data_3VJ7
#
_model_server_result.job_id            kDKeHEya19WQKVWDU5ROPQ 
_model_server_result.datetime_utc      '2024-11-16 08:44:22' 
_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          3vj7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":117}' 
#
_entry.id    3VJ7 
#
_exptl.entry_id    3VJ7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 3'-MONOPHOSPHATE" 
_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         90 
_cell.entry_id            3VJ7 
_cell.length_a            29.688 
_cell.length_b            49.45 
_cell.length_c            64.619 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VJ7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            B 
_struct_conn.ptnr1_label_atom_id            P 
_struct_conn.ptnr1_label_comp_id            3PD 
_struct_conn.ptnr1_label_seq_id             . 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             3PD 
_struct_conn.ptnr1_auth_seq_id              1 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            C 
_struct_conn.ptnr2_label_atom_id            O5' 
_struct_conn.ptnr2_label_comp_id            UM3 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             UM3 
_struct_conn.ptnr2_auth_seq_id              117 
_struct_conn.ptnr2_symmetry                 1_555 
_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                1.59 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UM3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 3'-MONOPHOSPHATE" 
_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 UM3 sing 363 n y 
N1 C6 UM3 sing 364 n y 
N1 C1' UM3 sing 365 n n 
C2 N3 UM3 sing 366 n y 
C2 O2 UM3 doub 367 n n 
N3 C4 UM3 sing 368 n y 
N3 HN3 UM3 sing 369 n n 
C4 C5 UM3 sing 370 n y 
C4 O4 UM3 doub 371 n n 
C5 C6 UM3 doub 372 n y 
C5 H5 UM3 sing 373 n n 
C6 H6 UM3 sing 374 n n 
C1' C2' UM3 sing 375 n n 
C1' O4' UM3 sing 376 n n 
C1' H1' UM3 sing 377 n n 
C2' C3' UM3 sing 378 n n 
C2' "H2'1" UM3 sing 379 n n 
C2' "H2'2" UM3 sing 380 n n 
C3' C4' UM3 sing 381 n n 
C3' O3' UM3 sing 382 n n 
C3' H3' UM3 sing 383 n n 
C4' O4' UM3 sing 384 n n 
C4' C5' UM3 sing 385 n n 
C4' H4' UM3 sing 386 n n 
O3' P UM3 sing 387 n n 
C5' O5' UM3 sing 388 n n 
C5' "H5'1" UM3 sing 389 n n 
C5' "H5'2" UM3 sing 390 n n 
O5' HO5' UM3 sing 391 n n 
P O1P UM3 doub 392 n n 
P O2P UM3 sing 393 n n 
P O3P UM3 sing 394 n n 
O2P HOP2 UM3 sing 395 n n 
O3P HOP3 UM3 sing 396 n n 
#
_atom_sites.entry_id                     3VJ7 
_atom_sites.fract_transf_matrix[1][1]    0.033684 
_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]    0.020222 
_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]    0.015475 
_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
B 2 3PD A 1 1 1 3PD 3PD . 
C 3 UM3 A 1 117 1 UM3 UM3 . 
D 4 HOH A 1 118 1 HOH HOH . 
D 4 HOH A 2 119 2 HOH HOH . 
D 4 HOH A 3 120 3 HOH HOH . 
D 4 HOH A 4 121 4 HOH HOH . 
D 4 HOH A 5 122 5 HOH HOH . 
D 4 HOH A 6 123 6 HOH HOH . 
D 4 HOH A 7 124 7 HOH HOH . 
D 4 HOH A 8 125 8 HOH HOH . 
D 4 HOH A 9 126 9 HOH HOH . 
D 4 HOH A 10 127 10 HOH HOH . 
D 4 HOH A 11 128 11 HOH HOH . 
D 4 HOH A 12 129 12 HOH HOH . 
D 4 HOH A 13 130 13 HOH HOH . 
D 4 HOH A 14 131 14 HOH HOH . 
D 4 HOH A 15 132 15 HOH HOH . 
D 4 HOH A 16 133 16 HOH HOH . 
D 4 HOH A 17 134 17 HOH HOH . 
D 4 HOH A 18 135 18 HOH HOH . 
D 4 HOH A 19 136 19 HOH HOH . 
D 4 HOH A 20 137 20 HOH HOH . 
D 4 HOH A 21 138 21 HOH HOH . 
D 4 HOH A 22 139 22 HOH HOH . 
D 4 HOH A 23 140 23 HOH HOH . 
D 4 HOH A 24 141 24 HOH HOH . 
