data_4WTC
#
_model_server_result.job_id            8gp_rILkTiU6Q7NF2ocvlA 
_model_server_result.datetime_utc      '2024-11-25 17:05:15' 
_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          4wtc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":605}' 
#
_entry.id    4WTC 
#
_exptl.entry_id    4WTC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          5 
_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         120 
_cell.entry_id            4WTC 
_cell.length_a            141.34 
_cell.length_b            141.34 
_cell.length_c            90.8 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WTC 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             H 
_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 B O3' U 8 P U 8 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc2 J O HOH . P HOH 102 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? 
metalc ? metalc3 C OD1 ASP 222 A ASP 220 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc4 C OD2 ASP 222 A ASP 220 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? 
metalc ? metalc5 C O THR 223 A THR 221 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc6 C OE2 GLU 239 A GLU 237 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc7 C ND1 HIS 256 A HIS 254 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc8 C OD1 ASP 320 A ASP 318 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc9 C OD2 ASP 320 A ASP 318 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc10 C OD1 ASP 321 A ASP 319 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc11 D MN MN . A MN 601 1_555 H O1A CDP . A CDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
metalc ? metalc12 E MN MN . A MN 602 1_555 H O1B CDP . A CDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc13 E MN MN . A MN 602 1_555 H O1A CDP . A CDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc14 E MN MN . A MN 602 1_555 K O HOH . A HOH 731 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
hydrog WATSON-CRICK hydrog1 A N1 A 3 T A 3 1_555 B N3 U 8 P U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N6 A 3 T A 3 1_555 B O4 U 8 P U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A N1 A 4 T A 4 1_555 B N3 U 7 P U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N6 A 4 T A 4 1_555 B O4 U 7 P U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N1 A 5 T A 5 1_555 B N3 U 6 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N6 A 5 T A 5 1_555 B O4 U 6 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N3 U 6 T U 6 1_555 B N1 A 5 P A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A O4 U 6 T U 6 1_555 B N6 A 5 P A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N3 U 7 T U 7 1_555 B N1 A 4 P A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A O4 U 7 T U 7 1_555 B N6 A 4 P A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 109 n n 
PB O1B CDP doub 110 n n 
PB O2B CDP sing 111 n n 
PB O3A CDP sing 112 n n 
O3A PA CDP sing 113 n n 
PA O1A CDP doub 114 n n 
PA O2A CDP sing 115 n n 
PA O5' CDP sing 116 n n 
O5' C5' CDP sing 117 n n 
C5' C4' CDP sing 118 n n 
C5' "H5'1" CDP sing 119 n n 
C5' "H5'2" CDP sing 120 n n 
C4' O4' CDP sing 121 n n 
C4' C3' CDP sing 122 n n 
C4' H4' CDP sing 123 n n 
O4' C1' CDP sing 124 n n 
C3' O3' CDP sing 125 n n 
C3' C2' CDP sing 126 n n 
C3' H3' CDP sing 127 n n 
O3' HA CDP sing 128 n n 
C2' O2' CDP sing 129 n n 
C2' C1' CDP sing 130 n n 
C2' H2' CDP sing 131 n n 
O2' HB CDP sing 132 n n 
C1' N1 CDP sing 133 n n 
C1' H1' CDP sing 134 n n 
N1 C2 CDP sing 135 n n 
N1 C6 CDP sing 136 n n 
C2 O2 CDP doub 137 n n 
C2 N3 CDP sing 138 n n 
N3 C4 CDP doub 139 n n 
C4 N4 CDP sing 140 n n 
C4 C5 CDP sing 141 n n 
N4 H4N1 CDP sing 142 n n 
N4 H4N2 CDP sing 143 n n 
C5 C6 CDP doub 144 n n 
C5 H5 CDP sing 145 n n 
C6 H6 CDP sing 146 n n 
HO1 O2A CDP sing 147 n n 
HO2 O2B CDP sing 148 n n 
HO3 O3B CDP sing 149 n n 
#
_atom_sites.entry_id                     4WTC 
_atom_sites.fract_transf_matrix[1][1]    0.007075 
_atom_sites.fract_transf_matrix[1][2]    0.004085 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00817 
_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]    0.011013 
_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 3 MN A 1 601 1 MN MN . 
E 3 MN A 1 602 2 MN MN . 
F 3 MN A 1 603 3 MN MN . 
G 4 CL A 1 604 4 CL CL . 
H 5 CDP A 1 605 1 CDP CDP . 
I 6 HOH T 1 101 26 HOH HOH . 
J 6 HOH P 1 101 23 HOH HOH . 
J 6 HOH P 2 102 27 HOH HOH . 
J 6 HOH P 3 103 33 HOH HOH . 
K 6 HOH A 1 701 7 HOH HOH . 
K 6 HOH A 2 702 9 HOH HOH . 
K 6 HOH A 3 703 31 HOH HOH . 
K 6 HOH A 4 704 36 HOH HOH . 
K 6 HOH A 5 705 6 HOH HOH . 
K 6 HOH A 6 706 10 HOH HOH . 
K 6 HOH A 7 707 35 HOH HOH . 
K 6 HOH A 8 708 55 HOH HOH . 
K 6 HOH A 9 709 2 HOH HOH . 
K 6 HOH A 10 710 51 HOH HOH . 
K 6 HOH A 11 711 47 HOH HOH . 
K 6 HOH A 12 712 17 HOH HOH . 
K 6 HOH A 13 713 1 HOH HOH . 
K 6 HOH A 14 714 3 HOH HOH . 
K 6 HOH A 15 715 4 HOH HOH . 
