data_3Q89
#
_model_server_result.job_id            DJTVdaNeQj9MGX5cDWYbLQ 
_model_server_result.datetime_utc      '2024-10-18 23:31:51' 
_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          3q89 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":158}' 
#
_entry.id    3Q89 
#
_exptl.entry_id    3Q89 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          3 
_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          108.23 
_cell.angle_gamma         90 
_cell.entry_id            3Q89 
_cell.length_a            186.613 
_cell.length_b            73.055 
_cell.length_c            102.272 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3Q89 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
? monomeric 1 author_defined_assembly 6 
? monomeric 1 author_defined_assembly 7 
? monomeric 1 author_defined_assembly 8 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,M 1 1 
B,I,J,N 2 1 
C,O 3 1 
D,P 4 1 
E,K,L,Q 5 1 
F,R 6 1 
G,S 7 1 
H,T 8 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
? 3 J N N 
? 3 L 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 J O2B CDP . B CDP 158 1_555 I MG MG . B MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
metalc ? metalc2 J O1A CDP . B CDP 158 1_555 I MG MG . B MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? 
metalc ? metalc3 L O2A CDP . E CDP 158 1_555 K MG MG . E MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? 
#
_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                     3Q89 
_atom_sites.fract_transf_matrix[1][1]    0.005359 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001765 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013688 
_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]    0.010295 
_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
I 2 MG B 1 159 159 MG MG . 
J 3 CDP B 1 158 1 CDP CDP . 
K 2 MG E 1 159 159 MG MG . 
L 3 CDP E 1 158 1 CDP CDP . 
M 4 HOH A 1 158 158 HOH HOH . 
M 4 HOH A 2 159 159 HOH HOH . 
M 4 HOH A 3 160 160 HOH HOH . 
M 4 HOH A 4 161 161 HOH HOH . 
M 4 HOH A 5 162 162 HOH HOH . 
M 4 HOH A 6 163 163 HOH HOH . 
M 4 HOH A 7 164 164 HOH HOH . 
M 4 HOH A 8 165 165 HOH HOH . 
M 4 HOH A 9 166 166 HOH HOH . 
M 4 HOH A 10 167 167 HOH HOH . 
M 4 HOH A 11 168 168 HOH HOH . 
M 4 HOH A 12 169 169 HOH HOH . 
N 4 HOH B 1 160 160 HOH HOH . 
N 4 HOH B 2 161 161 HOH HOH . 
N 4 HOH B 3 162 162 HOH HOH . 
N 4 HOH B 4 163 163 HOH HOH . 
N 4 HOH B 5 164 164 HOH HOH . 
N 4 HOH B 6 165 165 HOH HOH . 
N 4 HOH B 7 166 166 HOH HOH . 
N 4 HOH B 8 167 167 HOH HOH . 
N 4 HOH B 9 168 168 HOH HOH . 
N 4 HOH B 10 169 169 HOH HOH . 
N 4 HOH B 11 170 170 HOH HOH . 
N 4 HOH B 12 171 171 HOH HOH . 
N 4 HOH B 13 172 172 HOH HOH . 
N 4 HOH B 14 173 173 HOH HOH . 
N 4 HOH B 15 174 174 HOH HOH . 
O 4 HOH C 1 158 158 HOH HOH . 
O 4 HOH C 2 159 159 HOH HOH . 
O 4 HOH C 3 160 160 HOH HOH . 
O 4 HOH C 4 161 161 HOH HOH . 
O 4 HOH C 5 162 162 HOH HOH . 
O 4 HOH C 6 163 163 HOH HOH . 
O 4 HOH C 7 164 164 HOH HOH . 
O 4 HOH C 8 165 165 HOH HOH . 
O 4 HOH C 9 166 166 HOH HOH . 
O 4 HOH C 10 167 167 HOH HOH . 
O 4 HOH C 11 168 168 HOH HOH . 
P 4 HOH D 1 158 158 HOH HOH . 
P 4 HOH D 2 159 159 HOH HOH . 
P 4 HOH D 3 160 160 HOH HOH . 
P 4 HOH D 4 161 161 HOH HOH . 
P 4 HOH D 5 162 162 HOH HOH . 
P 4 HOH D 6 163 163 HOH HOH . 
P 4 HOH D 7 164 164 HOH HOH . 
P 4 HOH D 8 165 165 HOH HOH . 
P 4 HOH D 9 166 166 HOH HOH . 
Q 4 HOH E 1 160 160 HOH HOH . 
Q 4 HOH E 2 161 161 HOH HOH . 
Q 4 HOH E 3 162 162 HOH HOH . 
