data_1RAG
#
_model_server_result.job_id            6VkAP71Io0zJCkYF-SO7lw 
_model_server_result.datetime_utc      '2024-12-26 17:14:01' 
_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          1rag 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":999}' 
#
_entry.id    1RAG 
#
_exptl.entry_id    1RAG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              483.156 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            1RAG 
_cell.length_a            122.13 
_cell.length_b            122.13 
_cell.length_c            142.51 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RAG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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    1,2,3 
#
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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 122.13 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 61.065 105.767683 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 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 SG CYS 109 B CYS 109 1_555 E ZN ZN . B ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc2 B SG CYS 114 B CYS 114 1_555 E ZN ZN . B ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc3 B SG CYS 138 B CYS 138 1_555 E ZN ZN . B ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc4 B SG CYS 141 B CYS 141 1_555 E ZN ZN . B ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc5 D SG CYS 109 D CYS 109 1_555 G ZN ZN . D ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc6 D SG CYS 114 D CYS 114 1_555 G ZN ZN . D ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc7 D SG CYS 138 D CYS 138 1_555 G ZN ZN . D ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc8 D SG CYS 141 D CYS 141 1_555 G ZN ZN . D ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
#
_chem_comp.formula           'C9 H16 N3 O14 P3' 
_chem_comp.formula_weight    483.156 
_chem_comp.id                CTP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-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
N1 C2 CTP sing 70 n n 
N1 C6 CTP sing 71 n n 
N1 C1' CTP sing 72 n n 
C2 N3 CTP sing 73 n n 
C2 O2 CTP doub 74 n n 
N3 C4 CTP doub 75 n n 
C4 C5 CTP sing 76 n n 
C4 N4 CTP sing 77 n n 
C5 C6 CTP doub 78 n n 
C5 H5 CTP sing 79 n n 
C6 H6 CTP sing 80 n n 
N4 HN41 CTP sing 81 n n 
N4 HN42 CTP sing 82 n n 
C1' C2' CTP sing 83 n n 
C1' O4' CTP sing 84 n n 
C1' H1' CTP sing 85 n n 
C2' O2' CTP sing 86 n n 
C2' C3' CTP sing 87 n n 
C2' H2' CTP sing 88 n n 
O2' HO2' CTP sing 89 n n 
C3' C4' CTP sing 90 n n 
C3' O3' CTP sing 91 n n 
C3' H3' CTP sing 92 n n 
C4' O4' CTP sing 93 n n 
C4' C5' CTP sing 94 n n 
C4' H4' CTP sing 95 n n 
O3' HO3' CTP sing 96 n n 
C5' O5' CTP sing 97 n n 
C5' "H5'1" CTP sing 98 n n 
C5' "H5'2" CTP sing 99 n n 
O5' PA CTP sing 100 n n 
PA O1A CTP doub 101 n n 
PA O2A CTP sing 102 n n 
PA O3A CTP sing 103 n n 
O2A HOA2 CTP sing 104 n n 
O3A PB CTP sing 105 n n 
PB O1B CTP doub 106 n n 
PB O2B CTP sing 107 n n 
PB O3B CTP sing 108 n n 
O2B HOB2 CTP sing 109 n n 
O3B PG CTP sing 110 n n 
PG O1G CTP doub 111 n n 
PG O2G CTP sing 112 n n 
PG O3G CTP sing 113 n n 
O2G HOG2 CTP sing 114 n n 
O3G HOG3 CTP sing 115 n n 
#
_atom_sites.entry_id                     1RAG 
_atom_sites.fract_transf_matrix[1][1]    0.008188 
_atom_sites.fract_transf_matrix[1][2]    0.004727 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009455 
_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]    0.007017 
_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
E 3 ZN B 1 154 109 ZN ZN . 
F 4 CTP B 1 999 999 CTP CTP . 
G 3 ZN D 1 154 109 ZN ZN . 
H 4 CTP D 1 999 999 CTP CTP . 
I 5 HOH A 1 311 345 HOH HOH . 
I 5 HOH A 2 312 358 HOH HOH . 
I 5 HOH A 3 313 360 HOH HOH . 
I 5 HOH A 4 314 361 HOH HOH . 
I 5 HOH A 5 315 363 HOH HOH . 
I 5 HOH A 6 316 373 HOH HOH . 
I 5 HOH A 7 317 381 HOH HOH . 
I 5 HOH A 8 318 388 HOH HOH . 
I 5 HOH A 9 319 403 HOH HOH . 
I 5 HOH A 10 320 405 HOH HOH . 
