data_1YQN
#
_model_server_result.job_id            o6elOfciz17Y5O1vHqhfdw 
_model_server_result.datetime_utc      '2024-11-25 22:52:11' 
_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          1yqn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":200}' 
#
_entry.id    1YQN 
#
_exptl.entry_id    1YQN 
_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         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            1YQN 
_cell.length_a            143.778 
_cell.length_b            143.778 
_cell.length_c            143.778 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YQN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        199 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 21 3' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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 
_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' 7_555 -z+1/2,-x,y+1/2 0 0 -1 -1 0 0 0 1 0 71.889 0 71.889 
3 'crystal symmetry operation' 10_545 -y,z-1/2,-x+1/2 0 -1 0 0 0 1 -1 0 0 0 -71.889 71.889 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 OD1 ASP 10 A ASP 8 1_555 B ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc2 A NE2 HIS 12 A HIS 10 1_555 B ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc3 A ND1 HIS 44 A HIS 42 1_555 B ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc4 A OE2 GLU 137 A GLU 135 1_555 C MN MN . A MN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? 
metalc ? metalc5 D O2B CDP . A CDP 200 1_555 B ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? 
metalc ? metalc6 D O2A CDP . A CDP 200 1_555 C MN MN . A MN 500 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? 
metalc ? metalc7 D O1B CDP . A CDP 200 1_555 C MN MN . A MN 500 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? 
metalc ? metalc8 D O2A CDP . A CDP 200 10_545 C MN MN . A MN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? 
metalc ? metalc9 D O1B CDP . A CDP 200 10_545 C MN MN . A MN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? 
metalc ? metalc10 C MN MN . A MN 500 1_555 F O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc11 C MN MN . A MN 500 1_555 F O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? 
metalc ? metalc12 C MN MN . A MN 500 1_555 F O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
#
_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                     1YQN 
_atom_sites.fract_transf_matrix[1][1]    0.006955 
_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]    0.006955 
_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]    0.006955 
_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 ZN A 1 400 400 ZN ZN . 
C 3 MN A 1 500 500 MN MN . 
D 4 CDP A 1 200 200 CDP CDP . 
E 5 GPP A 1 300 300 GPP GPP . 
F 6 HOH A 1 601 601 HOH HOH . 
F 6 HOH A 2 602 602 HOH HOH . 
F 6 HOH A 3 603 603 HOH HOH . 
F 6 HOH A 4 604 604 HOH HOH . 
F 6 HOH A 5 605 605 HOH HOH . 
F 6 HOH A 6 606 606 HOH HOH . 
F 6 HOH A 7 607 607 HOH HOH . 
F 6 HOH A 8 608 608 HOH HOH . 
F 6 HOH A 9 609 609 HOH HOH . 
F 6 HOH A 10 610 610 HOH HOH . 
F 6 HOH A 11 611 611 HOH HOH . 
F 6 HOH A 12 612 612 HOH HOH . 
F 6 HOH A 13 613 613 HOH HOH . 
F 6 HOH A 14 614 614 HOH HOH . 
F 6 HOH A 15 615 615 HOH HOH . 
F 6 HOH A 16 616 616 HOH HOH . 
F 6 HOH A 17 617 617 HOH HOH . 
F 6 HOH A 18 618 618 HOH HOH . 
F 6 HOH A 19 619 619 HOH HOH . 
F 6 HOH A 20 620 620 HOH HOH . 
F 6 HOH A 21 621 621 HOH HOH . 
F 6 HOH A 22 622 622 HOH HOH . 
F 6 HOH A 23 623 623 HOH HOH . 
F 6 HOH A 24 624 624 HOH HOH . 
F 6 HOH A 25 625 625 HOH HOH . 
F 6 HOH A 26 626 626 HOH HOH . 
F 6 HOH A 27 627 627 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 . . . D 4 30.748 -7.51 56.844 1 78.72 ? O3B CDP 200 A 1 
HETATM 2 P PB CDP . . . D 4 29.289 -7.38 57.516 1 78.34 ? PB CDP 200 A 1 
HETATM 3 O O1B CDP . . . D 4 29.177 -6.095 58.327 1 79.42 ? O1B CDP 200 A 1 
HETATM 4 O O2B CDP . . . D 4 28.224 -7.43 56.45 1 78.15 ? O2B CDP 200 A 1 
HETATM 5 O O3A CDP . . . D 4 29.184 -8.677 58.486 1 76.96 ? O3A CDP 200 A 1 
HETATM 6 P PA CDP . . . D 4 28.704 -8.578 60.025 1 74.46 ? PA CDP 200 A 1 
HETATM 7 O O1A CDP . . . D 4 27.4 -9.309 60.21 1 79.42 ? O1A CDP 200 A 1 
HETATM 8 O O2A CDP . . . D 4 28.613 -7.115 60.456 1 78.15 ? O2A CDP 200 A 1 
HETATM 9 O O5' CDP . . . D 4 29.844 -9.387 60.797 1 73.54 ? O5' CDP 200 A 1 
HETATM 10 C C5' CDP . . . D 4 31.177 -9.278 60.36 1 71.95 ? C5' CDP 200 A 1 
HETATM 11 C C4' CDP . . . D 4 32.029 -10.434 60.874 1 70.49 ? C4' CDP 200 A 1 
HETATM 12 O O4' CDP . . . D 4 31.826 -10.731 62.248 1 69.4 ? O4' CDP 200 A 1 
HETATM 13 C C3' CDP . . . D 4 31.729 -11.724 60.143 1 69.88 ? C3' CDP 200 A 1 
HETATM 14 O O3' CDP . . . D 4 32.366 -11.756 58.887 1 70.68 ? O3' CDP 200 A 1 
HETATM 15 C C2' CDP . . . D 4 32.254 -12.756 61.115 1 69.36 ? C2' CDP 200 A 1 
HETATM 16 O O2' CDP . . . D 4 33.651 -12.875 60.98 1 69.4 ? O2' CDP 200 A 1 
HETATM 17 C C1' CDP . . . D 4 31.978 -12.123 62.467 1 68.4 ? C1' CDP 200 A 1 
HETATM 18 N N1 CDP . . . D 4 30.794 -12.717 63.138 1 67.74 ? N1 CDP 200 A 1 
HETATM 19 C C2 CDP . . . D 4 30.987 -13.445 64.303 1 68.1 ? C2 CDP 200 A 1 
HETATM 20 O O2 CDP . . . D 4 32.123 -13.718 64.689 1 68.3 ? O2 CDP 200 A 1 
HETATM 21 N N3 CDP . . . D 4 29.901 -13.871 65.054 1 68.33 ? N3 CDP 200 A 1 
HETATM 22 C C4 CDP . . . D 4 28.612 -13.517 64.698 1 67.75 ? C4 CDP 200 A 1 
HETATM 23 N N4 CDP . . . D 4 27.577 -13.961 65.409 1 67.19 ? N4 CDP 200 A 1 
HETATM 24 C C5 CDP . . . D 4 28.421 -12.694 63.59 1 67.22 ? C5 CDP 200 A 1 
HETATM 25 C C6 CDP . . . D 4 29.522 -12.299 62.829 1 67.45 ? C6 CDP 200 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           25 
#