data_3C3C
#
_model_server_result.job_id            6LPy5CoQqDDMOb1lqR-1tA 
_model_server_result.datetime_utc      '2024-11-24 12:00:42' 
_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          3c3c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":419}' 
#
_entry.id    3C3C 
#
_exptl.entry_id    3C3C 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          4 
_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         78.95 
_cell.angle_beta          84.51 
_cell.angle_gamma         83.23 
_cell.entry_id            3C3C 
_cell.length_a            35.789 
_cell.length_b            55.824 
_cell.length_c            94.497 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3C3C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_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,C,D,E,G 1 1 
B,F,H 2 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_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
disulf ? disulf1 B SG CYS 102 B CYS 98 1_555 B SG CYS 111 B CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc1 A OD1 ASP 222 A ASP 218 1_555 C MG MG . A MG 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? 
#
_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 87 n n 
PB O1B CDP doub 88 n n 
PB O2B CDP sing 89 n n 
PB O3A CDP sing 90 n n 
O3A PA CDP sing 91 n n 
PA O1A CDP doub 92 n n 
PA O2A CDP sing 93 n n 
PA O5' CDP sing 94 n n 
O5' C5' CDP sing 95 n n 
C5' C4' CDP sing 96 n n 
C5' "H5'1" CDP sing 97 n n 
C5' "H5'2" CDP sing 98 n n 
C4' O4' CDP sing 99 n n 
C4' C3' CDP sing 100 n n 
C4' H4' CDP sing 101 n n 
O4' C1' CDP sing 102 n n 
C3' O3' CDP sing 103 n n 
C3' C2' CDP sing 104 n n 
C3' H3' CDP sing 105 n n 
O3' HA CDP sing 106 n n 
C2' O2' CDP sing 107 n n 
C2' C1' CDP sing 108 n n 
C2' H2' CDP sing 109 n n 
O2' HB CDP sing 110 n n 
C1' N1 CDP sing 111 n n 
C1' H1' CDP sing 112 n n 
N1 C2 CDP sing 113 n n 
N1 C6 CDP sing 114 n n 
C2 O2 CDP doub 115 n n 
C2 N3 CDP sing 116 n n 
N3 C4 CDP doub 117 n n 
C4 N4 CDP sing 118 n n 
C4 C5 CDP sing 119 n n 
N4 H4N1 CDP sing 120 n n 
N4 H4N2 CDP sing 121 n n 
C5 C6 CDP doub 122 n n 
C5 H5 CDP sing 123 n n 
C6 H6 CDP sing 124 n n 
HO1 O2A CDP sing 125 n n 
HO2 O2B CDP sing 126 n n 
HO3 O3B CDP sing 127 n n 
#
_atom_sites.entry_id                     3C3C 
_atom_sites.fract_transf_matrix[1][1]    0.027942 
_atom_sites.fract_transf_matrix[1][2]    -0.003319 
_atom_sites.fract_transf_matrix[1][3]    -0.002117 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018039 
_atom_sites.fract_transf_matrix[2][3]    -0.00335 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.010813 
_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
C 2 MG A 1 417 1 MG MG . 
D 3 3PG A 1 418 1 3PG MP3 . 
E 4 CDP A 1 419 1 CDP CDP . 
F 3 3PG B 1 417 1 3PG MP3 . 
G 5 HOH A 1 420 2 HOH HOH . 
G 5 HOH A 2 421 4 HOH HOH . 
G 5 HOH A 3 422 5 HOH HOH . 
G 5 HOH A 4 423 6 HOH HOH . 
G 5 HOH A 5 424 7 HOH HOH . 
G 5 HOH A 6 425 8 HOH HOH . 
G 5 HOH A 7 426 10 HOH HOH . 
G 5 HOH A 8 427 13 HOH HOH . 
G 5 HOH A 9 428 14 HOH HOH . 
G 5 HOH A 10 429 15 HOH HOH . 
G 5 HOH A 11 430 16 HOH HOH . 
G 5 HOH A 12 431 17 HOH HOH . 
G 5 HOH A 13 432 18 HOH HOH . 
G 5 HOH A 14 433 19 HOH HOH . 
G 5 HOH A 15 434 21 HOH HOH . 
G 5 HOH A 16 435 22 HOH HOH . 
G 5 HOH A 17 436 26 HOH HOH . 
