data_5JPT
#
_model_server_result.job_id            iDmgyx3t1O-2Gh-wUIGiVQ 
_model_server_result.datetime_utc      '2025-01-10 13:00:26' 
_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          5jpt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":801}' 
#
_entry.id    5JPT 
#
_exptl.entry_id    5JPT 
_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         120 
_cell.entry_id            5JPT 
_cell.length_a            118.07 
_cell.length_b            118.07 
_cell.length_c            252.15 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JPT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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,F,G,J 1 1 
B,H,I,K 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 
#
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 H 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 OG1 THR 123 A THR 123 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc2 A NE2 HIS 479 A HIS 479 1_555 G NI NI . A NI 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? 
metalc ? metalc3 C O3B CDP . A CDP 801 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc4 D MG MG . A MG 802 1_555 J O HOH . A HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc5 D MG MG . A MG 802 1_555 J O HOH . A HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc6 D MG MG . A MG 802 1_555 J O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc7 D MG MG . A MG 802 1_555 J O HOH . A HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc8 B OG1 THR 123 B THR 123 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc9 H O1B CDP . B CDP 801 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc10 I MG MG . B MG 802 1_555 K O HOH . B HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc11 I MG MG . B MG 802 1_555 K O HOH . B HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc12 I MG MG . B MG 802 1_555 K O HOH . B HOH 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc13 I MG MG . B MG 802 1_555 K O HOH . B HOH 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
#
_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 76 n n 
PB O1B CDP doub 77 n n 
PB O2B CDP sing 78 n n 
PB O3A CDP sing 79 n n 
O3A PA CDP sing 80 n n 
PA O1A CDP doub 81 n n 
PA O2A CDP sing 82 n n 
PA O5' CDP sing 83 n n 
O5' C5' CDP sing 84 n n 
C5' C4' CDP sing 85 n n 
C5' "H5'1" CDP sing 86 n n 
C5' "H5'2" CDP sing 87 n n 
C4' O4' CDP sing 88 n n 
C4' C3' CDP sing 89 n n 
C4' H4' CDP sing 90 n n 
O4' C1' CDP sing 91 n n 
C3' O3' CDP sing 92 n n 
C3' C2' CDP sing 93 n n 
C3' H3' CDP sing 94 n n 
O3' HA CDP sing 95 n n 
C2' O2' CDP sing 96 n n 
C2' C1' CDP sing 97 n n 
C2' H2' CDP sing 98 n n 
O2' HB CDP sing 99 n n 
C1' N1 CDP sing 100 n n 
C1' H1' CDP sing 101 n n 
N1 C2 CDP sing 102 n n 
N1 C6 CDP sing 103 n n 
C2 O2 CDP doub 104 n n 
C2 N3 CDP sing 105 n n 
N3 C4 CDP doub 106 n n 
C4 N4 CDP sing 107 n n 
C4 C5 CDP sing 108 n n 
N4 H4N1 CDP sing 109 n n 
N4 H4N2 CDP sing 110 n n 
C5 C6 CDP doub 111 n n 
C5 H5 CDP sing 112 n n 
C6 H6 CDP sing 113 n n 
HO1 O2A CDP sing 114 n n 
HO2 O2B CDP sing 115 n n 
HO3 O3B CDP sing 116 n n 
#
_atom_sites.entry_id                     5JPT 
_atom_sites.fract_transf_matrix[1][1]    0.00847 
_atom_sites.fract_transf_matrix[1][2]    0.00489 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00978 
_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]    0.003966 
_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 1 801 1750 CDP CDP . 
D 3 MG A 1 802 1751 MG MG . 
E 4 GOL A 1 803 1752 GOL GOL . 
F 5 ACT A 1 804 1753 ACT ACT . 
G 6 NI A 1 805 1754 NI NI . 
H 2 CDP B 1 801 1750 CDP CDP . 
I 3 MG B 1 802 1751 MG MG . 
J 7 HOH A 1 901 1763 HOH HOH . 
J 7 HOH A 2 902 1764 HOH HOH . 
J 7 HOH A 3 903 1756 HOH HOH . 
J 7 HOH A 4 904 1759 HOH HOH . 
J 7 HOH A 5 905 1769 HOH HOH . 
J 7 HOH A 6 906 1768 HOH HOH . 
J 7 HOH A 7 907 1758 HOH HOH . 
J 7 HOH A 8 908 1762 HOH HOH . 
J 7 HOH A 9 909 1761 HOH HOH . 