K 6 HOH A 16 716 5 HOH HOH . 
K 6 HOH A 17 717 8 HOH HOH . 
K 6 HOH A 18 718 11 HOH HOH . 
K 6 HOH A 19 719 12 HOH HOH . 
K 6 HOH A 20 720 13 HOH HOH . 
K 6 HOH A 21 721 14 HOH HOH . 
K 6 HOH A 22 722 15 HOH HOH . 
K 6 HOH A 23 723 16 HOH HOH . 
K 6 HOH A 24 724 18 HOH HOH . 
K 6 HOH A 25 725 19 HOH HOH . 
K 6 HOH A 26 726 20 HOH HOH . 
K 6 HOH A 27 727 21 HOH HOH . 
K 6 HOH A 28 728 22 HOH HOH . 
K 6 HOH A 29 729 24 HOH HOH . 
K 6 HOH A 30 730 25 HOH HOH . 
K 6 HOH A 31 731 28 HOH HOH . 
K 6 HOH A 32 732 29 HOH HOH . 
K 6 HOH A 33 733 30 HOH HOH . 
K 6 HOH A 34 734 32 HOH HOH . 
K 6 HOH A 35 735 34 HOH HOH . 
K 6 HOH A 36 736 37 HOH HOH . 
K 6 HOH A 37 737 38 HOH HOH . 
K 6 HOH A 38 738 39 HOH HOH . 
K 6 HOH A 39 739 40 HOH HOH . 
K 6 HOH A 40 740 41 HOH HOH . 
K 6 HOH A 41 741 42 HOH HOH . 
K 6 HOH A 42 742 43 HOH HOH . 
K 6 HOH A 43 743 44 HOH HOH . 
K 6 HOH A 44 744 45 HOH HOH . 
K 6 HOH A 45 745 46 HOH HOH . 
K 6 HOH A 46 746 48 HOH HOH . 
K 6 HOH A 47 747 49 HOH HOH . 
K 6 HOH A 48 748 50 HOH HOH . 
K 6 HOH A 49 749 52 HOH HOH . 
K 6 HOH A 50 750 53 HOH HOH . 
K 6 HOH A 51 751 54 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 . . . H 5 43.376 -41.639 2.303 1 43.52 ? O3B CDP 605 A 1 
HETATM 2 P PB CDP . . . H 5 42.709 -42.993 2.486 1 46.78 ? PB CDP 605 A 1 
HETATM 3 O O1B CDP . . . H 5 42.841 -43.963 1.334 1 35.32 ? O1B CDP 605 A 1 
HETATM 4 O O2B CDP . . . H 5 41.279 -42.779 2.953 1 44.07 ? O2B CDP 605 A 1 
HETATM 5 O O3A CDP . . . H 5 43.448 -43.666 3.789 1 41.6 ? O3A CDP 605 A 1 
HETATM 6 P PA CDP . . . H 5 44.205 -45.091 3.783 1 39.56 ? PA CDP 605 A 1 
HETATM 7 O O1A CDP . . . H 5 44.756 -45.405 2.417 1 43.52 ? O1A CDP 605 A 1 
HETATM 8 O O2A CDP . . . H 5 45.1 -45.244 4.931 1 43.72 ? O2A CDP 605 A 1 
HETATM 9 O O5' CDP . . . H 5 43.029 -46.11 4.166 1 47.52 ? O5' CDP 605 A 1 
HETATM 10 C C5' CDP . . . H 5 42.053 -46.598 3.222 1 45.35 ? C5' CDP 605 A 1 
HETATM 11 C C4' CDP . . . H 5 40.645 -46.669 3.849 1 44.7 ? C4' CDP 605 A 1 
HETATM 12 O O4' CDP . . . H 5 40.611 -47.526 5 1 42.18 ? O4' CDP 605 A 1 
HETATM 13 C C3' CDP . . . H 5 40.052 -45.347 4.331 1 43.94 ? C3' CDP 605 A 1 
HETATM 14 O O3' CDP . . . H 5 39.471 -44.552 3.294 1 42.44 ? O3' CDP 605 A 1 
HETATM 15 C C2' CDP . . . H 5 39.009 -45.857 5.291 1 44.86 ? C2' CDP 605 A 1 
HETATM 16 O O2' CDP . . . H 5 37.831 -46.35 4.625 1 45.93 ? O2' CDP 605 A 1 
HETATM 17 C C1' CDP . . . H 5 39.689 -47.031 5.962 1 43.54 ? C1' CDP 605 A 1 
HETATM 18 N N1 CDP . . . H 5 40.26 -46.503 7.21 1 46.92 ? N1 CDP 605 A 1 
HETATM 19 C C2 CDP . . . H 5 39.434 -46.487 8.367 1 47.94 ? C2 CDP 605 A 1 
HETATM 20 O O2 CDP . . . H 5 38.292 -46.943 8.292 1 51.23 ? O2 CDP 605 A 1 
HETATM 21 N N3 CDP . . . H 5 39.841 -46.009 9.558 1 46.72 ? N3 CDP 605 A 1 
HETATM 22 C C4 CDP . . . H 5 41.098 -45.517 9.635 1 47.64 ? C4 CDP 605 A 1 
HETATM 23 N N4 CDP . . . H 5 41.521 -45.028 10.813 1 49.2 ? N4 CDP 605 A 1 
HETATM 24 C C5 CDP . . . H 5 41.949 -45.505 8.526 1 45.44 ? C5 CDP 605 A 1 
HETATM 25 C C6 CDP . . . H 5 41.504 -46.001 7.298 1 46.83 ? C6 CDP 605 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           25 
#