G 5 HOH A 18 437 27 HOH HOH . 
G 5 HOH A 19 438 30 HOH HOH . 
G 5 HOH A 20 439 33 HOH HOH . 
G 5 HOH A 21 440 34 HOH HOH . 
G 5 HOH A 22 441 38 HOH HOH . 
G 5 HOH A 23 442 39 HOH HOH . 
G 5 HOH A 24 443 40 HOH HOH . 
G 5 HOH A 25 444 41 HOH HOH . 
G 5 HOH A 26 445 42 HOH HOH . 
G 5 HOH A 27 446 43 HOH HOH . 
G 5 HOH A 28 447 46 HOH HOH . 
G 5 HOH A 29 448 47 HOH HOH . 
G 5 HOH A 30 449 48 HOH HOH . 
G 5 HOH A 31 450 51 HOH HOH . 
G 5 HOH A 32 451 54 HOH HOH . 
G 5 HOH A 33 452 58 HOH HOH . 
G 5 HOH A 34 453 61 HOH HOH . 
G 5 HOH A 35 454 67 HOH HOH . 
G 5 HOH A 36 455 70 HOH HOH . 
G 5 HOH A 37 456 71 HOH HOH . 
G 5 HOH A 38 457 77 HOH HOH . 
G 5 HOH A 39 458 80 HOH HOH . 
G 5 HOH A 40 459 83 HOH HOH . 
G 5 HOH A 41 460 85 HOH HOH . 
G 5 HOH A 42 461 86 HOH HOH . 
G 5 HOH A 43 462 89 HOH HOH . 
G 5 HOH A 44 463 92 HOH HOH . 
G 5 HOH A 45 464 93 HOH HOH . 
G 5 HOH A 46 465 97 HOH HOH . 
G 5 HOH A 47 466 98 HOH HOH . 
G 5 HOH A 48 467 99 HOH HOH . 
G 5 HOH A 49 468 100 HOH HOH . 
G 5 HOH A 50 469 101 HOH HOH . 
G 5 HOH A 51 470 107 HOH HOH . 
G 5 HOH A 52 471 110 HOH HOH . 
G 5 HOH A 53 472 113 HOH HOH . 
G 5 HOH A 54 473 114 HOH HOH . 
G 5 HOH A 55 474 116 HOH HOH . 
G 5 HOH A 56 475 118 HOH HOH . 
G 5 HOH A 57 476 119 HOH HOH . 
G 5 HOH A 58 477 121 HOH HOH . 
G 5 HOH A 59 478 123 HOH HOH . 
G 5 HOH A 60 479 124 HOH HOH . 
G 5 HOH A 61 480 125 HOH HOH . 
G 5 HOH A 62 481 127 HOH HOH . 
G 5 HOH A 63 482 130 HOH HOH . 
G 5 HOH A 64 483 131 HOH HOH . 
G 5 HOH A 65 484 132 HOH HOH . 
G 5 HOH A 66 485 133 HOH HOH . 
G 5 HOH A 67 486 134 HOH HOH . 
G 5 HOH A 68 487 135 HOH HOH . 
G 5 HOH A 69 488 137 HOH HOH . 
G 5 HOH A 70 489 139 HOH HOH . 
G 5 HOH A 71 490 141 HOH HOH . 
G 5 HOH A 72 491 150 HOH HOH . 
G 5 HOH A 73 492 152 HOH HOH . 
G 5 HOH A 74 493 155 HOH HOH . 
G 5 HOH A 75 494 157 HOH HOH . 
G 5 HOH A 76 495 158 HOH HOH . 
G 5 HOH A 77 496 160 HOH HOH . 
G 5 HOH A 78 497 161 HOH HOH . 
G 5 HOH A 79 498 164 HOH HOH . 
G 5 HOH A 80 499 165 HOH HOH . 
G 5 HOH A 81 500 166 HOH HOH . 
G 5 HOH A 82 501 169 HOH HOH . 
G 5 HOH A 83 502 170 HOH HOH . 
G 5 HOH A 84 503 172 HOH HOH . 
G 5 HOH A 85 504 173 HOH HOH . 
G 5 HOH A 86 505 175 HOH HOH . 
G 5 HOH A 87 506 177 HOH HOH . 
G 5 HOH A 88 507 182 HOH HOH . 
G 5 HOH A 89 508 185 HOH HOH . 