I 5 HOH A 11 321 408 HOH HOH . 
I 5 HOH A 12 322 422 HOH HOH . 
I 5 HOH A 13 323 426 HOH HOH . 
I 5 HOH A 14 324 428 HOH HOH . 
I 5 HOH A 15 325 438 HOH HOH . 
I 5 HOH A 16 326 439 HOH HOH . 
I 5 HOH A 17 327 440 HOH HOH . 
I 5 HOH A 18 328 450 HOH HOH . 
I 5 HOH A 19 329 454 HOH HOH . 
I 5 HOH A 20 330 475 HOH HOH . 
I 5 HOH A 21 331 479 HOH HOH . 
I 5 HOH A 22 332 486 HOH HOH . 
I 5 HOH A 23 333 540 HOH HOH . 
I 5 HOH A 24 334 541 HOH HOH . 
I 5 HOH A 25 335 555 HOH HOH . 
I 5 HOH A 26 336 577 HOH HOH . 
I 5 HOH A 27 337 578 HOH HOH . 
I 5 HOH A 28 338 586 HOH HOH . 
I 5 HOH A 29 339 159 HOH HOH . 
I 5 HOH A 30 340 212 HOH HOH . 
I 5 HOH A 31 341 216 HOH HOH . 
J 5 HOH B 1 1000 156 HOH HOH . 
J 5 HOH B 2 1001 168 HOH HOH . 
J 5 HOH B 3 1002 192 HOH HOH . 
J 5 HOH B 4 1003 230 HOH HOH . 
J 5 HOH B 5 1004 240 HOH HOH . 
J 5 HOH B 6 1005 249 HOH HOH . 
J 5 HOH B 7 1006 277 HOH HOH . 
J 5 HOH B 8 1007 279 HOH HOH . 
J 5 HOH B 9 1008 292 HOH HOH . 
K 5 HOH C 1 311 465 HOH HOH . 
K 5 HOH C 2 312 311 HOH HOH . 
K 5 HOH C 3 313 317 HOH HOH . 
K 5 HOH C 4 314 322 HOH HOH . 
K 5 HOH C 5 315 323 HOH HOH . 
K 5 HOH C 6 316 333 HOH HOH . 
K 5 HOH C 7 317 334 HOH HOH . 
K 5 HOH C 8 318 339 HOH HOH . 
K 5 HOH C 9 319 343 HOH HOH . 
K 5 HOH C 10 320 350 HOH HOH . 
K 5 HOH C 11 321 357 HOH HOH . 
K 5 HOH C 12 322 367 HOH HOH . 
K 5 HOH C 13 323 369 HOH HOH . 
K 5 HOH C 14 324 372 HOH HOH . 
K 5 HOH C 15 325 378 HOH HOH . 
K 5 HOH C 16 326 383 HOH HOH . 
K 5 HOH C 17 327 389 HOH HOH . 
K 5 HOH C 18 328 404 HOH HOH . 
K 5 HOH C 19 329 430 HOH HOH . 
K 5 HOH C 20 330 433 HOH HOH . 
K 5 HOH C 21 331 435 HOH HOH . 
K 5 HOH C 22 332 439 HOH HOH . 
K 5 HOH C 23 333 440 HOH HOH . 
K 5 HOH C 24 334 443 HOH HOH . 
K 5 HOH C 25 335 448 HOH HOH . 
K 5 HOH C 26 336 477 HOH HOH . 
K 5 HOH C 27 337 492 HOH HOH . 
K 5 HOH C 28 338 514 HOH HOH . 
K 5 HOH C 29 339 519 HOH HOH . 
K 5 HOH C 30 340 524 HOH HOH . 
K 5 HOH C 31 341 530 HOH HOH . 
K 5 HOH C 32 342 537 HOH HOH . 
K 5 HOH C 33 343 545 HOH HOH . 
K 5 HOH C 34 344 560 HOH HOH . 
K 5 HOH C 35 345 561 HOH HOH . 
K 5 HOH C 36 346 566 HOH HOH . 
K 5 HOH C 37 347 572 HOH HOH . 
K 5 HOH C 38 348 573 HOH HOH . 
K 5 HOH C 39 349 581 HOH HOH . 
K 5 HOH C 40 350 592 HOH HOH . 
K 5 HOH C 41 351 603 HOH HOH . 
K 5 HOH C 42 352 607 HOH HOH . 
K 5 HOH C 43 353 173 HOH HOH . 
L 5 HOH D 1 1000 312 HOH HOH . 
L 5 HOH D 2 1001 158 HOH HOH . 
