data_2OKE
#
_model_server_result.job_id            5ocuphEtFmk7IzrrJcTHmg 
_model_server_result.datetime_utc      '2024-11-05 00:16:11' 
_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          2oke 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":200}' 
#
_entry.id    2OKE 
#
_exptl.entry_id    2OKE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.157 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            2OKE 
_cell.length_a            120.46 
_cell.length_b            120.46 
_cell.length_c            50.1 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2OKE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_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,G,H,I,J,K,L 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 G N N 
? 3 H 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
metalc ? metalc1 B OE1 GLN 25 B GLN 25 1_555 F MG MG . B MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? 
metalc ? metalc2 F MG MG . B MG 300 1_555 K O HOH . B HOH 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.147 ? 
metalc ? metalc3 F MG MG . B MG 300 1_555 H O1G DUP . C DUP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc4 F MG MG . B MG 300 1_555 H N3A DUP . C DUP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? 
metalc ? metalc5 F MG MG . B MG 300 1_555 H O1B DUP . C DUP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? 
#
_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 83 n n 
C4 C5 DUP sing 84 n y 
C4 N3 DUP sing 85 n y 
C5 C6 DUP doub 86 n y 
C5 H5 DUP sing 87 n n 
C6 N1 DUP sing 88 n y 
C6 H6 DUP sing 89 n n 
N3 C2 DUP sing 90 n y 
N3 HN3 DUP sing 91 n n 
C2 O2 DUP doub 92 n n 
C2 N1 DUP sing 93 n y 
N1 C1' DUP sing 94 n n 
C1' C2' DUP sing 95 n n 
C1' O4' DUP sing 96 n n 
C1' H1' DUP sing 97 n n 
C2' C3' DUP sing 98 n n 
C2' "H2'1" DUP sing 99 n n 
C2' "H2'2" DUP sing 100 n n 
C3' O3' DUP sing 101 n n 
C3' C4' DUP sing 102 n n 
C3' H1 DUP sing 103 n n 
O3' H3' DUP sing 104 n n 
O4' C4' DUP sing 105 n n 
C4' C5' DUP sing 106 n n 
C4' H4' DUP sing 107 n n 
C5' O5' DUP sing 108 n n 
C5' "H5'1" DUP sing 109 n n 
C5' "H5'2" DUP sing 110 n n 
O5' PA DUP sing 111 n n 
PA O1A DUP doub 112 n n 
PA O2A DUP sing 113 n n 
PA N3A DUP sing 114 n n 
O2A H2A DUP sing 115 n n 
N3A PB DUP sing 116 n n 
N3A H3A DUP sing 117 n n 
PB O1B DUP doub 118 n n 
PB O2B DUP sing 119 n n 
PB O3B DUP sing 120 n n 
O2B H2B DUP sing 121 n n 
O3B PG DUP sing 122 n n 
PG O2G DUP doub 123 n n 
PG O1G DUP sing 124 n n 
PG O3G DUP sing 125 n n 
O1G H1G DUP sing 126 n n 
O3G H3G DUP sing 127 n n 
#
_atom_sites.entry_id                     2OKE 
_atom_sites.fract_transf_matrix[1][1]    0.008302 
_atom_sites.fract_transf_matrix[1][2]    0.004793 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009586 
_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]    0.01996 
_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
D 2 CL A 1 301 301 CL CL . 
E 3 DUP A 1 200 200 DUP DUP . 
F 4 MG B 1 300 300 MG MG . 
G 3 DUP B 1 201 201 DUP DUP . 
H 3 DUP C 1 202 202 DUP DUP . 
I 5 EDO C 1 401 401 EDO EDO . 
J 6 HOH A 1 302 4 HOH HOH . 
J 6 HOH A 2 303 9 HOH HOH . 
J 6 HOH A 3 304 12 HOH HOH . 
J 6 HOH A 4 305 17 HOH HOH . 
J 6 HOH A 5 306 22 HOH HOH . 
J 6 HOH A 6 307 31 HOH HOH . 
J 6 HOH A 7 308 36 HOH HOH . 
J 6 HOH A 8 309 38 HOH HOH . 
J 6 HOH A 9 310 40 HOH HOH . 
J 6 HOH A 10 311 48 HOH HOH . 
J 6 HOH A 11 312 51 HOH HOH . 
J 6 HOH A 12 313 53 HOH HOH . 
J 6 HOH A 13 314 56 HOH HOH . 
J 6 HOH A 14 315 59 HOH HOH . 
J 6 HOH A 15 316 67 HOH HOH . 
J 6 HOH A 16 317 70 HOH HOH . 
J 6 HOH A 17 318 71 HOH HOH . 
J 6 HOH A 18 319 73 HOH HOH . 
J 6 HOH A 19 320 76 HOH HOH . 
J 6 HOH A 20 321 78 HOH HOH . 
J 6 HOH A 21 322 83 HOH HOH . 
J 6 HOH A 22 323 87 HOH HOH . 