H 5 HOH B 1 418 1 HOH HOH . 
H 5 HOH B 2 419 9 HOH HOH . 
H 5 HOH B 3 420 11 HOH HOH . 
H 5 HOH B 4 421 12 HOH HOH . 
H 5 HOH B 5 422 20 HOH HOH . 
H 5 HOH B 6 423 23 HOH HOH . 
H 5 HOH B 7 424 24 HOH HOH . 
H 5 HOH B 8 425 25 HOH HOH . 
H 5 HOH B 9 426 28 HOH HOH . 
H 5 HOH B 10 427 29 HOH HOH . 
H 5 HOH B 11 428 31 HOH HOH . 
H 5 HOH B 12 429 32 HOH HOH . 
H 5 HOH B 13 430 35 HOH HOH . 
H 5 HOH B 14 431 36 HOH HOH . 
H 5 HOH B 15 432 37 HOH HOH . 
H 5 HOH B 16 433 44 HOH HOH . 
H 5 HOH B 17 434 45 HOH HOH . 
H 5 HOH B 18 435 49 HOH HOH . 
H 5 HOH B 19 436 50 HOH HOH . 
H 5 HOH B 20 437 52 HOH HOH . 
H 5 HOH B 21 438 53 HOH HOH . 
H 5 HOH B 22 439 55 HOH HOH . 
H 5 HOH B 23 440 56 HOH HOH . 
H 5 HOH B 24 441 57 HOH HOH . 
H 5 HOH B 25 442 59 HOH HOH . 
H 5 HOH B 26 443 60 HOH HOH . 
H 5 HOH B 27 444 62 HOH HOH . 
H 5 HOH B 28 445 63 HOH HOH . 
H 5 HOH B 29 446 64 HOH HOH . 
H 5 HOH B 30 447 65 HOH HOH . 
H 5 HOH B 31 448 66 HOH HOH . 
H 5 HOH B 32 449 68 HOH HOH . 
H 5 HOH B 33 450 69 HOH HOH . 
H 5 HOH B 34 451 73 HOH HOH . 
H 5 HOH B 35 452 74 HOH HOH . 
H 5 HOH B 36 453 75 HOH HOH . 
H 5 HOH B 37 454 76 HOH HOH . 
H 5 HOH B 38 455 78 HOH HOH . 
H 5 HOH B 39 456 79 HOH HOH . 
H 5 HOH B 40 457 81 HOH HOH . 
H 5 HOH B 41 458 82 HOH HOH . 
H 5 HOH B 42 459 84 HOH HOH . 
H 5 HOH B 43 460 87 HOH HOH . 
H 5 HOH B 44 461 88 HOH HOH . 
H 5 HOH B 45 462 90 HOH HOH . 
H 5 HOH B 46 463 91 HOH HOH . 
H 5 HOH B 47 464 94 HOH HOH . 
H 5 HOH B 48 465 95 HOH HOH . 
H 5 HOH B 49 466 96 HOH HOH . 
H 5 HOH B 50 467 102 HOH HOH . 
H 5 HOH B 51 468 104 HOH HOH . 
H 5 HOH B 52 469 105 HOH HOH . 
H 5 HOH B 53 470 106 HOH HOH . 
H 5 HOH B 54 471 108 HOH HOH . 
H 5 HOH B 55 472 111 HOH HOH . 
H 5 HOH B 56 473 112 HOH HOH . 
H 5 HOH B 57 474 115 HOH HOH . 
H 5 HOH B 58 475 120 HOH HOH . 
H 5 HOH B 59 476 122 HOH HOH . 
H 5 HOH B 60 477 126 HOH HOH . 
H 5 HOH B 61 478 129 HOH HOH . 
H 5 HOH B 62 479 138 HOH HOH . 
H 5 HOH B 63 480 140 HOH HOH . 
H 5 HOH B 64 481 142 HOH HOH . 
H 5 HOH B 65 482 143 HOH HOH . 
H 5 HOH B 66 483 144 HOH HOH . 
H 5 HOH B 67 484 145 HOH HOH . 
H 5 HOH B 68 485 147 HOH HOH . 
H 5 HOH B 69 486 149 HOH HOH . 
H 5 HOH B 70 487 151 HOH HOH . 
H 5 HOH B 71 488 153 HOH HOH . 
