data_5VDS
#
_model_server_result.job_id            jVRUkXvizwRkODRb8SWIHQ 
_model_server_result.datetime_utc      '2024-11-29 07:54:47' 
_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          5vds 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    5VDS 
#
_exptl.entry_id    5VDS 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              614.348 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "3',3'-cdUMP" 
_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          104.81 
_cell.angle_gamma         90 
_cell.entry_id            5VDS 
_cell.length_a            215.45 
_cell.length_b            48.408 
_cell.length_c            86.086 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VDS 
_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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 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
? 3 D N N 
? 3 F 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 A NE2 HIS 231 A HIS 390 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc2 A SG CYS 237 A CYS 396 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc3 A SG CYS 238 A CYS 397 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc4 A SG CYS 245 A CYS 404 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc5 B NE2 HIS 231 B HIS 390 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc6 B SG CYS 237 B CYS 396 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
metalc ? metalc7 B SG CYS 238 B CYS 397 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc8 B SG CYS 245 B CYS 404 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
#
_chem_comp.formula           'C18 H24 N4 O16 P2' 
_chem_comp.formula_weight    614.348 
_chem_comp.id                9BJ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "3',3'-cdUMP" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1-{(2R,6R,8R,10aR,12R,13R,13aS)-6-[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-1,2-dihydroxyethyl]-2,8,13-trihydroxy-2,8-dioxohexahydro-2H,4H,8H,10H-2lambda~5~,8lambda~5~-furo[3,2-d][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-12-yl}pyrimidine-2,4(1H,3H)-dione 
#
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
C10 C08 9BJ sing 1 n n 
C10 N11 9BJ sing 2 n n 
C10 O19 9BJ sing 3 n n 
C13 C12 9BJ doub 4 n n 
C13 C14 9BJ sing 5 n n 
C21 C22 9BJ sing 6 n n 
C21 O20 9BJ sing 7 n n 
C21 C38 9BJ sing 8 n n 
C22 C23 9BJ sing 9 n n 
O01 P02 9BJ doub 10 n n 
P02 O03 9BJ sing 11 n n 
P02 O20 9BJ sing 12 n n 
P02 O40 9BJ sing 13 n n 
O03 C04 9BJ sing 14 n n 
C04 C05 9BJ sing 15 n n 
C05 C06 9BJ sing 16 n n 
C05 O19 9BJ sing 17 n n 
C06 O07 9BJ sing 18 n n 
C06 C08 9BJ sing 19 n n 
O07 P25 9BJ sing 20 n n 
C08 O09 9BJ sing 21 n n 
N11 C12 9BJ sing 22 n n 
N11 C16 9BJ sing 23 n n 
C14 N15 9BJ sing 24 n n 
C14 O18 9BJ doub 25 n n 
N15 C16 9BJ sing 26 n n 
C16 O17 9BJ doub 27 n n 
C23 O24 9BJ sing 28 n n 
O24 P25 9BJ sing 29 n n 
P25 O26 9BJ doub 30 n n 
P25 O27 9BJ sing 31 n n 
O28 C29 9BJ sing 32 n n 
C29 N30 9BJ sing 33 n n 
C29 C38 9BJ sing 34 n n 
N30 C31 9BJ sing 35 n n 
N30 C35 9BJ sing 36 n n 
C31 N32 9BJ sing 37 n n 
C31 O37 9BJ doub 38 n n 
N32 C33 9BJ sing 39 n n 
C33 C34 9BJ sing 40 n n 
C33 O36 9BJ doub 41 n n 
C34 C35 9BJ doub 42 n n 
C38 O39 9BJ sing 43 n n 
C10 H1 9BJ sing 44 n n 
C13 H2 9BJ sing 45 n n 
C21 H3 9BJ sing 46 n n 
C22 H4 9BJ sing 47 n n 
C22 H5 9BJ sing 48 n n 
C04 H6 9BJ sing 49 n n 
C04 H7 9BJ sing 50 n n 
C05 H8 9BJ sing 51 n n 
C06 H9 9BJ sing 52 n n 
C08 H10 9BJ sing 53 n n 
O09 H11 9BJ sing 54 n n 
C12 H12 9BJ sing 55 n n 
N15 H13 9BJ sing 56 n n 
C23 H14 9BJ sing 57 n n 
C23 H15 9BJ sing 58 n n 
O27 H16 9BJ sing 59 n n 
O28 H17 9BJ sing 60 n n 
C29 H18 9BJ sing 61 n n 
N32 H19 9BJ sing 62 n n 
C34 H20 9BJ sing 63 n n 
C35 H21 9BJ sing 64 n n 
C38 H22 9BJ sing 65 n n 
O39 H23 9BJ sing 66 n n 
O40 H24 9BJ sing 67 n n 
#
_atom_sites.entry_id                     5VDS 
_atom_sites.fract_transf_matrix[1][1]    0.004641 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001228 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020658 
_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]    0.012016 
_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 ZN A 1 601 601 ZN ZN . 
