data_4MVD
#
_model_server_result.job_id            Eby02e4fKpRjBzsRO2RJrA 
_model_server_result.datetime_utc      '2024-12-02 02:39:43' 
_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          4mvd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":401}' 
#
_entry.id    4MVD 
#
_exptl.entry_id    4MVD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              488.324 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM" 
_entity.pdbx_number_of_molecules    8 
_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            4MVD 
_cell.length_a            107.78 
_cell.length_b            107.78 
_cell.length_c            575.71 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4MVD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 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,B,C,D,I,J,K,L 1 1 
E,F,G,H,M,N,O,P 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 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
#
_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 70 n n 
N1 C6 CDC sing 71 n n 
N1 C1' CDC sing 72 n n 
C2 N3 CDC sing 73 n n 
C2 O2 CDC doub 74 n n 
N3 C4 CDC doub 75 n n 
C4 C5 CDC sing 76 n n 
C4 N4 CDC sing 77 n n 
C5 C6 CDC doub 78 n n 
C5 H5 CDC sing 79 n n 
C6 H6 CDC sing 80 n n 
N4 H41 CDC sing 81 n n 
N4 H42 CDC sing 82 n n 
C1' C2' CDC sing 83 n n 
C1' O4' CDC sing 84 n n 
C1' H1' CDC sing 85 n n 
C2' O2' CDC sing 86 n n 
C2' C3' CDC sing 87 n n 
C2' H2' CDC sing 88 n n 
O2' "HO'2" CDC sing 89 n n 
C3' C4' CDC sing 90 n n 
C3' O3' CDC sing 91 n n 
C3' H3' CDC sing 92 n n 
C4' O4' CDC sing 93 n n 
C4' C5' CDC sing 94 n n 
C4' H4' CDC sing 95 n n 
O3' H3T CDC sing 96 n n 
C5' O5' CDC sing 97 n n 
C5' "H5'1" CDC sing 98 n n 
C5' "H5'2" CDC sing 99 n n 
O5' PA CDC sing 100 n n 
PA O1A CDC doub 101 n n 
PA O2A CDC sing 102 n n 
PA O3A CDC sing 103 n n 
O2A HO2A CDC sing 104 n n 
O3A PB CDC sing 105 n n 
PB O1B CDC sing 106 n n 
PB O2B CDC sing 107 n n 
PB O3B CDC doub 108 n n 
O1B C14 CDC sing 109 n n 
C14 C15 CDC sing 110 n n 
C14 H141 CDC sing 111 n n 
C14 H142 CDC sing 112 n n 
C15 N11 CDC sing 113 n n 
C15 H151 CDC sing 114 n n 
C15 H152 CDC sing 115 n n 
N11 C16 CDC sing 116 n n 
N11 C17 CDC sing 117 n n 
N11 C18 CDC sing 118 n n 
C16 H161 CDC sing 119 n n 
C16 H162 CDC sing 120 n n 
C16 H163 CDC sing 121 n n 
C17 H171 CDC sing 122 n n 
C17 H172 CDC sing 123 n n 
C17 H173 CDC sing 124 n n 
C18 H181 CDC sing 125 n n 
C18 H182 CDC sing 126 n n 
C18 H183 CDC sing 127 n n 
#
_atom_sites.entry_id                     4MVD 
_atom_sites.fract_transf_matrix[1][1]    0.009278 
_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]    0.009278 
_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]    0.001737 
_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 CDC B 1 401 300 CDC CDC . 
J 2 CDC A 1 401 300 CDC CDC . 
K 2 CDC D 1 401 300 CDC CDC . 
L 2 CDC C 1 401 300 CDC CDC . 
M 2 CDC F 1 401 300 CDC CDC . 
N 2 CDC E 1 401 300 CDC CDC . 
O 2 CDC H 1 401 300 CDC CDC . 
P 2 CDC G 1 401 300 CDC CDC . 
