data_4WTK
#
_model_server_result.job_id            65w86ftPGdsTMqLFebRiTA 
_model_server_result.datetime_utc      '2024-10-10 11:22:36' 
_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          4wtk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":605}' 
#
_entry.id    4WTK 
#
_exptl.entry_id    4WTK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          6 
_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            4WTK 
_cell.length_a            140.23 
_cell.length_b            140.23 
_cell.length_c            92.54 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WTK 
_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,L,M,N 
_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                      6 
_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' G 2 P G 2 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc2 C OD2 ASP 222 A ASP 220 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc3 C OD1 ASP 222 A ASP 220 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc4 C O THR 223 A THR 221 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc5 C OE2 GLU 239 A GLU 237 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc6 C ND1 HIS 256 A HIS 254 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc7 C OD1 ASP 320 A ASP 318 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc8 C OD2 ASP 320 A ASP 318 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc9 C OD1 ASP 321 A ASP 319 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc10 D MN MN . A MN 601 1_555 H O1A CDP . A CDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc11 D MN MN . A MN 601 1_555 N O HOH . A HOH 766 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc12 E MN MN . A MN 602 1_555 H O1B CDP . A CDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc13 E MN MN . A MN 602 1_555 H O1A CDP . A CDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc14 E MN MN . A MN 602 1_555 N O HOH . A HOH 799 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
hydrog WATSON-CRICK hydrog1 A N3 C 3 T C 3 1_555 B N1 G 2 P G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 C 3 T C 3 1_555 B O6 G 2 P G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 C 3 T C 3 1_555 B N2 G 2 P G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N3 C 4 T C 4 1_555 B N1 G 1 P G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N4 C 4 T C 4 1_555 B O6 G 1 P G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O2 C 4 T C 4 1_555 B N2 G 1 P G 1 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 189 n n 
PB O1B CDP doub 190 n n 
PB O2B CDP sing 191 n n 
PB O3A CDP sing 192 n n 
O3A PA CDP sing 193 n n 
PA O1A CDP doub 194 n n 
PA O2A CDP sing 195 n n 
PA O5' CDP sing 196 n n 
O5' C5' CDP sing 197 n n 
C5' C4' CDP sing 198 n n 
C5' "H5'1" CDP sing 199 n n 
C5' "H5'2" CDP sing 200 n n 
C4' O4' CDP sing 201 n n 
C4' C3' CDP sing 202 n n 
C4' H4' CDP sing 203 n n 
O4' C1' CDP sing 204 n n 
C3' O3' CDP sing 205 n n 
C3' C2' CDP sing 206 n n 
C3' H3' CDP sing 207 n n 
O3' HA CDP sing 208 n n 
C2' O2' CDP sing 209 n n 
C2' C1' CDP sing 210 n n 
C2' H2' CDP sing 211 n n 
O2' HB CDP sing 212 n n 
C1' N1 CDP sing 213 n n 
C1' H1' CDP sing 214 n n 
N1 C2 CDP sing 215 n n 
N1 C6 CDP sing 216 n n 
C2 O2 CDP doub 217 n n 
C2 N3 CDP sing 218 n n 
N3 C4 CDP doub 219 n n 
C4 N4 CDP sing 220 n n 
C4 C5 CDP sing 221 n n 
N4 H4N1 CDP sing 222 n n 
N4 H4N2 CDP sing 223 n n 
C5 C6 CDP doub 224 n n 
C5 H5 CDP sing 225 n n 
C6 H6 CDP sing 226 n n 
HO1 O2A CDP sing 227 n n 
HO2 O2B CDP sing 228 n n 
HO3 O3B CDP sing 229 n n 
#
_atom_sites.entry_id                     4WTK 
_atom_sites.fract_transf_matrix[1][1]    0.007131 
_atom_sites.fract_transf_matrix[1][2]    0.004117 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008234 
_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]    0.010806 
_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 4 MN A 1 601 1 MN MN . 
E 4 MN A 1 602 2 MN MN . 
F 4 MN A 1 603 3 MN MN . 
G 5 CL A 1 604 4 CL CL . 
H 6 CDP A 1 605 1 CDP CDP . 
I 7 PG6 A 1 606 1 PG6 PG6 . 
J 8 B3P A 1 607 2 B3P B3P . 
K 9 EDO A 1 608 1 EDO EDO . 
L 10 HOH T 1 101 99 HOH HOH . 
M 10 HOH P 1 101 69 HOH HOH . 
M 10 HOH P 2 102 98 HOH HOH . 
M 10 HOH P 3 103 100 HOH HOH . 
M 10 HOH P 4 104 101 HOH HOH . 
N 10 HOH A 1 701 28 HOH HOH . 
N 10 HOH A 2 702 16 HOH HOH . 
N 10 HOH A 3 703 82 HOH HOH . 
N 10 HOH A 4 704 8 HOH HOH . 
N 10 HOH A 5 705 6 HOH HOH . 
N 10 HOH A 6 706 37 HOH HOH . 
N 10 HOH A 7 707 78 HOH HOH . 
