data_8URP
#
_model_server_result.job_id            Z3AuwIocfivauJL6s_TQgw 
_model_server_result.datetime_utc      '2025-04-25 21:35:02' 
_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          8urp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1005}' 
#
_entry.id    8URP 
#
_exptl.entry_id    8URP 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              488.324 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM" 
_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         90 
_cell.entry_id            8URP 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8URP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,G,H,I,J,K,L,M,N,O,P,Q,R 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 G N N 
? 4 O 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
covale ? covale1 A C ACE 1 A ACE 1 1_555 A N GLY 2 A GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 B C ACE 1 B ACE 1 1_555 B N GLY 2 B GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
metalc ? metalc1 A O ASP 96 A ASP 96 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? 
metalc ? metalc2 A OD1 ASP 96 A ASP 96 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc3 A OD1 ASP 96 A ASP 96 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc4 A OD2 ASP 96 A ASP 96 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? 
metalc ? metalc5 A OD1 ASP 99 A ASP 99 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? 
metalc ? metalc6 A OD2 ASP 117 A ASP 117 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc7 A OD1 ASP 117 A ASP 117 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc8 A OD1 ASP 121 A ASP 121 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? 
metalc ? metalc9 A OD2 ASP 121 A ASP 121 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc10 C MG MG . A MG 1001 1_555 G O3B CDC . A CDC 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc11 C MG MG . A MG 1001 1_555 G O2A CDC . A CDC 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc12 B O ASP 96 B ASP 96 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc13 B OD1 ASP 96 B ASP 96 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc14 B OD1 ASP 96 B ASP 96 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
metalc ? metalc15 B OD2 ASP 96 B ASP 96 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? 
metalc ? metalc16 B OD1 ASP 99 B ASP 99 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc17 B OD2 ASP 99 B ASP 99 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? 
metalc ? metalc18 B OD2 ASP 117 B ASP 117 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc19 B OD1 ASP 117 B ASP 117 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc20 B OD1 ASP 121 B ASP 121 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
metalc ? metalc21 B OD2 ASP 121 B ASP 121 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
metalc ? metalc22 L MG MG . B MG 402 1_555 O O1A CDC . B CDC 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc23 L MG MG . B MG 402 1_555 O O3B CDC . B CDC 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? 
#
_chem_comp.formula           'C14 H26 N4 O11 P2' 
_chem_comp.formula_weight    488.324 
_chem_comp.id                CDC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM" 
_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
N1 C2 CDC sing 76 n n 
N1 C6 CDC sing 77 n n 
N1 C1' CDC sing 78 n n 
C2 N3 CDC sing 79 n n 
C2 O2 CDC doub 80 n n 
N3 C4 CDC doub 81 n n 
C4 C5 CDC sing 82 n n 
C4 N4 CDC sing 83 n n 
C5 C6 CDC doub 84 n n 
C5 H5 CDC sing 85 n n 
C6 H6 CDC sing 86 n n 
N4 H41 CDC sing 87 n n 
N4 H42 CDC sing 88 n n 
C1' C2' CDC sing 89 n n 
C1' O4' CDC sing 90 n n 
C1' H1' CDC sing 91 n n 
C2' O2' CDC sing 92 n n 
C2' C3' CDC sing 93 n n 
C2' H2' CDC sing 94 n n 
O2' "HO'2" CDC sing 95 n n 
C3' C4' CDC sing 96 n n 
C3' O3' CDC sing 97 n n 
C3' H3' CDC sing 98 n n 
C4' O4' CDC sing 99 n n 
C4' C5' CDC sing 100 n n 
C4' H4' CDC sing 101 n n 
O3' H3T CDC sing 102 n n 
C5' O5' CDC sing 103 n n 
C5' "H5'1" CDC sing 104 n n 
C5' "H5'2" CDC sing 105 n n 
O5' PA CDC sing 106 n n 
PA O1A CDC doub 107 n n 
PA O2A CDC sing 108 n n 
PA O3A CDC sing 109 n n 
O2A HO2A CDC sing 110 n n 
O3A PB CDC sing 111 n n 
PB O1B CDC sing 112 n n 
PB O2B CDC sing 113 n n 
PB O3B CDC doub 114 n n 
O1B C14 CDC sing 115 n n 
C14 C15 CDC sing 116 n n 
C14 H141 CDC sing 117 n n 
C14 H142 CDC sing 118 n n 
C15 N11 CDC sing 119 n n 
C15 H151 CDC sing 120 n n 
C15 H152 CDC sing 121 n n 
N11 C16 CDC sing 122 n n 
N11 C17 CDC sing 123 n n 
N11 C18 CDC sing 124 n n 
C16 H161 CDC sing 125 n n 
C16 H162 CDC sing 126 n n 
C16 H163 CDC sing 127 n n 
C17 H171 CDC sing 128 n n 
C17 H172 CDC sing 129 n n 
C17 H173 CDC sing 130 n n 
C18 H181 CDC sing 131 n n 
C18 H182 CDC sing 132 n n 
C18 H183 CDC sing 133 n n 
#
_atom_sites.entry_id                     8URP 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 MG A 1 1001 1001 MG MG . 
D 2 MG A 1 1002 1002 MG MG . 
E 3 PCW A 1 1003 1005 PCW PCW . 
F 3 PCW A 1 1004 1006 PCW PCW . 
G 4 CDC A 1 1005 1009 CDC CDC . 