D 4 HOH A 25 142 25 HOH HOH . 
D 4 HOH A 26 143 26 HOH HOH . 
D 4 HOH A 27 144 27 HOH HOH . 
D 4 HOH A 28 145 28 HOH HOH . 
D 4 HOH A 29 146 29 HOH HOH . 
D 4 HOH A 30 147 30 HOH HOH . 
D 4 HOH A 31 148 31 HOH HOH . 
D 4 HOH A 32 149 32 HOH HOH . 
D 4 HOH A 33 150 33 HOH HOH . 
D 4 HOH A 34 151 34 HOH HOH . 
D 4 HOH A 35 152 35 HOH HOH . 
D 4 HOH A 36 153 36 HOH HOH . 
D 4 HOH A 37 154 37 HOH HOH . 
D 4 HOH A 38 155 38 HOH HOH . 
D 4 HOH A 39 156 39 HOH HOH . 
D 4 HOH A 40 157 40 HOH HOH . 
D 4 HOH A 41 158 41 HOH HOH . 
D 4 HOH A 42 159 42 HOH HOH . 
D 4 HOH A 43 160 43 HOH HOH . 
D 4 HOH A 44 161 44 HOH HOH . 
D 4 HOH A 45 162 45 HOH HOH . 
D 4 HOH A 46 163 46 HOH HOH . 
D 4 HOH A 47 164 47 HOH HOH . 
D 4 HOH A 48 165 48 HOH HOH . 
D 4 HOH A 49 166 49 HOH HOH . 
D 4 HOH A 50 167 50 HOH HOH . 
D 4 HOH A 51 168 51 HOH HOH . 
D 4 HOH A 52 169 52 HOH HOH . 
D 4 HOH A 53 170 53 HOH HOH . 
D 4 HOH A 54 171 54 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 UM3 . . . C 3 6.21 13.525 5.167 1 10.29 ? N1 UM3 117 A 1 
HETATM 2 C C2 UM3 . . . C 3 4.911 12.939 5.278 1 10.04 ? C2 UM3 117 A 1 
HETATM 3 N N3 UM3 . . . C 3 3.867 13.727 4.754 1 9.71 ? N3 UM3 117 A 1 
HETATM 4 C C4 UM3 . . . C 3 3.992 14.992 4.154 1 10.59 ? C4 UM3 117 A 1 
HETATM 5 C C5 UM3 . . . C 3 5.361 15.523 4.074 1 10.23 ? C5 UM3 117 A 1 
HETATM 6 C C6 UM3 . . . C 3 6.407 14.796 4.566 1 10.8 ? C6 UM3 117 A 1 
HETATM 7 O O2 UM3 . . . C 3 4.69 11.847 5.792 1 13.91 ? O2 UM3 117 A 1 
HETATM 8 O O4 UM3 . . . C 3 3.005 15.57 3.751 1 10.07 ? O4 UM3 117 A 1 
HETATM 9 C C1' UM3 . . . C 3 7.356 12.702 5.75 1 11.17 ? C1' UM3 117 A 1 
HETATM 10 C C2' UM3 . . . C 3 8.496 12.26 4.825 1 10.77 ? C2' UM3 117 A 1 
HETATM 11 C C3' UM3 . . . C 3 9.714 12.336 5.785 1 14.44 ? C3' UM3 117 A 1 
HETATM 12 C C4' UM3 . . . C 3 9.352 13.555 6.648 1 15.61 ? C4' UM3 117 A 1 
HETATM 13 O O3' UM3 . . . C 3 9.77 11.214 6.693 1 17.28 ? O3' UM3 117 A 1 
HETATM 14 O O4' UM3 . . . C 3 7.912 13.487 6.791 1 10.38 ? O4' UM3 117 A 1 
HETATM 15 C C5' UM3 . . . C 3 9.892 14.872 6.174 1 18.41 ? C5' UM3 117 A 1 
HETATM 16 O O5' UM3 . . . C 3 11.191 15.018 6.797 1 19.08 ? O5' UM3 117 A 1 
HETATM 17 P P UM3 . . . C 3 10.193 9.859 6.074 1 16.72 ? P UM3 117 A 1 
HETATM 18 O O1P UM3 . . . C 3 10.194 8.886 7.128 1 14.57 ? O1P UM3 117 A 1 
HETATM 19 O O2P UM3 . . . C 3 11.52 9.997 5.545 1 19.09 ? O2P UM3 117 A 1 
HETATM 20 O O3P UM3 . . . C 3 9.302 9.422 5.025 1 17.87 ? O3P UM3 117 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           20 
#