J 6 HOH A 23 324 101 HOH HOH . 
J 6 HOH A 24 325 104 HOH HOH . 
J 6 HOH A 25 326 106 HOH HOH . 
J 6 HOH A 26 327 108 HOH HOH . 
J 6 HOH A 27 328 110 HOH HOH . 
J 6 HOH A 28 329 112 HOH HOH . 
J 6 HOH A 29 330 117 HOH HOH . 
J 6 HOH A 30 331 120 HOH HOH . 
K 6 HOH B 1 301 3 HOH HOH . 
K 6 HOH B 2 302 5 HOH HOH . 
K 6 HOH B 3 303 6 HOH HOH . 
K 6 HOH B 4 304 8 HOH HOH . 
K 6 HOH B 5 305 10 HOH HOH . 
K 6 HOH B 6 306 14 HOH HOH . 
K 6 HOH B 7 307 16 HOH HOH . 
K 6 HOH B 8 308 18 HOH HOH . 
K 6 HOH B 9 309 20 HOH HOH . 
K 6 HOH B 10 310 24 HOH HOH . 
K 6 HOH B 11 311 25 HOH HOH . 
K 6 HOH B 12 312 26 HOH HOH . 
K 6 HOH B 13 313 28 HOH HOH . 
K 6 HOH B 14 314 29 HOH HOH . 
K 6 HOH B 15 315 30 HOH HOH . 
K 6 HOH B 16 316 34 HOH HOH . 
K 6 HOH B 17 317 35 HOH HOH . 
K 6 HOH B 18 318 43 HOH HOH . 
K 6 HOH B 19 319 44 HOH HOH . 
K 6 HOH B 20 320 47 HOH HOH . 
K 6 HOH B 21 321 52 HOH HOH . 
K 6 HOH B 22 322 54 HOH HOH . 
K 6 HOH B 23 323 55 HOH HOH . 
K 6 HOH B 24 324 57 HOH HOH . 
K 6 HOH B 25 325 58 HOH HOH . 
K 6 HOH B 26 326 60 HOH HOH . 
K 6 HOH B 27 327 61 HOH HOH . 
K 6 HOH B 28 328 64 HOH HOH . 
K 6 HOH B 29 329 65 HOH HOH . 
K 6 HOH B 30 330 66 HOH HOH . 
K 6 HOH B 31 331 69 HOH HOH . 
K 6 HOH B 32 332 75 HOH HOH . 
K 6 HOH B 33 333 77 HOH HOH . 
K 6 HOH B 34 334 79 HOH HOH . 
K 6 HOH B 35 335 80 HOH HOH . 
K 6 HOH B 36 336 81 HOH HOH . 
K 6 HOH B 37 337 82 HOH HOH . 
K 6 HOH B 38 338 85 HOH HOH . 
K 6 HOH B 39 339 86 HOH HOH . 
K 6 HOH B 40 340 97 HOH HOH . 
K 6 HOH B 41 341 99 HOH HOH . 
K 6 HOH B 42 342 100 HOH HOH . 
K 6 HOH B 43 343 111 HOH HOH . 
K 6 HOH B 44 344 116 HOH HOH . 
K 6 HOH B 45 345 118 HOH HOH . 
K 6 HOH B 46 346 119 HOH HOH . 
K 6 HOH B 47 347 121 HOH HOH . 
L 6 HOH C 1 402 1 HOH HOH . 
L 6 HOH C 2 403 2 HOH HOH . 
L 6 HOH C 3 404 7 HOH HOH . 
L 6 HOH C 4 405 11 HOH HOH . 
L 6 HOH C 5 406 13 HOH HOH . 
L 6 HOH C 6 407 15 HOH HOH . 
L 6 HOH C 7 408 19 HOH HOH . 
L 6 HOH C 8 409 21 HOH HOH . 
L 6 HOH C 9 410 23 HOH HOH . 
L 6 HOH C 10 411 27 HOH HOH . 
L 6 HOH C 11 412 32 HOH HOH . 
L 6 HOH C 12 413 33 HOH HOH . 
L 6 HOH C 13 414 37 HOH HOH . 
L 6 HOH C 14 415 39 HOH HOH . 
L 6 HOH C 15 416 41 HOH HOH . 
L 6 HOH C 16 417 42 HOH HOH . 
L 6 HOH C 17 418 45 HOH HOH . 
L 6 HOH C 18 419 46 HOH HOH . 
L 6 HOH C 19 420 49 HOH HOH . 
L 6 HOH C 20 421 50 HOH HOH . 
L 6 HOH C 21 422 62 HOH HOH . 
L 6 HOH C 22 423 63 HOH HOH . 
L 6 HOH C 23 424 68 HOH HOH . 
L 6 HOH C 24 425 72 HOH HOH . 
L 6 HOH C 25 426 74 HOH HOH . 
L 6 HOH C 26 427 84 HOH HOH . 
