data_3VTK
#
_model_server_result.job_id            FbhJajA0BTYgMAHnmsjcbw 
_model_server_result.datetime_utc      '2024-11-13 10:51:04' 
_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          3vtk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    3VTK 
#
_exptl.entry_id    3VTK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              434.078 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5-IODO-2'-DEOXYURIDINE-5'-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            3VTK 
_cell.length_a            83.7 
_cell.length_b            83.7 
_cell.length_c            156.3 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VTK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 41' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 6_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 83.7 0 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 
#
_chem_comp.formula           'C9 H12 I N2 O8 P' 
_chem_comp.formula_weight    434.078 
_chem_comp.id                5IU 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'dna linking' 
_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 5IU sing 1 n n 
N1 C6 5IU sing 2 n n 
N1 C1' 5IU sing 3 n n 
C2 N3 5IU sing 4 n n 
C2 O2 5IU doub 5 n n 
N3 C4 5IU sing 6 n n 
N3 HN3 5IU sing 7 n n 
C4 C5 5IU sing 8 n n 
C4 O4 5IU doub 9 n n 
C5 C6 5IU doub 10 n n 
C5 I5 5IU sing 11 n n 
C6 H6 5IU sing 12 n n 
C1' C2' 5IU sing 13 n n 
C1' O4' 5IU sing 14 n n 
C1' H1' 5IU sing 15 n n 
C2' C3' 5IU sing 16 n n 
C2' H2' 5IU sing 17 n n 
C2' "H2''" 5IU sing 18 n n 
C3' C4' 5IU sing 19 n n 
C3' O3' 5IU sing 20 n n 
C3' H3' 5IU sing 21 n n 
C4' O4' 5IU sing 22 n n 
C4' C5' 5IU sing 23 n n 
C4' H4' 5IU sing 24 n n 
O3' HO3' 5IU sing 25 n n 
C5' O5' 5IU sing 26 n n 
C5' H5' 5IU sing 27 n n 
C5' "H5''" 5IU sing 28 n n 
O5' P 5IU sing 29 n n 
P OP1 5IU doub 30 n n 
P OP2 5IU sing 31 n n 
P OP3 5IU sing 32 n n 
OP2 HOP2 5IU sing 33 n n 
OP3 HOP3 5IU sing 34 n n 
#
_atom_sites.entry_id                     3VTK 
_atom_sites.fract_transf_matrix[1][1]    0.011947 
_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]    0.011947 
_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]    0.006398 
_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 ADP A 1 400 400 ADP ADP . 
C 3 5IU A 1 500 500 5IU 5IU . 
D 4 HOH A 1 601 601 HOH HOH . 
D 4 HOH A 2 602 602 HOH HOH . 
D 4 HOH A 3 603 603 HOH HOH . 
D 4 HOH A 4 604 604 HOH HOH . 
D 4 HOH A 5 605 605 HOH HOH . 
D 4 HOH A 6 606 606 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 5IU . . . C 3 39.382 15.046 31.269 1 18.58 ? N1 5IU 500 A 1 
HETATM 2 C C2 5IU . . . C 3 38.777 13.858 30.872 1 20.27 ? C2 5IU 500 A 1 
HETATM 3 N N3 5IU . . . C 3 38.687 12.833 31.766 1 25.52 ? N3 5IU 500 A 1 
HETATM 4 C C4 5IU . . . C 3 39.147 12.911 33.064 1 23.6 ? C4 5IU 500 A 1 
HETATM 5 C C5 5IU . . . C 3 39.764 14.13 33.48 1 20.22 ? C5 5IU 500 A 1 
HETATM 6 C C6 5IU . . . C 3 39.886 15.192 32.534 1 22.38 ? C6 5IU 500 A 1 
HETATM 7 O O2 5IU . . . C 3 38.311 13.699 29.754 1 22.16 ? O2 5IU 500 A 1 
HETATM 8 O O4 5IU . . . C 3 39.008 11.923 33.825 1 21.3 ? O4 5IU 500 A 1 
HETATM 9 I I5 5IU . . . C 3 40.485 14.312 35.463 1 15.96 ? I5 5IU 500 A 1 
HETATM 10 C C1' 5IU . . . C 3 39.547 16.172 30.27 1 14.29 ? C1' 5IU 500 A 1 
HETATM 11 C C2' 5IU . . . C 3 38.556 17.322 30.416 1 11.56 ? C2' 5IU 500 A 1 
HETATM 12 C C3' 5IU . . . C 3 39.413 18.498 30 1 18.39 ? C3' 5IU 500 A 1 
HETATM 13 C C4' 5IU . . . C 3 40.712 18.204 30.667 1 15.9 ? C4' 5IU 500 A 1 
HETATM 14 O O3' 5IU . . . C 3 39.652 18.573 28.605 1 25.79 ? O3' 5IU 500 A 1 
HETATM 15 O O4' 5IU . . . C 3 40.832 16.761 30.6 1 13.03 ? O4' 5IU 500 A 1 
HETATM 16 C C5' 5IU . . . C 3 40.83 18.656 32.126 1 26.1 ? C5' 5IU 500 A 1 
HETATM 17 O O5' 5IU . . . C 3 41.039 20.088 32.202 1 33.74 ? O5' 5IU 500 A 1 
HETATM 18 P P 5IU . . . C 3 40.226 21.046 33.254 1 37.52 ? P 5IU 500 A 1 
HETATM 19 O OP1 5IU . . . C 3 39.816 20.218 34.413 1 39.12 ? OP1 5IU 500 A 1 
HETATM 20 O OP2 5IU . . . C 3 39.019 21.618 32.589 1 38.41 ? OP2 5IU 500 A 1 
HETATM 21 O OP3 5IU . . . C 3 41.094 22.131 33.71 1 28.61 ? OP3 5IU 500 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#