data_2BPG
#
_model_server_result.job_id            pksHJjM0DuOhpLwsI_SZ8g 
_model_server_result.datetime_utc      '2024-10-26 18:27:20' 
_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          2bpg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":338}' 
#
_entry.id    2BPG 
#
_exptl.entry_id    2BPG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              451.158 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE" 
_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          106.4 
_cell.angle_gamma         90 
_cell.entry_id            2BPG 
_cell.length_a            106.3 
_cell.length_b            56.8 
_cell.length_c            86.7 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2BPG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
PISA trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,G,H,J 1 1 
C,D,F,I,K 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
? 5 H N N 
? 5 I 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 B OP1 DC 6 P DC 6 1_555 G MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? 
metalc ? metalc2 E O THR 101 A THR 101 1_555 G MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc3 E O VAL 103 A VAL 103 1_555 G MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc4 E O ILE 106 A ILE 106 1_555 G MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.031 ? 
hydrog WATSON-CRICK hydrog1 A N1 DG 2 T DG 5 1_555 B N3 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N2 DG 2 T DG 5 1_555 B O2 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O6 DG 2 T DG 5 1_555 B N4 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DG 3 T DG 6 1_555 B N3 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 DG 3 T DG 6 1_555 B O2 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 DG 3 T DG 6 1_555 B N4 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DC PAIR' hydrog7 A N2 DG 3 T DG 6 1_555 B O2 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DC-DG PAIR' hydrog8 A O2 DC 4 T DC 7 1_555 B N1 DG 5 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N1 DG 5 T DG 8 1_555 B N3 DC 4 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N2 DG 5 T DG 8 1_555 B O2 DC 4 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A O6 DG 5 T DG 8 1_555 B N4 DC 4 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N3 DC 6 T DC 9 1_555 B N1 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N4 DC 6 T DC 9 1_555 B O6 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A O2 DC 6 T DC 9 1_555 B N2 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N3 DC 7 T DC 10 1_555 B N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N4 DC 7 T DC 10 1_555 B O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A O2 DC 7 T DC 10 1_555 B N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DC PAIR' hydrog18 A N1 DG 8 T DG 11 1_555 B N3 DC 1 P DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 C N1 DG 2 C DG 5 1_555 D N3 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 C N2 DG 2 C DG 5 1_555 D O2 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 C O6 DG 2 C DG 5 1_555 D N4 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DC PAIR' hydrog22 C N1 DG 3 C DG 6 1_555 D N3 DC 6 D DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DC-DG PAIR' hydrog23 C O2 DC 4 C DC 7 1_555 D N2 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DC PAIR' hydrog24 C N1 DG 5 C DG 8 1_555 D N3 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog25 C N3 DC 6 C DC 9 1_555 D N1 DG 3 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog26 C N4 DC 6 C DC 9 1_555 D O6 DG 3 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog27 C O2 DC 6 C DC 9 1_555 D N2 DG 3 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog28 C N3 DC 7 C DC 10 1_555 D N1 DG 2 D DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog29 C N4 DC 7 C DC 10 1_555 D O6 DG 2 D DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog30 C O2 DC 7 C DC 10 1_555 D N2 DG 2 D DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog31 C N1 DG 8 C DG 11 1_555 D N3 DC 1 D DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog32 C N2 DG 8 C DG 11 1_555 D O2 DC 1 D DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog33 C O6 DG 8 C DG 11 1_555 D N4 DC 1 D DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C9 H16 N3 O12 P3' 
_chem_comp.formula_weight    451.158 
_chem_comp.id                DCT 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE" 
_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 DCT sing 118 n n 
N1 C6 DCT sing 119 n n 
N1 C1' DCT sing 120 n n 
C2 N3 DCT sing 121 n n 
C2 O2 DCT doub 122 n n 
N3 C4 DCT doub 123 n n 
C4 C5 DCT sing 124 n n 
C4 N4 DCT sing 125 n n 
C5 C6 DCT doub 126 n n 
C5 H5 DCT sing 127 n n 
C6 H6 DCT sing 128 n n 
N4 HN41 DCT sing 129 n n 
N4 HN42 DCT sing 130 n n 
C1' C2' DCT sing 131 n n 
C1' O4' DCT sing 132 n n 
C1' H1' DCT sing 133 n n 
C2' C3' DCT sing 134 n n 
C2' H2' DCT sing 135 n n 
C2' "H2''" DCT sing 136 n n 
C3' C4' DCT sing 137 n n 
C3' "H3'1" DCT sing 138 n n 
C3' "H3'2" DCT sing 139 n n 
C4' O4' DCT sing 140 n n 
C4' C5' DCT sing 141 n n 
C4' H4' DCT sing 142 n n 
C5' O5' DCT sing 143 n n 
C5' H5' DCT sing 144 n n 
C5' "H5''" DCT sing 145 n n 
O5' PA DCT sing 146 n n 
PA O1A DCT doub 147 n n 
PA O2A DCT sing 148 n n 
PA O3A DCT sing 149 n n 
O2A HOA2 DCT sing 150 n n 
O3A PB DCT sing 151 n n 
PB O1B DCT doub 152 n n 
PB O2B DCT sing 153 n n 
PB O3B DCT sing 154 n n 
O2B HOB2 DCT sing 155 n n 
O3B PG DCT sing 156 n n 
PG O1G DCT doub 157 n n 
PG O2G DCT sing 158 n n 
PG O3G DCT sing 159 n n 
O2G HOG2 DCT sing 160 n n 
O3G HOG3 DCT sing 161 n n 
#
_atom_sites.entry_id                     2BPG 
_atom_sites.fract_transf_matrix[1][1]    0.009407 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002769 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017606 
_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]    0.012023 
_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
G 4 MG A 1 500 500 MG MG . 