L 6 HOH C 27 428 88 HOH HOH . 
L 6 HOH C 28 429 89 HOH HOH . 
L 6 HOH C 29 430 90 HOH HOH . 
L 6 HOH C 30 431 91 HOH HOH . 
L 6 HOH C 31 432 92 HOH HOH . 
L 6 HOH C 32 433 93 HOH HOH . 
L 6 HOH C 33 434 94 HOH HOH . 
L 6 HOH C 34 435 95 HOH HOH . 
L 6 HOH C 35 436 96 HOH HOH . 
L 6 HOH C 36 437 98 HOH HOH . 
L 6 HOH C 37 438 102 HOH HOH . 
L 6 HOH C 38 439 105 HOH HOH . 
L 6 HOH C 39 440 107 HOH HOH . 
L 6 HOH C 40 441 109 HOH HOH . 
L 6 HOH C 41 442 113 HOH HOH . 
L 6 HOH C 42 443 114 HOH HOH . 
L 6 HOH C 43 444 115 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 . . . E 3 0.592 -32.979 0.653 1 44.34 ? O4 DUP 200 A 1 
HETATM 2 C C4 DUP . . . E 3 1.806 -33.273 0.644 1 44.44 ? C4 DUP 200 A 1 
HETATM 3 C C5 DUP . . . E 3 2.264 -34.267 -0.209 1 44.27 ? C5 DUP 200 A 1 
HETATM 4 C C6 DUP . . . E 3 3.618 -34.582 -0.212 1 44.49 ? C6 DUP 200 A 1 
HETATM 5 N N3 DUP . . . E 3 2.679 -32.63 1.457 1 44.58 ? N3 DUP 200 A 1 
HETATM 6 C C2 DUP . . . E 3 4.001 -32.931 1.463 1 44.48 ? C2 DUP 200 A 1 
HETATM 7 O O2 DUP . . . E 3 4.764 -32.308 2.238 1 43.96 ? O2 DUP 200 A 1 
HETATM 8 N N1 DUP . . . E 3 4.488 -33.943 0.594 1 44.63 ? N1 DUP 200 A 1 
HETATM 9 C C1' DUP . . . E 3 5.915 -34.309 0.574 1 44.85 ? C1' DUP 200 A 1 
HETATM 10 C C2' DUP . . . E 3 6.066 -35.807 0.811 1 45.48 ? C2' DUP 200 A 1 
HETATM 11 C C3' DUP . . . E 3 6.578 -36.387 -0.494 1 46.02 ? C3' DUP 200 A 1 
HETATM 12 O O3' DUP . . . E 3 7.702 -37.222 -0.22 1 45.28 ? O3' DUP 200 A 1 
HETATM 13 O O4' DUP . . . E 3 6.515 -34.013 -0.692 1 45.85 ? O4' DUP 200 A 1 
HETATM 14 C C4' DUP . . . E 3 6.958 -35.195 -1.366 1 47.13 ? C4' DUP 200 A 1 
HETATM 15 C C5' DUP . . . E 3 6.29 -35.268 -2.735 1 49.91 ? C5' DUP 200 A 1 
HETATM 16 O O5' DUP . . . E 3 7.242 -35.565 -3.758 1 53.82 ? O5' DUP 200 A 1 
HETATM 17 P PA DUP . . . E 3 7.88 -34.432 -4.719 1 56.01 ? PA DUP 200 A 1 
HETATM 18 O O1A DUP . . . E 3 7.984 -33.156 -3.91 1 55.97 ? O1A DUP 200 A 1 
HETATM 19 O O2A DUP . . . E 3 9.155 -35.02 -5.282 1 56.01 ? O2A DUP 200 A 1 
HETATM 20 N N3A DUP . . . E 3 6.863 -34.15 -6.016 1 57.6 ? N3A DUP 200 A 1 
HETATM 21 P PB DUP . . . E 3 6.845 -35.211 -7.309 1 59.6 ? PB DUP 200 A 1 
HETATM 22 O O1B DUP . . . E 3 5.648 -34.883 -8.173 1 59.02 ? O1B DUP 200 A 1 
HETATM 23 O O2B DUP . . . E 3 8.209 -35.218 -7.965 1 59.43 ? O2B DUP 200 A 1 
HETATM 24 O O3B DUP . . . E 3 6.633 -36.683 -6.689 1 60.12 ? O3B DUP 200 A 1 
HETATM 25 P PG DUP . . . E 3 5.243 -37.097 -5.986 1 61.02 ? PG DUP 200 A 1 
HETATM 26 O O2G DUP . . . E 3 5.636 -37.912 -4.777 1 60.96 ? O2G DUP 200 A 1 
HETATM 27 O O1G DUP . . . E 3 4.569 -35.798 -5.62 1 60.88 ? O1G DUP 200 A 1 
HETATM 28 O O3G DUP . . . E 3 4.558 -37.878 -7.083 1 61.05 ? O3G DUP 200 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#