N 10 HOH A 8 708 39 HOH HOH . 
N 10 HOH A 9 709 27 HOH HOH . 
N 10 HOH A 10 710 54 HOH HOH . 
N 10 HOH A 11 711 43 HOH HOH . 
N 10 HOH A 12 712 109 HOH HOH . 
N 10 HOH A 13 713 88 HOH HOH . 
N 10 HOH A 14 714 1 HOH HOH . 
N 10 HOH A 15 715 80 HOH HOH . 
N 10 HOH A 16 716 40 HOH HOH . 
N 10 HOH A 17 717 102 HOH HOH . 
N 10 HOH A 18 718 60 HOH HOH . 
N 10 HOH A 19 719 38 HOH HOH . 
N 10 HOH A 20 720 96 HOH HOH . 
N 10 HOH A 21 721 18 HOH HOH . 
N 10 HOH A 22 722 29 HOH HOH . 
N 10 HOH A 23 723 95 HOH HOH . 
N 10 HOH A 24 724 114 HOH HOH . 
N 10 HOH A 25 725 41 HOH HOH . 
N 10 HOH A 26 726 2 HOH HOH . 
N 10 HOH A 27 727 3 HOH HOH . 
N 10 HOH A 28 728 4 HOH HOH . 
N 10 HOH A 29 729 5 HOH HOH . 
N 10 HOH A 30 730 7 HOH HOH . 
N 10 HOH A 31 731 9 HOH HOH . 
N 10 HOH A 32 732 10 HOH HOH . 
N 10 HOH A 33 733 11 HOH HOH . 
N 10 HOH A 34 734 12 HOH HOH . 
N 10 HOH A 35 735 13 HOH HOH . 
N 10 HOH A 36 736 14 HOH HOH . 
N 10 HOH A 37 737 15 HOH HOH . 
N 10 HOH A 38 738 17 HOH HOH . 
N 10 HOH A 39 739 19 HOH HOH . 
N 10 HOH A 40 740 20 HOH HOH . 
N 10 HOH A 41 741 21 HOH HOH . 
N 10 HOH A 42 742 22 HOH HOH . 
N 10 HOH A 43 743 23 HOH HOH . 
N 10 HOH A 44 744 24 HOH HOH . 
N 10 HOH A 45 745 25 HOH HOH . 
N 10 HOH A 46 746 26 HOH HOH . 
N 10 HOH A 47 747 30 HOH HOH . 
N 10 HOH A 48 748 31 HOH HOH . 
N 10 HOH A 49 749 32 HOH HOH . 
N 10 HOH A 50 750 33 HOH HOH . 
N 10 HOH A 51 751 34 HOH HOH . 
N 10 HOH A 52 752 35 HOH HOH . 
N 10 HOH A 53 753 36 HOH HOH . 
N 10 HOH A 54 754 42 HOH HOH . 
N 10 HOH A 55 755 44 HOH HOH . 
N 10 HOH A 56 756 45 HOH HOH . 
N 10 HOH A 57 757 46 HOH HOH . 
N 10 HOH A 58 758 47 HOH HOH . 
N 10 HOH A 59 759 48 HOH HOH . 
N 10 HOH A 60 760 49 HOH HOH . 
N 10 HOH A 61 761 50 HOH HOH . 
N 10 HOH A 62 762 51 HOH HOH . 
N 10 HOH A 63 763 52 HOH HOH . 
N 10 HOH A 64 764 53 HOH HOH . 
N 10 HOH A 65 765 55 HOH HOH . 
N 10 HOH A 66 766 56 HOH HOH . 
N 10 HOH A 67 767 57 HOH HOH . 
N 10 HOH A 68 768 58 HOH HOH . 
N 10 HOH A 69 769 59 HOH HOH . 
N 10 HOH A 70 770 61 HOH HOH . 
N 10 HOH A 71 771 62 HOH HOH . 
N 10 HOH A 72 772 63 HOH HOH . 
N 10 HOH A 73 773 64 HOH HOH . 
N 10 HOH A 74 774 65 HOH HOH . 
N 10 HOH A 75 775 66 HOH HOH . 
N 10 HOH A 76 776 67 HOH HOH . 
N 10 HOH A 77 777 68 HOH HOH . 
N 10 HOH A 78 778 70 HOH HOH . 
N 10 HOH A 79 779 71 HOH HOH . 
N 10 HOH A 80 780 72 HOH HOH . 
N 10 HOH A 81 781 73 HOH HOH . 
N 10 HOH A 82 782 74 HOH HOH . 
N 10 HOH A 83 783 75 HOH HOH . 
N 10 HOH A 84 784 76 HOH HOH . 
N 10 HOH A 85 785 77 HOH HOH . 
N 10 HOH A 86 786 79 HOH HOH . 
N 10 HOH A 87 787 81 HOH HOH . 
N 10 HOH A 88 788 83 HOH HOH . 
N 10 HOH A 89 789 84 HOH HOH . 
N 10 HOH A 90 790 85 HOH HOH . 
