data_7O0N
#
_model_server_result.job_id            58t0Kg3rc_IhMF1CGu1Tyw 
_model_server_result.datetime_utc      '2024-10-30 03:19:50' 
_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          7o0n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    7O0N 
#
_exptl.entry_id    7O0N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-DIPHOSPHATE" 
_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         90 
_cell.entry_id            7O0N 
_cell.length_a            44.12 
_cell.length_b            80.37 
_cell.length_c            136.83 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7O0N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,M 
_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
? 2 C N N 
? 2 J 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 A OE1 GLU 92 A GLU 126 1_555 E MG MG . A MG 303 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc2 A OE2 GLU 92 A GLU 126 1_555 E MG MG . A MG 303 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.677 ? 
metalc ? metalc3 A OD1 ASN 93 A ASN 127 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc4 C O3B CDP . A CDP 301 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc5 C O2A CDP . A CDP 301 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? 
metalc ? metalc6 D O4P TS6 . A TS6 302 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc7 B OD1 ASN 93 B ASN 127 1_555 K MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc8 I O1P TS6 . B TS6 303 1_555 K MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? 
metalc ? metalc9 J O1B CDP . B CDP 304 1_555 K MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc10 J O1A CDP . B CDP 304 1_555 K MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? 
metalc ? metalc11 K MG MG . B MG 305 1_555 M O HOH . B HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
#
_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                     7O0N 
_atom_sites.fract_transf_matrix[1][1]    0.022665 
_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]    0.012442 
_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]    0.007308 
_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 CDP A 1 301 301 CDP CDP . 
D 3 TS6 A 1 302 302 TS6 TS6 . 
E 4 MG A 1 303 303 MG MG . 
F 5 PEG A 1 304 304 PEG PEG . 
G 6 GOL B 1 301 301 GOL GOL . 
H 6 GOL B 1 302 302 GOL GOL . 
I 3 TS6 B 1 303 303 TS6 TS6 . 
J 2 CDP B 1 304 304 CDP CDP . 
K 4 MG B 1 305 305 MG MG . 
L 7 HOH A 1 401 401 HOH HOH . 
L 7 HOH A 2 402 402 HOH HOH . 
L 7 HOH A 3 403 403 HOH HOH . 
L 7 HOH A 4 404 404 HOH HOH . 
L 7 HOH A 5 405 405 HOH HOH . 
L 7 HOH A 6 406 406 HOH HOH . 
L 7 HOH A 7 407 407 HOH HOH . 
L 7 HOH A 8 408 408 HOH HOH . 
L 7 HOH A 9 409 409 HOH HOH . 
L 7 HOH A 10 410 410 HOH HOH . 
L 7 HOH A 11 411 411 HOH HOH . 
L 7 HOH A 12 412 412 HOH HOH . 
L 7 HOH A 13 413 413 HOH HOH . 
L 7 HOH A 14 414 414 HOH HOH . 
L 7 HOH A 15 415 415 HOH HOH . 
L 7 HOH A 16 416 416 HOH HOH . 
L 7 HOH A 17 417 417 HOH HOH . 
L 7 HOH A 18 418 418 HOH HOH . 
L 7 HOH A 19 419 419 HOH HOH . 
L 7 HOH A 20 420 420 HOH HOH . 
L 7 HOH A 21 421 421 HOH HOH . 
L 7 HOH A 22 422 422 HOH HOH . 
L 7 HOH A 23 423 423 HOH HOH . 
L 7 HOH A 24 424 424 HOH HOH . 
L 7 HOH A 25 425 425 HOH HOH . 
L 7 HOH A 26 426 426 HOH HOH . 
L 7 HOH A 27 427 427 HOH HOH . 
L 7 HOH A 28 428 428 HOH HOH . 
L 7 HOH A 29 429 429 HOH HOH . 
L 7 HOH A 30 430 430 HOH HOH . 
M 7 HOH B 1 401 401 HOH HOH . 
M 7 HOH B 2 402 402 HOH HOH . 
M 7 HOH B 3 403 403 HOH HOH . 
M 7 HOH B 4 404 404 HOH HOH . 
M 7 HOH B 5 405 405 HOH HOH . 
M 7 HOH B 6 406 406 HOH HOH . 
M 7 HOH B 7 407 407 HOH HOH . 
M 7 HOH B 8 408 408 HOH HOH . 
M 7 HOH B 9 409 409 HOH HOH . 
M 7 HOH B 10 410 410 HOH HOH . 
M 7 HOH B 11 411 411 HOH HOH . 
M 7 HOH B 12 412 412 HOH HOH . 