D 3 9BJ A 1 602 1 9BJ LIG . 
E 2 ZN B 1 601 601 ZN ZN . 
F 3 9BJ B 1 602 1 9BJ LIG . 
G 4 HOH A 1 701 47 HOH HOH . 
G 4 HOH A 2 702 17 HOH HOH . 
G 4 HOH A 3 703 50 HOH HOH . 
G 4 HOH A 4 704 52 HOH HOH . 
G 4 HOH A 5 705 8 HOH HOH . 
G 4 HOH A 6 706 29 HOH HOH . 
G 4 HOH A 7 707 18 HOH HOH . 
G 4 HOH A 8 708 89 HOH HOH . 
G 4 HOH A 9 709 67 HOH HOH . 
G 4 HOH A 10 710 54 HOH HOH . 
G 4 HOH A 11 711 90 HOH HOH . 
G 4 HOH A 12 712 72 HOH HOH . 
G 4 HOH A 13 713 16 HOH HOH . 
G 4 HOH A 14 714 20 HOH HOH . 
G 4 HOH A 15 715 13 HOH HOH . 
G 4 HOH A 16 716 76 HOH HOH . 
G 4 HOH A 17 717 36 HOH HOH . 
G 4 HOH A 18 718 38 HOH HOH . 
G 4 HOH A 19 719 21 HOH HOH . 
G 4 HOH A 20 720 11 HOH HOH . 
G 4 HOH A 21 721 19 HOH HOH . 
G 4 HOH A 22 722 5 HOH HOH . 
G 4 HOH A 23 723 30 HOH HOH . 
G 4 HOH A 24 724 81 HOH HOH . 
G 4 HOH A 25 725 86 HOH HOH . 
G 4 HOH A 26 726 60 HOH HOH . 
G 4 HOH A 27 727 64 HOH HOH . 
G 4 HOH A 28 728 48 HOH HOH . 
G 4 HOH A 29 729 10 HOH HOH . 
G 4 HOH A 30 730 41 HOH HOH . 
G 4 HOH A 31 731 87 HOH HOH . 
G 4 HOH A 32 732 66 HOH HOH . 
G 4 HOH A 33 733 9 HOH HOH . 
G 4 HOH A 34 734 39 HOH HOH . 
G 4 HOH A 35 735 44 HOH HOH . 
G 4 HOH A 36 736 61 HOH HOH . 
G 4 HOH A 37 737 14 HOH HOH . 
H 4 HOH B 1 701 46 HOH HOH . 
H 4 HOH B 2 702 51 HOH HOH . 
H 4 HOH B 3 703 88 HOH HOH . 
H 4 HOH B 4 704 4 HOH HOH . 
H 4 HOH B 5 705 74 HOH HOH . 
H 4 HOH B 6 706 70 HOH HOH . 
H 4 HOH B 7 707 63 HOH HOH . 
H 4 HOH B 8 708 40 HOH HOH . 
H 4 HOH B 9 709 24 HOH HOH . 
H 4 HOH B 10 710 45 HOH HOH . 
H 4 HOH B 11 711 71 HOH HOH . 
H 4 HOH B 12 712 59 HOH HOH . 
H 4 HOH B 13 713 57 HOH HOH . 
H 4 HOH B 14 714 79 HOH HOH . 