H 5 HOH B 72 489 154 HOH HOH . 
H 5 HOH B 73 490 156 HOH HOH . 
H 5 HOH B 74 491 159 HOH HOH . 
H 5 HOH B 75 492 162 HOH HOH . 
H 5 HOH B 76 493 163 HOH HOH . 
H 5 HOH B 77 494 168 HOH HOH . 
H 5 HOH B 78 495 176 HOH HOH . 
H 5 HOH B 79 496 178 HOH HOH . 
H 5 HOH B 80 497 181 HOH HOH . 
H 5 HOH B 81 498 183 HOH HOH . 
H 5 HOH B 82 499 184 HOH HOH . 
H 5 HOH B 83 500 186 HOH HOH . 
H 5 HOH B 84 501 187 HOH HOH . 
H 5 HOH B 85 502 188 HOH HOH . 
H 5 HOH B 86 503 189 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 . . . E 4 10.145 0.418 29.495 1 93.49 ? O3B CDP 419 A 1 
HETATM 2 P PB CDP . . . E 4 9.619 -0.497 30.711 1 91.96 ? PB CDP 419 A 1 
HETATM 3 O O1B CDP . . . E 4 10.664 -1.399 31.246 1 93.92 ? O1B CDP 419 A 1 
HETATM 4 O O2B CDP . . . E 4 8.338 -1.29 30.144 1 92.52 ? O2B CDP 419 A 1 
HETATM 5 O O3A CDP . . . E 4 9.05 0.525 31.818 1 88.39 ? O3A CDP 419 A 1 
HETATM 6 P PA CDP . . . E 4 8.758 0.01 33.315 1 82.88 ? PA CDP 419 A 1 
HETATM 7 O O1A CDP . . . E 4 8.065 -1.297 33.347 1 84.17 ? O1A CDP 419 A 1 
HETATM 8 O O2A CDP . . . E 4 7.916 1.181 34.028 1 79.64 ? O2A CDP 419 A 1 
HETATM 9 O O5' CDP . . . E 4 10.187 -0.022 34.057 1 79.07 ? O5' CDP 419 A 1 
HETATM 10 C C5' CDP . . . E 4 11.324 0.59 33.444 1 72.91 ? C5' CDP 419 A 1 
HETATM 11 C C4' CDP . . . E 4 12.571 -0.281 33.607 1 68.54 ? C4' CDP 419 A 1 
HETATM 12 O O4' CDP . . . E 4 12.46 -1.055 34.811 1 67.6 ? O4' CDP 419 A 1 
HETATM 13 C C3' CDP . . . E 4 13.789 0.61 33.851 1 66.2 ? C3' CDP 419 A 1 
HETATM 14 O O3' CDP . . . E 4 14.524 0.759 32.633 1 65.19 ? O3' CDP 419 A 1 
HETATM 15 C C2' CDP . . . E 4 14.626 -0.179 34.86 1 62.72 ? C2' CDP 419 A 1 
HETATM 16 O O2' CDP . . . E 4 15.884 -0.521 34.272 1 57.74 ? O2' CDP 419 A 1 
HETATM 17 C C1' CDP . . . E 4 13.81 -1.45 35.098 1 63.53 ? C1' CDP 419 A 1 
HETATM 18 N N1 CDP . . . E 4 13.917 -1.846 36.52 1 61.3 ? N1 CDP 419 A 1 
HETATM 19 C C2 CDP . . . E 4 14.185 -3.177 36.859 1 61.07 ? C2 CDP 419 A 1 
HETATM 20 O O2 CDP . . . E 4 14.332 -4.02 35.975 1 59.27 ? O2 CDP 419 A 1 
HETATM 21 N N3 CDP . . . E 4 14.285 -3.546 38.205 1 61.95 ? N3 CDP 419 A 1 
HETATM 22 C C4 CDP . . . E 4 14.117 -2.583 39.206 1 62.97 ? C4 CDP 419 A 1 
HETATM 23 N N4 CDP . . . E 4 14.212 -2.932 40.486 1 65.48 ? N4 CDP 419 A 1 
HETATM 24 C C5 CDP . . . E 4 13.851 -1.262 38.865 1 61.78 ? C5 CDP 419 A 1 
HETATM 25 C C6 CDP . . . E 4 13.75 -0.891 37.529 1 60.42 ? C6 CDP 419 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#