data_8DHB
#
_model_server_result.job_id            rVQ20FSCvr8PBSu22-o_OQ 
_model_server_result.datetime_utc      '2024-11-14 03:47:37' 
_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          8dhb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":501}' 
#
_entry.id    8DHB 
#
_exptl.entry_id    8DHB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              444.185 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate' 
_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            8DHB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DHB 
_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    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_pdbx_struct_assembly.details               author_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 
_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    ? 
_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                      11 
_struct_asym.id                             K 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 J SG CYS 51 J CYS 8 1_555 J SG CYS 168 J CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc1 K O12 CZC . A CZC 501 1_555 L BE BEF . A BEF 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.779 ? 
#
_chem_comp.formula           'C10 H14 N4 O12 P2' 
_chem_comp.formula_weight    444.185 
_chem_comp.id                CZC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'xanthosine diphosphate' 
#
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
O12 P2 CZC doub 86 n n 
O11 P2 CZC sing 87 n n 
P2 O10 CZC sing 88 n n 
P2 O7 CZC sing 89 n n 
O7 P1 CZC sing 90 n n 
C6 O3 CZC sing 91 n n 
C6 C5 CZC sing 92 n n 
C6 C7 CZC sing 93 n n 
O2 C5 CZC sing 94 n n 
C8 C7 CZC sing 95 n n 
C8 O5 CZC sing 96 n n 
O9 P1 CZC doub 97 n n 
P1 O5 CZC sing 98 n n 
P1 O8 CZC sing 99 n n 
C5 C4 CZC sing 100 n n 
C7 O4 CZC sing 101 n n 
C4 O4 CZC sing 102 n n 
C4 N4 CZC sing 103 n n 
N4 C10 CZC sing 104 n y 
N4 C2 CZC sing 105 n y 
C10 N3 CZC doub 106 n y 
C2 N2 CZC sing 107 n n 
C2 C3 CZC doub 108 n y 
N2 C1 CZC sing 109 n n 
N3 C3 CZC sing 110 n y 
C3 C9 CZC sing 111 n n 
C1 O1 CZC doub 112 n n 
C1 N1 CZC sing 113 n n 
C9 N1 CZC sing 114 n n 
C9 O6 CZC doub 115 n n 
C4 H1 CZC sing 116 n n 
C5 H2 CZC sing 117 n n 
C6 H3 CZC sing 118 n n 
C7 H4 CZC sing 119 n n 
C8 H5 CZC sing 120 n n 
C8 H6 CZC sing 121 n n 
C10 H7 CZC sing 122 n n 
N1 H8 CZC sing 123 n n 
N2 H9 CZC sing 124 n n 
O2 H10 CZC sing 125 n n 
O3 H11 CZC sing 126 n n 
O8 H12 CZC sing 127 n n 
O10 H13 CZC sing 128 n n 
O11 H14 CZC sing 129 n n 
#
_atom_sites.entry_id                     8DHB 
_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
K 11 CZC A 1 501 502 CZC XDP . 
L 12 BEF A 1 502 503 BEF BEF . 
M 13 GDP B 1 500 500 GDP GDP . 
#
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 C1 CZC . . . K 11 218.126 254.34 227.779 1 54.69 ? C1 CZC 501 A 1 
HETATM 2 C C2 CZC . . . K 11 218.482 252.728 226.127 1 55.69 ? C2 CZC 501 A 1 
HETATM 3 C C3 CZC . . . K 11 218.134 251.736 226.959 1 55.72 ? C3 CZC 501 A 1 
HETATM 4 C C4 CZC . . . K 11 219.214 252.95 223.738 1 58.72 ? C4 CZC 501 A 1 
HETATM 5 C C5 CZC . . . K 11 220.692 253.292 223.665 1 59.88 ? C5 CZC 501 A 1 
HETATM 6 C C6 CZC . . . K 11 221.206 252.368 222.59 1 60.93 ? C6 CZC 501 A 1 
HETATM 7 C C7 CZC . . . K 11 219.994 252.216 221.687 1 60.88 ? C7 CZC 501 A 1 
HETATM 8 C C8 CZC . . . K 11 220.081 250.893 220.932 1 61.53 ? C8 CZC 501 A 1 
HETATM 9 C C9 CZC . . . K 11 217.768 252.001 228.225 1 55.7 ? C9 CZC 501 A 1 
HETATM 10 C C10 CZC . . . K 11 218.643 250.872 225.052 1 56.31 ? C10 CZC 501 A 1 
HETATM 11 N N1 CZC . . . K 11 217.758 253.332 228.673 1 55.31 ? N1 CZC 501 A 1 
HETATM 12 N N2 CZC . . . K 11 218.478 254.01 226.529 1 54.93 ? N2 CZC 501 A 1 
HETATM 13 N N3 CZC . . . K 11 218.236 250.592 226.286 1 55.78 ? N3 CZC 501 A 1 
HETATM 14 N N4 CZC . . . K 11 218.804 252.189 224.957 1 56.83 ? N4 CZC 501 A 1 
HETATM 15 O O1 CZC . . . K 11 218.128 255.579 228.156 1 54.06 ? O1 CZC 501 A 1 
HETATM 16 O O2 CZC . . . K 11 220.803 254.648 223.205 1 59.95 ? O2 CZC 501 A 1 
HETATM 17 O O3 CZC . . . K 11 222.289 253 221.857 1 61.45 ? O3 CZC 501 A 1 
HETATM 18 O O4 CZC . . . K 11 218.887 252.143 222.581 1 59.7 ? O4 CZC 501 A 1 
HETATM 19 O O5 CZC . . . K 11 219.316 249.892 221.603 1 62.15 ? O5 CZC 501 A 1 
HETATM 20 O O6 CZC . . . K 11 217.441 251.103 229.007 1 55.44 ? O6 CZC 501 A 1 
HETATM 21 O O7 CZC . . . K 11 218.519 248.196 219.935 1 63.69 ? O7 CZC 501 A 1 
HETATM 22 O O8 CZC . . . K 11 219.086 247.505 222.307 1 62.8 -1 O8 CZC 501 A 1 
HETATM 23 O O9 CZC . . . K 11 220.894 248.216 220.632 1 63.63 ? O9 CZC 501 A 1 
HETATM 24 O O10 CZC . . . K 11 218.66 245.796 219.887 1 64.22 ? O10 CZC 501 A 1 
HETATM 25 O O11 CZC . . . K 11 216.597 246.934 220.698 1 64.16 -1 O11 CZC 501 A 1 
HETATM 26 O O12 CZC . . . K 11 217.224 247.058 218.304 1 64.27 ? O12 CZC 501 A 1 
HETATM 27 P P1 CZC . . . K 11 219.528 248.363 221.185 1 63.3 ? P1 CZC 501 A 1 
HETATM 28 P P2 CZC . . . K 11 217.675 246.867 219.701 1 64.14 ? P2 CZC 501 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#