Q 4 HOH E 4 163 163 HOH HOH . 
Q 4 HOH E 5 164 164 HOH HOH . 
Q 4 HOH E 6 165 165 HOH HOH . 
Q 4 HOH E 7 166 166 HOH HOH . 
Q 4 HOH E 8 167 167 HOH HOH . 
Q 4 HOH E 9 168 168 HOH HOH . 
R 4 HOH F 1 158 158 HOH HOH . 
R 4 HOH F 2 159 159 HOH HOH . 
R 4 HOH F 3 160 160 HOH HOH . 
R 4 HOH F 4 161 161 HOH HOH . 
S 4 HOH G 1 158 158 HOH HOH . 
S 4 HOH G 2 159 159 HOH HOH . 
S 4 HOH G 3 160 160 HOH HOH . 
S 4 HOH G 4 161 161 HOH HOH . 
S 4 HOH G 5 162 162 HOH HOH . 
T 4 HOH H 1 158 158 HOH HOH . 
T 4 HOH H 2 159 159 HOH HOH . 
T 4 HOH H 3 160 160 HOH HOH . 
T 4 HOH H 4 161 161 HOH HOH . 
T 4 HOH H 5 162 162 HOH HOH . 
T 4 HOH H 6 163 163 HOH HOH . 
T 4 HOH H 7 164 164 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 . . . L 3 44.096 -3.969 23.856 1 20 ? O3B CDP 158 E 1 
HETATM 2 P PB CDP . . . L 3 45.369 -3.439 23.363 1 20 ? PB CDP 158 E 1 
HETATM 3 O O1B CDP . . . L 3 46.569 -3.642 24.257 1 20 ? O1B CDP 158 E 1 
HETATM 4 O O2B CDP . . . L 3 45.54 -3.719 21.934 1 20 ? O2B CDP 158 E 1 
HETATM 5 O O3A CDP . . . L 3 45.222 -1.86 23.467 1 20 ? O3A CDP 158 E 1 
HETATM 6 P PA CDP . . . L 3 46.163 -0.989 24.422 1 20 ? PA CDP 158 E 1 
HETATM 7 O O1A CDP . . . L 3 45.775 -1.197 25.83 1 20 ? O1A CDP 158 E 1 
HETATM 8 O O2A CDP . . . L 3 47.595 -1.02 24.008 1 20 ? O2A CDP 158 E 1 
HETATM 9 O O5' CDP . . . L 3 45.545 0.349 24.005 1 20 ? O5' CDP 158 E 1 
HETATM 10 C C5' CDP . . . L 3 44.187 0.157 23.858 1 20 ? C5' CDP 158 E 1 
HETATM 11 C C4' CDP . . . L 3 43.714 -0.852 24.881 1 20 ? C4' CDP 158 E 1 
HETATM 12 O O4' CDP . . . L 3 43.29 -0.023 25.933 1 20 ? O4' CDP 158 E 1 
HETATM 13 C C3' CDP . . . L 3 42.457 -1.585 24.393 1 20 ? C3' CDP 158 E 1 
HETATM 14 O O3' CDP . . . L 3 42.354 -2.886 24.881 1 20 ? O3' CDP 158 E 1 
HETATM 15 C C2' CDP . . . L 3 41.292 -0.87 25.005 1 20 ? C2' CDP 158 E 1 
HETATM 16 O O2' CDP . . . L 3 40.505 -1.765 25.747 1 20 ? O2' CDP 158 E 1 
HETATM 17 C C1' CDP . . . L 3 41.888 0.198 25.87 1 20 ? C1' CDP 158 E 1 
HETATM 18 N N1 CDP . . . L 3 41.645 1.353 25.046 1 20 ? N1 CDP 158 E 1 
HETATM 19 C C2 CDP . . . L 3 40.469 2.05 25.211 1 20 ? C2 CDP 158 E 1 
HETATM 20 O O2 CDP . . . L 3 39.702 1.704 26.084 1 20 ? O2 CDP 158 E 1 
HETATM 21 N N3 CDP . . . L 3 40.185 3.1 24.463 1 20 ? N3 CDP 158 E 1 
HETATM 22 C C4 CDP . . . L 3 41.082 3.47 23.534 1 20 ? C4 CDP 158 E 1 
HETATM 23 N N4 CDP . . . L 3 40.855 4.546 22.757 1 20 ? N4 CDP 158 E 1 
HETATM 24 C C5 CDP . . . L 3 42.244 2.771 23.343 1 20 ? C5 CDP 158 E 1 
HETATM 25 C C6 CDP . . . L 3 42.506 1.691 24.125 1 20 ? C6 CDP 158 E 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           34 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#