data_5DDY
#
_model_server_result.job_id            OSEk2aD7JbgSeuBL5CySTA 
_model_server_result.datetime_utc      '2024-10-18 16:23:21' 
_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          5ddy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":603}' 
#
_entry.id    5DDY 
#
_exptl.entry_id    5DDY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.157 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_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            5DDY 
_cell.length_a            206.015 
_cell.length_b            206.015 
_cell.length_c            114.266 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DDY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,H,U 1 1 
B,I,J,K,L,V 2 1 
C,M,N,O,P 3 1 
D,Q,R,S,T 4 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
? 4 G N N 
? 4 K N N 
? 4 O N N 
? 4 S 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
disulf ? disulf1 A SG CYS 303 A CYS 543 1_555 D SG CYS 303 G CYS 543 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 B SG CYS 303 C CYS 543 1_555 C SG CYS 303 E CYS 543 3_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc1 A O SER 99 A SER 339 1_555 H MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? 
metalc ? metalc2 A OD1 ASP 187 A ASP 427 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc3 A OD2 ASP 189 A ASP 429 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc4 A OD1 ASP 189 A ASP 429 1_555 F MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? 
metalc ? metalc5 A OD2 ASP 250 A ASP 490 1_555 F MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc6 E MG MG . A MG 601 1_555 G O2G DCP . A DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? 
metalc ? metalc7 E MG MG . A MG 601 1_555 G O2A DCP . A DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc8 E MG MG . A MG 601 1_555 G O2B DCP . A DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc9 B O ASP 187 C ASP 427 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? 
metalc ? metalc10 B OD1 ASP 187 C ASP 427 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc11 B OD2 ASP 187 C ASP 427 1_555 J MN MN . C MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc12 B OD1 ASP 189 C ASP 429 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc13 B OD2 ASP 189 C ASP 429 1_555 J MN MN . C MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc14 B OD2 ASP 250 C ASP 490 1_555 J MN MN . C MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc15 I MG MG . C MG 601 1_555 K O2B DCP . C DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc16 I MG MG . C MG 601 1_555 K O2A DCP . C DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? 
metalc ? metalc17 I MG MG . C MG 601 1_555 K O2G DCP . C DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc18 J MN MN . C MN 602 1_555 K O2A DCP . C DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? 
metalc ? metalc19 C OD1 ASP 187 E ASP 427 1_555 M MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc20 C OD2 ASP 187 E ASP 427 1_555 N MN MN . E MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? 
metalc ? metalc21 C OD2 ASP 189 E ASP 429 1_555 M MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc22 C OD1 ASP 189 E ASP 429 1_555 N MN MN . E MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc23 C OD2 ASP 250 E ASP 490 1_555 N MN MN . E MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc24 M MG MG . E MG 601 1_555 O O2B DCP . E DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc25 M MG MG . E MG 601 1_555 O O2A DCP . E DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
metalc ? metalc26 M MG MG . E MG 601 1_555 O O2G DCP . E DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc27 D O ASP 187 G ASP 427 1_555 Q MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? 
metalc ? metalc28 D OD1 ASP 187 G ASP 427 1_555 Q MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
metalc ? metalc29 D OD2 ASP 189 G ASP 429 1_555 Q MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc30 D OD2 ASP 250 G ASP 490 1_555 R MN MN . G MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc31 Q MG MG . G MG 601 1_555 S O2B DCP . G DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc32 Q MG MG . G MG 601 1_555 S O2G DCP . G DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? 