M 7 HOH B 13 413 413 HOH HOH . 
M 7 HOH B 14 414 414 HOH HOH . 
M 7 HOH B 15 415 415 HOH HOH . 
M 7 HOH B 16 416 416 HOH HOH . 
M 7 HOH B 17 417 417 HOH HOH . 
M 7 HOH B 18 418 418 HOH HOH . 
M 7 HOH B 19 419 419 HOH HOH . 
M 7 HOH B 20 420 420 HOH HOH . 
M 7 HOH B 21 421 421 HOH HOH . 
M 7 HOH B 22 422 422 HOH HOH . 
M 7 HOH B 23 423 423 HOH HOH . 
M 7 HOH B 24 424 424 HOH HOH . 
M 7 HOH B 25 425 425 HOH HOH . 
M 7 HOH B 26 426 426 HOH HOH . 
M 7 HOH B 27 427 427 HOH HOH . 
M 7 HOH B 28 428 428 HOH HOH . 
M 7 HOH B 29 429 429 HOH HOH . 
M 7 HOH B 30 430 430 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 2 17.535 16.042 22.696 1 29.97 ? O3B CDP 301 A 1 
HETATM 2 P PB CDP . . . C 2 18.279 16.23 21.4 1 34.41 ? PB CDP 301 A 1 
HETATM 3 O O1B CDP . . . C 2 18.666 14.938 20.736 1 34.56 ? O1B CDP 301 A 1 
HETATM 4 O O2B CDP . . . C 2 19.481 17.092 21.571 1 31.26 ? O2B CDP 301 A 1 
HETATM 5 O O3A CDP . . . C 2 17.292 16.904 20.284 1 34.18 ? O3A CDP 301 A 1 
HETATM 6 P PA CDP . . . C 2 15.854 17.621 20.522 1 32.25 ? PA CDP 301 A 1 
HETATM 7 O O1A CDP . . . C 2 15.595 18.384 19.251 1 35.35 ? O1A CDP 301 A 1 
HETATM 8 O O2A CDP . . . C 2 14.763 16.618 20.813 1 28.74 ? O2A CDP 301 A 1 
HETATM 9 O O5' CDP . . . C 2 15.889 18.665 21.772 1 32.65 ? O5' CDP 301 A 1 
HETATM 10 C C5' CDP . . . C 2 16.861 19.687 21.785 1 36.19 ? C5' CDP 301 A 1 
HETATM 11 C C4' CDP . . . C 2 17.142 20.049 23.121 1 30.23 ? C4' CDP 301 A 1 
HETATM 12 O O4' CDP . . . C 2 18.348 20.936 23.198 1 32.38 ? O4' CDP 301 A 1 
HETATM 13 C C3' CDP . . . C 2 15.982 20.962 23.736 1 34.97 ? C3' CDP 301 A 1 
HETATM 14 O O3' CDP . . . C 2 15.799 20.495 25.144 1 32.91 ? O3' CDP 301 A 1 
HETATM 15 C C2' CDP . . . C 2 16.407 22.16 23.645 1 34.82 ? C2' CDP 301 A 1 
HETATM 16 O O2' CDP . . . C 2 15.885 23.09 24.668 1 30.7 ? O2' CDP 301 A 1 
HETATM 17 C C1' CDP . . . C 2 18.004 21.975 23.934 1 35.14 ? C1' CDP 301 A 1 
HETATM 18 N N1 CDP . . . C 2 18.869 23.012 23.537 1 34.71 ? N1 CDP 301 A 1 
HETATM 19 C C2 CDP . . . C 2 20.059 23.31 24.367 1 35.94 ? C2 CDP 301 A 1 
HETATM 20 O O2 CDP . . . C 2 20.251 22.742 25.4 1 34.39 ? O2 CDP 301 A 1 
HETATM 21 N N3 CDP . . . C 2 20.998 24.351 23.902 1 37.03 ? N3 CDP 301 A 1 
HETATM 22 C C4 CDP . . . C 2 20.772 25.033 22.663 1 28.59 ? C4 CDP 301 A 1 
HETATM 23 N N4 CDP . . . C 2 21.668 26.034 22.218 1 33.39 ? N4 CDP 301 A 1 
HETATM 24 C C5 CDP . . . C 2 19.596 24.726 21.834 1 34.44 ? C5 CDP 301 A 1 
HETATM 25 C C6 CDP . . . C 2 18.664 23.699 22.281 1 31.34 ? C6 CDP 301 A 1 
#
_model_server_stats.io_time_ms              70 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           333 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#