data_3VJ7
#
_model_server_result.job_id            VkmaKDPDQioYnvuoLuYM3A 
_model_server_result.datetime_utc      '2024-11-16 08:50:48' 
_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":"B","auth_seq_id":1}' 
#
_entry.id    3VJ7 
#
_exptl.entry_id    3VJ7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE 
_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                      2 
_struct_asym.id                             B 
_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           'C10 H14 N5 O7 P' 
_chem_comp.formula_weight    347.221 
_chem_comp.id                3PD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE" 
#
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
O5' C5' 3PD sing 1 n n 
O5' H5' 3PD sing 2 n n 
C5' C4' 3PD sing 3 n n 
C5' "H5'1" 3PD sing 4 n n 
C5' "H5'2" 3PD sing 5 n n 
C4' O4' 3PD sing 6 n n 
C4' C3' 3PD sing 7 n n 
C4' H4' 3PD sing 8 n n 
O4' C1' 3PD sing 9 n n 
C1' C2' 3PD sing 10 n n 
C1' N9 3PD sing 11 n n 
C1' H1' 3PD sing 12 n n 
C2' C3' 3PD sing 13 n n 
C2' "H2'1" 3PD sing 14 n n 
C2' "H2'2" 3PD sing 15 n n 
C3' O3' 3PD sing 16 n n 
C3' H3' 3PD sing 17 n n 
O3' P 3PD sing 18 n n 
N9 C4 3PD sing 19 n y 
N9 C8 3PD sing 20 n y 
C4 N3 3PD sing 21 n y 
C4 C5 3PD doub 22 n y 
N3 C2 3PD doub 23 n y 
C2 N2 3PD sing 24 n n 
C2 N1 3PD sing 25 n y 
N2 HN21 3PD sing 26 n n 
N2 HN22 3PD sing 27 n n 
N1 C6 3PD sing 28 n y 
N1 HN1 3PD sing 29 n n 
C6 O6 3PD doub 30 n n 
C6 C5 3PD sing 31 n y 
C5 N7 3PD sing 32 n y 
N7 C8 3PD doub 33 n y 
C8 H8 3PD sing 34 n n 
P O1P 3PD sing 35 n n 
P O2P 3PD sing 36 n n 
P O1 3PD doub 37 n n 
O1P H1P 3PD sing 38 n n 
O2P H2P 3PD sing 39 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 O O5' 3PD . . . B 2 11.46 13.495 1.349 1 21.4 ? O5' 3PD 1 A 1 
HETATM 2 C C5' 3PD . . . B 2 12.41 12.82 2.168 1 17.93 ? C5' 3PD 1 A 1 
HETATM 3 C C4' 3PD . . . B 2 13.418 13.789 2.773 1 17.43 ? C4' 3PD 1 A 1 
HETATM 4 O O4' 3PD . . . B 2 14.374 14.275 1.783 1 14.99 ? O4' 3PD 1 A 1 
HETATM 5 C C1' 3PD . . . B 2 14.683 15.623 1.991 1 16.09 ? C1' 3PD 1 A 1 
HETATM 6 C C2' 3PD . . . B 2 13.877 16.153 3.19 1 15.6 ? C2' 3PD 1 A 1 
HETATM 7 C C3' 3PD . . . B 2 12.818 15.047 3.435 1 18.18 ? C3' 3PD 1 A 1 
HETATM 8 O O3' 3PD . . . B 2 12.658 14.724 4.833 1 18.53 ? O3' 3PD 1 A 1 
HETATM 9 N N9 3PD . . . B 2 14.499 16.385 0.683 1 14 ? N9 3PD 1 A 1 
HETATM 10 C C4 3PD . . . B 2 13.329 16.682 -0.026 1 15.41 ? C4 3PD 1 A 1 
HETATM 11 N N3 3PD . . . B 2 12.014 16.335 0.338 1 13.55 ? N3 3PD 1 A 1 
HETATM 12 C C2 3PD . . . B 2 11.072 16.779 -0.555 1 14.46 ? C2 3PD 1 A 1 
HETATM 13 N N2 3PD . . . B 2 9.769 16.546 -0.38 1 14.56 ? N2 3PD 1 A 1 
HETATM 14 N N1 3PD . . . B 2 11.411 17.514 -1.705 1 14.6 ? N1 3PD 1 A 1 
HETATM 15 C C6 3PD . . . B 2 12.741 17.883 -2.1 1 16.64 ? C6 3PD 1 A 1 
HETATM 16 O O6 3PD . . . B 2 12.896 18.531 -3.139 1 17.41 ? O6 3PD 1 A 1 
HETATM 17 C C5 3PD . . . B 2 13.748 17.42 -1.162 1 16.71 ? C5 3PD 1 A 1 
HETATM 18 N N7 3PD . . . B 2 15.126 17.563 -1.175 1 17.05 ? N7 3PD 1 A 1 
HETATM 19 C C8 3PD . . . B 2 15.513 16.946 -0.081 1 14.67 ? C8 3PD 1 A 1 
HETATM 20 P P 3PD . . . B 2 12.374 15.754 6.031 1 16.9 ? P 3PD 1 A 1 
HETATM 21 O O1P 3PD . . . B 2 13.561 15.779 6.884 1 18.33 ? O1P 3PD 1 A 1 
HETATM 22 O O1 3PD . . . B 2 11.882 17.066 5.551 1 16.72 ? O1 3PD 1 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           22 
#