' CDP 301 A 1 
HETATM 14 O O3' CDP . . . C 3 22.362 3.59 28.573 1 16.61 ? O3' CDP 301 A 1 
HETATM 15 C C2' CDP . . . C 3 22.429 5.231 26.79 1 15.16 ? C2' CDP 301 A 1 
HETATM 16 O O2' CDP . . . C 3 23.164 5.999 27.717 1 16.79 ? O2' CDP 301 A 1 
HETATM 17 C C1' CDP . . . C 3 23.409 4.419 25.982 1 16.38 ? C1' CDP 301 A 1 
HETATM 18 N N1 CDP . . . C 3 23.909 4.949 24.707 1 16.14 ? N1 CDP 301 A 1 
HETATM 19 C C2 CDP . . . C 3 25.283 4.839 24.433 1 16.52 ? C2 CDP 301 A 1 
HETATM 20 O O2 CDP . . . C 3 26.088 4.482 25.322 1 16.58 ? O2 CDP 301 A 1 
HETATM 21 N N3 CDP . . . C 3 25.747 5.229 23.225 1 15.83 ? N3 CDP 301 A 1 
HETATM 22 C C4 CDP . . . C 3 24.889 5.637 22.27 1 14.01 ? C4 CDP 301 A 1 
HETATM 23 N N4 CDP . . . C 3 25.395 5.96 21.054 1 16.88 ? N4 CDP 301 A 1 
HETATM 24 C C5 CDP . . . C 3 23.521 5.723 22.507 1 16.72 ? C5 CDP 301 A 1 
HETATM 25 C C6 CDP . . . C 3 23.037 5.358 23.751 1 15.64 ? C6 CDP 301 A 1 
#
_model_server_stats.io_time_ms              54 
_model_server_stats.parse_time_ms           28 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           25 
#