H 4 HOH B 15 715 15 HOH HOH . 
H 4 HOH B 16 716 22 HOH HOH . 
H 4 HOH B 17 717 75 HOH HOH . 
H 4 HOH B 18 718 68 HOH HOH . 
H 4 HOH B 19 719 42 HOH HOH . 
H 4 HOH B 20 720 27 HOH HOH . 
H 4 HOH B 21 721 6 HOH HOH . 
H 4 HOH B 22 722 26 HOH HOH . 
H 4 HOH B 23 723 37 HOH HOH . 
H 4 HOH B 24 724 43 HOH HOH . 
H 4 HOH B 25 725 3 HOH HOH . 
H 4 HOH B 26 726 65 HOH HOH . 
H 4 HOH B 27 727 53 HOH HOH . 
H 4 HOH B 28 728 33 HOH HOH . 
H 4 HOH B 29 729 69 HOH HOH . 
H 4 HOH B 30 730 12 HOH HOH . 
H 4 HOH B 31 731 2 HOH HOH . 
H 4 HOH B 32 732 7 HOH HOH . 
H 4 HOH B 33 733 23 HOH HOH . 
H 4 HOH B 34 734 1 HOH HOH . 
H 4 HOH B 35 735 32 HOH HOH . 
H 4 HOH B 36 736 84 HOH HOH . 
H 4 HOH B 37 737 82 HOH HOH . 
H 4 HOH B 38 738 31 HOH HOH . 
H 4 HOH B 39 739 56 HOH HOH . 
H 4 HOH B 40 740 73 HOH HOH . 
H 4 HOH B 41 741 55 HOH HOH . 
H 4 HOH B 42 742 62 HOH HOH . 
H 4 HOH B 43 743 34 HOH HOH . 
H 4 HOH B 44 744 28 HOH HOH . 
H 4 HOH B 45 745 85 HOH HOH . 
H 4 HOH B 46 746 25 HOH HOH . 
H 4 HOH B 47 747 78 HOH HOH . 
H 4 HOH B 48 748 49 HOH HOH . 
H 4 HOH B 49 749 80 HOH HOH . 
H 4 HOH B 50 750 58 HOH HOH . 
H 4 HOH B 51 751 35 HOH HOH . 
H 4 HOH B 52 752 83 HOH HOH . 
H 4 HOH B 53 753 77 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 C C10 9BJ . . . D 3 -23.383 3.054 27.609 1 84.08 ? C10 9BJ 602 A 1 
HETATM 2 C C13 9BJ . . . D 3 -21.379 1.638 24.55 1 98.87 ? C13 9BJ 602 A 1 
HETATM 3 C C21 9BJ . . . D 3 -27.506 -1.524 25.37 1 61.14 ? C21 9BJ 602 A 1 
HETATM 4 C C22 9BJ . . . D 3 -28.725 -1.235 25.627 1 62.04 ? C22 9BJ 602 A 1 
HETATM 5 O O01 9BJ . . . D 3 -24.246 -2.446 26.301 1 70.35 -1 O01 9BJ 602 A 1 
HETATM 6 P P02 9BJ . . . D 3 -25.376 -1.755 27.036 1 70.55 ? P02 9BJ 602 A 1 
HETATM 7 O O03 9BJ . . . D 3 -25.195 -0.091 27.154 1 74.14 ? O03 9BJ 602 A 1 
HETATM 8 C C04 9BJ . . . D 3 -25.554 0.549 28.382 1 77.54 ? C04 9BJ 602 A 1 
HETATM 9 C C05 9BJ . . . D 3 -25.171 1.88 28.34 1 78.21 ? C05 9BJ 602 A 1 
HETATM 10 C C06 9BJ . . . D 3 -25.578 2.568 26.934 1 76.78 ? C06 9BJ 602 A 1 
HETATM 11 O O07 9BJ . . . D 3 -26.995 3.058 26.974 1 72.01 ? O07 9BJ 602 A 1 
HETATM 12 C C08 9BJ . . . D 3 -24.79 3.521 26.83 1 80.61 ? C08 9BJ 602 A 1 
HETATM 13 O O09 9BJ . . . D 3 -25.35 4.72 27.482 1 81.36 ? O09 9BJ 602 A 1 