J 7 HOH A 10 910 1755 HOH HOH . 
J 7 HOH A 11 911 1760 HOH HOH . 
J 7 HOH A 12 912 1767 HOH HOH . 
J 7 HOH A 13 913 1757 HOH HOH . 
J 7 HOH A 14 914 1765 HOH HOH . 
J 7 HOH A 15 915 1766 HOH HOH . 
K 7 HOH B 1 901 1758 HOH HOH . 
K 7 HOH B 2 902 1757 HOH HOH . 
K 7 HOH B 3 903 1760 HOH HOH . 
K 7 HOH B 4 904 1762 HOH HOH . 
K 7 HOH B 5 905 1759 HOH HOH . 
K 7 HOH B 6 906 1756 HOH HOH . 
K 7 HOH B 7 907 1761 HOH HOH . 
K 7 HOH B 8 908 1755 HOH HOH . 
K 7 HOH B 9 909 1752 HOH HOH . 
K 7 HOH B 10 910 1754 HOH HOH . 
K 7 HOH B 11 911 1753 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 2 32.683 0.225 16.426 1 41.75 ? O3B CDP 801 B 1 
HETATM 2 P PB CDP . . . H 2 32.373 1.514 15.675 1 39.56 ? PB CDP 801 B 1 
HETATM 3 O O1B CDP . . . H 2 32.616 1.289 14.188 1 41.7 ? O1B CDP 801 B 1 
HETATM 4 O O2B CDP . . . H 2 33.275 2.626 16.187 1 38.15 -1 O2B CDP 801 B 1 
HETATM 5 O O3A CDP . . . H 2 30.843 1.927 15.917 1 37.01 ? O3A CDP 801 B 1 
HETATM 6 P PA CDP . . . H 2 29.607 1.361 15.044 1 41.61 ? PA CDP 801 B 1 
HETATM 7 O O1A CDP . . . H 2 29.674 1.953 13.66 1 43.76 ? O1A CDP 801 B 1 
HETATM 8 O O2A CDP . . . H 2 29.702 -0.126 14.942 1 48.17 -1 O2A CDP 801 B 1 
HETATM 9 O O5' CDP . . . H 2 28.242 1.778 15.725 1 45.46 ? O5' CDP 801 B 1 
HETATM 10 C C5' CDP . . . H 2 27.776 1.078 16.863 1 48.85 ? C5' CDP 801 B 1 
HETATM 11 C C4' CDP . . . H 2 26.277 0.859 16.763 1 49 ? C4' CDP 801 B 1 
HETATM 12 O O4' CDP . . . H 2 25.917 0.177 15.351 1 47.01 ? O4' CDP 801 B 1 
HETATM 13 C C3' CDP . . . H 2 25.874 0.059 17.699 1 50.58 ? C3' CDP 801 B 1 
HETATM 14 O O3' CDP . . . H 2 24.582 0.54 18.277 1 50.86 ? O3' CDP 801 B 1 
HETATM 15 C C2' CDP . . . H 2 25.664 -1.314 17.026 1 51.59 ? C2' CDP 801 B 1 
HETATM 16 O O2' CDP . . . H 2 24.644 -2.018 17.627 1 51.12 ? O2' CDP 801 B 1 
HETATM 17 C C1' CDP . . . H 2 25.306 -0.958 15.6 1 51.6 ? C1' CDP 801 B 1 
HETATM 18 N N1 CDP . . . H 2 25.802 -2.033 14.711 1 50.69 ? N1 CDP 801 B 1 
HETATM 19 C C2 CDP . . . H 2 24.871 -3.011 14.166 1 49.09 ? C2 CDP 801 B 1 
HETATM 20 O O2 CDP . . . H 2 23.686 -2.943 14.438 1 52.54 ? O2 CDP 801 B 1 
HETATM 21 N N3 CDP . . . H 2 25.367 -4.084 13.284 1 48.96 ? N3 CDP 801 B 1 
HETATM 22 C C4 CDP . . . H 2 26.752 -4.166 12.967 1 46.2 ? C4 CDP 801 B 1 
HETATM 23 N N4 CDP . . . H 2 27.218 -5.19 12.126 1 47.53 ? N4 CDP 801 B 1 
HETATM 24 C C5 CDP . . . H 2 27.698 -3.187 13.516 1 43.49 ? C5 CDP 801 B 1 
HETATM 25 C C6 CDP . . . H 2 27.202 -2.113 14.398 1 47.6 ? C6 CDP 801 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           720 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#