#
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 . . . N 2 -25.731 7.922 116.767 1 30.54 ? N1 CDC 401 E 1 
HETATM 2 C C2 CDC . . . N 2 -26.882 7.243 116.702 1 44.77 ? C2 CDC 401 E 1 
HETATM 3 N N3 CDC . . . N 2 -27.896 7.67 115.916 1 43.44 ? N3 CDC 401 E 1 
HETATM 4 C C4 CDC . . . N 2 -27.757 8.795 115.183 1 57.27 ? C4 CDC 401 E 1 
HETATM 5 C C5 CDC . . . N 2 -26.566 9.511 115.241 1 41.23 ? C5 CDC 401 E 1 
HETATM 6 C C6 CDC . . . N 2 -25.544 9.044 116.059 1 20.46 ? C6 CDC 401 E 1 
HETATM 7 O O2 CDC . . . N 2 -27.023 6.105 117.441 1 31.56 ? O2 CDC 401 E 1 
HETATM 8 N N4 CDC . . . N 2 -28.778 9.218 114.394 1 66.03 ? N4 CDC 401 E 1 
HETATM 9 C C1' CDC . . . N 2 -24.674 7.411 117.641 1 36.05 ? C1' CDC 401 E 1 
HETATM 10 C C2' CDC . . . N 2 -23.521 6.833 116.845 1 21.31 ? C2' CDC 401 E 1 
HETATM 11 O O2' CDC . . . N 2 -23.713 5.432 116.633 1 41.73 ? O2' CDC 401 E 1 
HETATM 12 C C3' CDC . . . N 2 -22.334 7.061 117.749 1 21.58 ? C3' CDC 401 E 1 
HETATM 13 C C4' CDC . . . N 2 -22.724 8.209 118.668 1 13.78 ? C4' CDC 401 E 1 
HETATM 14 O O4' CDC . . . N 2 -24.119 8.449 118.458 1 34.9 ? O4' CDC 401 E 1 
HETATM 15 O O3' CDC . . . N 2 -22.14 5.883 118.533 1 28.76 ? O3' CDC 401 E 1 
HETATM 16 C C5' CDC . . . N 2 -21.9 9.459 118.369 1 16.41 ? C5' CDC 401 E 1 
HETATM 17 O O5' CDC . . . N 2 -21.744 9.627 116.955 1 31.97 ? O5' CDC 401 E 1 
HETATM 18 P PA CDC . . . N 2 -20.908 10.871 116.35 1 24.86 ? PA CDC 401 E 1 
HETATM 19 O O1A CDC . . . N 2 -21.179 12.066 117.238 1 47.74 ? O1A CDC 401 E 1 
HETATM 20 O O2A CDC . . . N 2 -21.163 10.981 114.864 1 9.27 ? O2A CDC 401 E 1 
HETATM 21 O O3A CDC . . . N 2 -19.367 10.437 116.538 1 17.48 ? O3A CDC 401 E 1 
HETATM 22 P PB CDC . . . N 2 -18.616 9.536 115.428 1 32.48 ? PB CDC 401 E 1 
HETATM 23 O O1B CDC . . . N 2 -17.185 9.305 116.106 1 37.45 ? O1B CDC 401 E 1 
HETATM 24 O O2B CDC . . . N 2 -19.27 8.179 115.385 1 24.68 ? O2B CDC 401 E 1 
HETATM 25 O O3B CDC . . . N 2 -18.423 10.335 114.155 1 23.34 ? O3B CDC 401 E 1 
HETATM 26 C C14 CDC . . . N 2 -16.995 8.107 116.853 1 36.79 ? C14 CDC 401 E 1 
HETATM 27 C C15 CDC . . . N 2 -15.819 8.269 117.806 1 48.16 ? C15 CDC 401 E 1 
HETATM 28 N N11 CDC . . . N 2 -14.548 8.127 117.081 1 25.98 ? N11 CDC 401 E 1 
HETATM 29 C C16 CDC . . . N 2 -14.659 7.097 116.038 1 24 ? C16 CDC 401 E 1 
HETATM 30 C C17 CDC . . . N 2 -13.514 7.727 118.042 1 24.12 ? C17 CDC 401 E 1 
HETATM 31 C C18 CDC . . . N 2 -14.17 9.405 116.464 1 23.63 ? C18 CDC 401 E 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           31 
#