HETATM 14 N N11 9BJ . . . D 3 -22.447 2.964 26.461 1 92.72 ? N11 9BJ 602 A 1 
HETATM 15 C C12 9BJ . . . D 3 -22.328 1.723 25.709 1 96.31 ? C12 9BJ 602 A 1 
HETATM 16 C C14 9BJ . . . D 3 -20.555 2.829 24.175 1 99.8 ? C14 9BJ 602 A 1 
HETATM 17 N N15 9BJ . . . D 3 -20.678 4.064 24.933 1 97.29 ? N15 9BJ 602 A 1 
HETATM 18 C C16 9BJ . . . D 3 -21.623 4.145 26.083 1 96.05 ? C16 9BJ 602 A 1 
HETATM 19 O O17 9BJ . . . D 3 -21.719 5.155 26.697 1 98.39 ? O17 9BJ 602 A 1 
HETATM 20 O O18 9BJ . . . D 3 -19.801 2.765 23.258 1 100.89 ? O18 9BJ 602 A 1 
HETATM 21 O O19 9BJ . . . D 3 -23.673 2.015 28.377 1 80.17 ? O19 9BJ 602 A 1 
HETATM 22 O O20 9BJ . . . D 3 -26.892 -2.243 26.528 1 64.95 ? O20 9BJ 602 A 1 
HETATM 23 C C23 9BJ . . . D 3 -28.822 0.175 26.164 1 65.58 ? C23 9BJ 602 A 1 
HETATM 24 O O24 9BJ . . . D 3 -28.042 1.04 25.333 1 67.24 ? O24 9BJ 602 A 1 
HETATM 25 P P25 9BJ . . . D 3 -27.983 2.683 25.68 1 68.08 ? P25 9BJ 602 A 1 
HETATM 26 O O26 9BJ . . . D 3 -27.751 3.553 24.462 1 72.05 -1 O26 9BJ 602 A 1 
HETATM 27 O O27 9BJ . . . D 3 -29.377 3.044 26.137 1 63.99 ? O27 9BJ 602 A 1 
HETATM 28 O O28 9BJ . . . D 3 -29.57 -1.374 24.194 1 59.86 ? O28 9BJ 602 A 1 
HETATM 29 C C29 9BJ . . . D 3 -28.793 -1.931 23.314 1 53.45 ? C29 9BJ 602 A 1 
HETATM 30 N N30 9BJ . . . D 3 -28.126 -1.161 22.221 1 42.52 ? N30 9BJ 602 A 1 
HETATM 31 C C31 9BJ . . . D 3 -27.747 -1.834 20.947 1 37.53 ? C31 9BJ 602 A 1 
HETATM 32 N N32 9BJ . . . D 3 -27.092 -1.054 19.854 1 33.34 ? N32 9BJ 602 A 1 
HETATM 33 C C33 9BJ . . . D 3 -26.822 0.366 20.025 1 35.09 ? C33 9BJ 602 A 1 
HETATM 34 C C34 9BJ . . . D 3 -27.203 1.048 21.3 1 33.57 ? C34 9BJ 602 A 1 
HETATM 35 C C35 9BJ . . . D 3 -27.86 0.26 22.393 1 35.78 ? C35 9BJ 602 A 1 
HETATM 36 O O36 9BJ . . . D 3 -26.299 0.987 19.156 1 36.97 ? O36 9BJ 602 A 1 
HETATM 37 O O37 9BJ . . . D 3 -27.964 -2.992 20.797 1 38.91 ? O37 9BJ 602 A 1 
HETATM 38 C C38 9BJ . . . D 3 -27.576 -2.468 24.114 1 57.71 ? C38 9BJ 602 A 1 
HETATM 39 O O39 9BJ . . . D 3 -27.798 -3.726 24.497 1 57.78 ? O39 9BJ 602 A 1 
HETATM 40 O O40 9BJ . . . D 3 -25.278 -2.253 28.456 1 70.55 ? O40 9BJ 602 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           40 
#