L 5 HOH D 3 1002 164 HOH HOH . 
L 5 HOH D 4 1003 176 HOH HOH . 
L 5 HOH D 5 1004 190 HOH HOH . 
L 5 HOH D 6 1005 192 HOH HOH . 
L 5 HOH D 7 1006 213 HOH HOH . 
L 5 HOH D 8 1007 265 HOH HOH . 
L 5 HOH D 9 1008 304 HOH HOH . 
L 5 HOH D 10 1009 319 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 N N1 CTP . . . H 4 25.279 93.092 44.167 1 72.82 ? N1 CTP 999 D 1 
HETATM 2 C C2 CTP . . . H 4 24.261 92.211 44.053 1 72.94 ? C2 CTP 999 D 1 
HETATM 3 N N3 CTP . . . H 4 23.129 92.34 44.732 1 72.65 ? N3 CTP 999 D 1 
HETATM 4 C C4 CTP . . . H 4 22.944 93.336 45.569 1 72.99 ? C4 CTP 999 D 1 
HETATM 5 C C5 CTP . . . H 4 23.925 94.283 45.701 1 71.67 ? C5 CTP 999 D 1 
HETATM 6 C C6 CTP . . . H 4 25.087 94.111 44.985 1 72.63 ? C6 CTP 999 D 1 
HETATM 7 O O2 CTP . . . H 4 24.306 91.283 43.237 1 72.82 ? O2 CTP 999 D 1 
HETATM 8 N N4 CTP . . . H 4 21.833 93.379 46.297 1 73.94 ? N4 CTP 999 D 1 
HETATM 9 C C1' CTP . . . H 4 26.591 92.792 43.596 1 69.89 ? C1' CTP 999 D 1 
HETATM 10 C C2' CTP . . . H 4 26.813 93.688 42.418 1 69.41 ? C2' CTP 999 D 1 
HETATM 11 O O2' CTP . . . H 4 26.477 92.888 41.298 1 68.61 ? O2' CTP 999 D 1 
HETATM 12 C C3' CTP . . . H 4 28.295 94.057 42.467 1 68.82 ? C3' CTP 999 D 1 
HETATM 13 C C4' CTP . . . H 4 28.791 93.449 43.788 1 68.69 ? C4' CTP 999 D 1 
HETATM 14 O O4' CTP . . . H 4 27.642 93.032 44.502 1 73.12 ? O4' CTP 999 D 1 
HETATM 15 O O3' CTP . . . H 4 28.998 93.427 41.398 1 67.21 ? O3' CTP 999 D 1 
HETATM 16 C C5' CTP . . . H 4 29.523 94.406 44.709 1 70.35 ? C5' CTP 999 D 1 
HETATM 17 O O5' CTP . . . H 4 30.115 95.514 44.033 1 84.93 ? O5' CTP 999 D 1 
HETATM 18 P PA CTP . . . H 4 29.796 97.022 44.616 1 65.69 ? PA CTP 999 D 1 
HETATM 19 O O1A CTP . . . H 4 28.241 97.087 44.857 1 61.2 ? O1A CTP 999 D 1 
HETATM 20 O O2A CTP . . . H 4 30.629 97.269 45.947 1 66.57 ? O2A CTP 999 D 1 
HETATM 21 O O3A CTP . . . H 4 30.25 98.163 43.515 1 86.93 ? O3A CTP 999 D 1 
HETATM 22 P PB CTP . . . H 4 31.606 97.771 42.647 1 79.85 ? PB CTP 999 D 1 
HETATM 23 O O1B CTP . . . H 4 32.395 99.111 42.385 1 79.88 ? O1B CTP 999 D 1 
HETATM 24 O O2B CTP . . . H 4 31.14 97.095 41.293 1 81.12 ? O2B CTP 999 D 1 
HETATM 25 O O3B CTP . . . H 4 32.648 96.734 43.408 1 80.91 ? O3B CTP 999 D 1 
HETATM 26 P PG CTP . . . H 4 34.132 96.635 42.665 1 92.14 ? PG CTP 999 D 1 
HETATM 27 O O1G CTP . . . H 4 34.073 97.167 41.171 1 93.01 ? O1G CTP 999 D 1 
HETATM 28 O O2G CTP . . . H 4 34.531 95.102 42.667 1 92.7 ? O2G CTP 999 D 1 
HETATM 29 O O3G CTP . . . H 4 35.148 97.49 43.528 1 92.89 ? O3G CTP 999 D 1 
#
_model_server_stats.io_time_ms              58 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           29 
#