H 5 DCT A 1 338 338 DCT DCT . 
I 5 DCT B 1 338 338 DCT DCT . 
J 6 HOH A 1 401 401 HOH HOH . 
K 6 HOH B 1 400 400 HOH HOH . 
K 6 HOH B 2 402 402 HOH HOH . 
K 6 HOH B 3 403 403 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 DCT . . . I 5 -20.947 34.803 59.133 1 4.14 ? N1 DCT 338 B 1 
HETATM 2 C C2 DCT . . . I 5 -21.467 34.271 57.964 1 11.99 ? C2 DCT 338 B 1 
HETATM 3 N N3 DCT . . . I 5 -20.587 34.005 56.955 1 16.94 ? N3 DCT 338 B 1 
HETATM 4 C C4 DCT . . . I 5 -19.286 34.281 57.066 1 18.04 ? C4 DCT 338 B 1 
HETATM 5 C C5 DCT . . . I 5 -18.76 34.851 58.244 1 10.58 ? C5 DCT 338 B 1 
HETATM 6 C C6 DCT . . . I 5 -19.614 35.123 59.281 1 4.45 ? C6 DCT 338 B 1 
HETATM 7 O O2 DCT . . . I 5 -22.665 33.99 57.866 1 13.79 ? O2 DCT 338 B 1 
HETATM 8 N N4 DCT . . . I 5 -18.484 34.001 56.02 1 23.31 ? N4 DCT 338 B 1 
HETATM 9 C C1' DCT . . . I 5 -22.025 35.451 60.042 1 2.07 ? C1' DCT 338 B 1 
HETATM 10 C C2' DCT . . . I 5 -22.873 34.439 60.779 1 3.34 ? C2' DCT 338 B 1 
HETATM 11 C C3' DCT . . . I 5 -23.071 35.075 62.172 1 1.17 ? C3' DCT 338 B 1 
HETATM 12 C C4' DCT . . . I 5 -22.018 36.149 62.296 1 1.16 ? C4' DCT 338 B 1 
HETATM 13 O O4' DCT . . . I 5 -21.38 36.261 60.98 1 2.12 ? O4' DCT 338 B 1 
HETATM 14 C C5' DCT . . . I 5 -20.948 35.932 63.347 1 1 ? C5' DCT 338 B 1 
HETATM 15 O O5' DCT . . . I 5 -20.085 37.07 63.467 1 1 ? O5' DCT 338 B 1 
HETATM 16 P PA DCT . . . I 5 -19.335 37.46 64.812 1 1.73 ? PA DCT 338 B 1 
HETATM 17 O O1A DCT . . . I 5 -20.243 37.578 65.973 1 1 ? O1A DCT 338 B 1 
HETATM 18 O O2A DCT . . . I 5 -18.352 38.537 64.619 1 5.98 ? O2A DCT 338 B 1 
HETATM 19 O O3A DCT . . . I 5 -18.646 36.19 64.944 1 4.97 ? O3A DCT 338 B 1 
HETATM 20 P PB DCT . . . I 5 -18.925 35.036 65.91 1 10.8 ? PB DCT 338 B 1 
HETATM 21 O O1B DCT . . . I 5 -18.765 33.783 65.108 1 15.48 ? O1B DCT 338 B 1 
HETATM 22 O O2B DCT . . . I 5 -20.176 35.272 66.686 1 6.66 ? O2B DCT 338 B 1 
HETATM 23 O O3B DCT . . . I 5 -17.752 35.324 66.856 1 13.1 ? O3B DCT 338 B 1 
HETATM 24 P PG DCT . . . I 5 -17.631 36.471 67.944 1 10.91 ? PG DCT 338 B 1 
HETATM 25 O O1G DCT . . . I 5 -18.887 37.355 67.899 1 1 ? O1G DCT 338 B 1 
HETATM 26 O O2G DCT . . . I 5 -17.291 35.836 69.196 1 12.04 ? O2G DCT 338 B 1 
HETATM 27 O O3G DCT . . . I 5 -16.352 37.259 67.371 1 14.22 ? O3G DCT 338 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#