H 5 PCF A 1 1006 1010 PCF PCF . 
I 3 PCW A 1 1007 1006 PCW PCW . 
J 3 PCW A 1 1008 1007 PCW PCW . 
K 3 PCW B 1 401 1007 PCW PCW . 
L 2 MG B 1 402 1001 MG MG . 
M 2 MG B 1 403 1002 MG MG . 
N 3 PCW B 1 404 1005 PCW PCW . 
O 4 CDC B 1 405 1009 CDC CDC . 
P 5 PCF B 1 406 1010 PCF PCF . 
Q 6 HOH A 1 1101 1011 HOH HOH . 
Q 6 HOH A 2 1102 1012 HOH HOH . 
Q 6 HOH A 3 1103 1013 HOH HOH . 
Q 6 HOH A 4 1104 1014 HOH HOH . 
Q 6 HOH A 5 1105 1008 HOH HOH . 
R 6 HOH B 1 501 1012 HOH HOH . 
R 6 HOH B 2 502 1011 HOH HOH . 
R 6 HOH B 3 503 1013 HOH HOH . 
R 6 HOH B 4 504 1008 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 N N1 CDC . . . G 4 118.528 146.88 163.196 1 64.56 ? N1 CDC 1005 A 1 
HETATM 2 C C2 CDC . . . G 4 117.886 147.635 162.085 1 68.66 ? C2 CDC 1005 A 1 
HETATM 3 N N3 CDC . . . G 4 118.717 148.498 161.196 1 68.9 ? N3 CDC 1005 A 1 
HETATM 4 C C4 CDC . . . G 4 120.152 148.605 161.408 1 60.17 ? C4 CDC 1005 A 1 
HETATM 5 C C5 CDC . . . G 4 120.794 147.858 162.51 1 64.94 ? C5 CDC 1005 A 1 
HETATM 6 C C6 CDC . . . G 4 119.971 146.996 163.401 1 68.84 ? C6 CDC 1005 A 1 
HETATM 7 O O2 CDC . . . G 4 116.711 147.547 161.909 1 75.5 ? O2 CDC 1005 A 1 
HETATM 8 N N4 CDC . . . G 4 120.961 149.447 160.539 1 62 ? N4 CDC 1005 A 1 
HETATM 9 C C1' CDC . . . G 4 117.722 146.046 164.05 1 68.25 ? C1' CDC 1005 A 1 
HETATM 10 C C2' CDC . . . G 4 117.724 144.516 163.504 1 69.16 ? C2' CDC 1005 A 1 
HETATM 11 O O2' CDC . . . G 4 116.43 143.889 163.781 1 72.72 ? O2' CDC 1005 A 1 
HETATM 12 C C3' CDC . . . G 4 118.653 143.904 164.161 1 66.64 ? C3' CDC 1005 A 1 
HETATM 13 C C4' CDC . . . G 4 118.603 144.566 165.547 1 70.14 ? C4' CDC 1005 A 1 
HETATM 14 O O4' CDC . . . G 4 118.193 146.022 165.26 1 78.06 ? O4' CDC 1005 A 1 
HETATM 15 O O3' CDC . . . G 4 118.333 142.43 164.268 1 72.28 ? O3' CDC 1005 A 1 
HETATM 16 C C5' CDC . . . G 4 119.887 144.538 166.163 1 68.5 ? C5' CDC 1005 A 1 
HETATM 17 O O5' CDC . . . G 4 119.827 145.259 167.381 1 67.15 ? O5' CDC 1005 A 1 
HETATM 18 P PA CDC . . . G 4 121.266 145.712 168.131 1 77.24 ? PA CDC 1005 A 1 
HETATM 19 O O1A CDC . . . G 4 120.951 146.55 169.338 1 75.46 ? O1A CDC 1005 A 1 
HETATM 20 O O2A CDC . . . G 4 122.107 146.526 167.164 1 70.85 ? O2A CDC 1005 A 1 
HETATM 21 O O3A CDC . . . G 4 122.092 144.35 168.614 1 72.72 ? O3A CDC 1005 A 1 
HETATM 22 P PB CDC . . . G 4 123.371 143.634 167.786 1 78.86 ? PB CDC 1005 A 1 
HETATM 23 O O1B CDC . . . G 4 124.711 143.558 168.784 1 76.28 ? O1B CDC 1005 A 1 
HETATM 24 O O2B CDC . . . G 4 122.982 142.224 167.383 1 71.64 ? O2B CDC 1005 A 1 
HETATM 25 O O3B CDC . . . G 4 123.714 144.436 166.545 1 69.64 ? O3B CDC 1005 A 1 
HETATM 26 C C14 CDC . . . G 4 125.061 144.724 169.567 1 69.81 ? C14 CDC 1005 A 1 
HETATM 27 C C15 CDC . . . G 4 125.516 144.279 171.014 1 71.41 ? C15 CDC 1005 A 1 
HETATM 28 N N11 CDC . . . G 4 124.42 144.5 171.993 1 74.89 ? N11 CDC 1005 A 1 
HETATM 29 C C16 CDC . . . G 4 123.337 143.586 171.73 1 72.64 ? C16 CDC 1005 A 1 
HETATM 30 C C17 CDC . . . G 4 124.938 144.255 173.371 1 72.11 ? C17 CDC 1005 A 1 
HETATM 31 C C18 CDC . . . G 4 123.949 145.853 171.9 1 73.35 ? C18 CDC 1005 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           31 
#