N 10 HOH A 91 791 86 HOH HOH . 
N 10 HOH A 92 792 87 HOH HOH . 
N 10 HOH A 93 793 89 HOH HOH . 
N 10 HOH A 94 794 90 HOH HOH . 
N 10 HOH A 95 795 91 HOH HOH . 
N 10 HOH A 96 796 92 HOH HOH . 
N 10 HOH A 97 797 93 HOH HOH . 
N 10 HOH A 98 798 94 HOH HOH . 
N 10 HOH A 99 799 97 HOH HOH . 
N 10 HOH A 100 800 103 HOH HOH . 
N 10 HOH A 101 801 104 HOH HOH . 
N 10 HOH A 102 802 105 HOH HOH . 
N 10 HOH A 103 803 106 HOH HOH . 
N 10 HOH A 104 804 107 HOH HOH . 
N 10 HOH A 105 805 108 HOH HOH . 
N 10 HOH A 106 806 110 HOH HOH . 
N 10 HOH A 107 807 111 HOH HOH . 
N 10 HOH A 108 808 112 HOH HOH . 
N 10 HOH A 109 809 113 HOH HOH . 
N 10 HOH A 110 810 115 HOH HOH . 
N 10 HOH A 111 811 116 HOH HOH . 
N 10 HOH A 112 812 117 HOH HOH . 
N 10 HOH A 113 813 118 HOH HOH . 
N 10 HOH A 114 814 119 HOH HOH . 
N 10 HOH A 115 815 120 HOH HOH . 
N 10 HOH A 116 816 121 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 6 42.773 -41.012 2.012 1 48.07 ? O3B CDP 605 A 1 
HETATM 2 P PB CDP . . . H 6 42.292 -42.391 2.412 1 47.1 ? PB CDP 605 A 1 
HETATM 3 O O1B CDP . . . H 6 42.31 -43.465 1.345 1 35.22 ? O1B CDP 605 A 1 
HETATM 4 O O2B CDP . . . H 6 41.012 -42.214 3.196 1 47.38 ? O2B CDP 605 A 1 
HETATM 5 O O3A CDP . . . H 6 43.412 -42.913 3.489 1 47.1 ? O3A CDP 605 A 1 
HETATM 6 P PA CDP . . . H 6 43.845 -44.458 3.713 1 45.59 ? PA CDP 605 A 1 
HETATM 7 O O1A CDP . . . H 6 44.386 -45.024 2.41 1 49.41 ? O1A CDP 605 A 1 
HETATM 8 O O2A CDP . . . H 6 44.647 -44.663 4.949 1 49.93 ? O2A CDP 605 A 1 
HETATM 9 O O5' CDP . . . H 6 42.444 -45.114 4.161 1 48.74 ? O5' CDP 605 A 1 
HETATM 10 C C5' CDP . . . H 6 41.587 -45.818 3.273 1 49.31 ? C5' CDP 605 A 1 
HETATM 11 C C4' CDP . . . H 6 40.228 -45.986 3.938 1 51.33 ? C4' CDP 605 A 1 
HETATM 12 O O4' CDP . . . H 6 40.298 -46.8 5.14 1 54.52 ? O4' CDP 605 A 1 
HETATM 13 C C3' CDP . . . H 6 39.579 -44.684 4.361 1 49.45 ? C3' CDP 605 A 1 
HETATM 14 O O3' CDP . . . H 6 39.003 -43.97 3.262 1 45.02 ? O3' CDP 605 A 1 
HETATM 15 C C2' CDP . . . H 6 38.579 -45.21 5.376 1 51.15 ? C2' CDP 605 A 1 
HETATM 16 O O2' CDP . . . H 6 37.373 -45.716 4.753 1 52.4 ? O2' CDP 605 A 1 
HETATM 17 C C1' CDP . . . H 6 39.339 -46.339 6.082 1 50.42 ? C1' CDP 605 A 1 
HETATM 18 N N1 CDP . . . H 6 39.929 -45.767 7.293 1 52.53 ? N1 CDP 605 A 1 
HETATM 19 C C2 CDP . . . H 6 39.09 -45.66 8.433 1 54.27 ? C2 CDP 605 A 1 
HETATM 20 O O2 CDP . . . H 6 37.914 -46.083 8.402 1 55.4 ? O2 CDP 605 A 1 
HETATM 21 N N3 CDP . . . H 6 39.544 -45.114 9.577 1 54.16 ? N3 CDP 605 A 1 
HETATM 22 C C4 CDP . . . H 6 40.814 -44.654 9.647 1 55.95 ? C4 CDP 605 A 1 
HETATM 23 N N4 CDP . . . H 6 41.225 -44.11 10.817 1 57.02 ? N4 CDP 605 A 1 
HETATM 24 C C5 CDP . . . H 6 41.666 -44.732 8.536 1 50.41 ? C5 CDP 605 A 1 
HETATM 25 C C6 CDP . . . H 6 41.195 -45.296 7.352 1 51.88 ? C6 CDP 605 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#