#
_chem_comp.formula           'C9 H16 N3 O13 P3' 
_chem_comp.formula_weight    467.157 
_chem_comp.id                DCP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" 
_chem_comp.type              non-polymer 
_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 DCP sing 83 n n 
N1 C6 DCP sing 84 n n 
N1 C1' DCP sing 85 n n 
C2 N3 DCP sing 86 n n 
C2 O2 DCP doub 87 n n 
N3 C4 DCP doub 88 n n 
C4 C5 DCP sing 89 n n 
C4 N4 DCP sing 90 n n 
C5 C6 DCP doub 91 n n 
C5 H5 DCP sing 92 n n 
C6 H6 DCP sing 93 n n 
N4 HN41 DCP sing 94 n n 
N4 HN42 DCP sing 95 n n 
C1' C2' DCP sing 96 n n 
C1' O4' DCP sing 97 n n 
C1' H1' DCP sing 98 n n 
C2' C3' DCP sing 99 n n 
C2' "H2'1" DCP sing 100 n n 
C2' "H2'2" DCP sing 101 n n 
C3' C4' DCP sing 102 n n 
C3' O3' DCP sing 103 n n 
C3' H3' DCP sing 104 n n 
C4' O4' DCP sing 105 n n 
C4' C5' DCP sing 106 n n 
C4' H4' DCP sing 107 n n 
O3' HO3' DCP sing 108 n n 
C5' O5' DCP sing 109 n n 
C5' "H5'1" DCP sing 110 n n 
C5' "H5'2" DCP sing 111 n n 
O5' PA DCP sing 112 n n 
PA O1A DCP doub 113 n n 
PA O2A DCP sing 114 n n 
PA O3A DCP sing 115 n n 
O2A HOA2 DCP sing 116 n n 
O3A PB DCP sing 117 n n 
PB O1B DCP doub 118 n n 
PB O2B DCP sing 119 n n 
PB O3B DCP sing 120 n n 
O2B HOB2 DCP sing 121 n n 
O3B PG DCP sing 122 n n 
PG O1G DCP doub 123 n n 
PG O2G DCP sing 124 n n 
PG O3G DCP sing 125 n n 
O2G HOG2 DCP sing 126 n n 
O3G HOG3 DCP sing 127 n n 
#
_atom_sites.entry_id                     5DDY 
_atom_sites.fract_transf_matrix[1][1]    0.004854 
_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]    0.004854 
_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]    0.008752 
_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
E 2 MG A 1 601 601 MG MG . 
F 3 MN A 1 602 602 MN MN . 
G 4 DCP A 1 603 603 DCP DCP . 
H 3 MN A 1 604 604 MN MN . 
I 2 MG C 1 601 601 MG MG . 
J 3 MN C 1 602 602 MN MN . 
K 4 DCP C 1 603 603 DCP DCP . 
L 3 MN C 1 604 604 MN MN . 
M 2 MG E 1 601 601 MG MG . 
N 3 MN E 1 602 602 MN MN . 
O 4 DCP E 1 603 603 DCP DCP . 
P 3 MN E 1 604 604 MN MN . 
Q 2 MG G 1 601 601 MG MG . 
R 3 MN G 1 602 602 MN MN . 
S 4 DCP G 1 603 603 DCP DCP . 
T 3 MN G 1 604 604 MN MN . 
U 5 HOH A 1 701 701 HOH HOH . 
U 5 HOH A 2 702 702 HOH HOH . 
V 5 HOH C 1 701 701 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 DCP . . . O 4 -37.247 -53.532 -31.075 1 133.51 ? N1 DCP 603 E 1 
HETATM 2 C C2 DCP . . . O 4 -37.962 -53.113 -29.921 1 136.28 ? C2 DCP 603 E 1 
HETATM 3 N N3 DCP . . . O 4 -37.603 -51.838 -29.315 1 142.7 ? N3 DCP 603 E 1 
HETATM 4 C C4 DCP . . . O 4 -36.631 -51.109 -29.852 1 135.97 ? C4 DCP 603 E 1 
HETATM 5 C C5 DCP . . . O 4 -35.882 -51.592 -31.099 1 133.98 ? C5 DCP 603 E 1 
HETATM 6 C C6 DCP . . . O 4 -36.213 -52.779 -31.666 1 133.46 ? C6 DCP 603 E 1 
HETATM 7 O O2 DCP . . . O 4 -38.859 -53.787 -29.43 1 136.43 ? O2 DCP 603 E 1 
HETATM 8 N N4 DCP . . . O 4 -36.275 -49.849 -29.258 1 129.69 ? N4 DCP 603 E 1 
HETATM 9 C C1' DCP . . . O 4 -37.614 -54.814 -31.698 1 129.68 ? C1' DCP 603 E 1 
HETATM 10 C C2' DCP . . . O 4 -38.732 -54.694 -32.694 1 133.28 ? C2' DCP 603 E 1 
HETATM 11 C C3' DCP . . . O 4 -37.998 -54.674 -33.994 1 138.65 ? C3' DCP 603 E 1 
HETATM 12 C C4' DCP . . . O 4 -36.879 -55.608 -33.708 1 141.17 ? C4' DCP 603 E 1 
HETATM 13 O O4' DCP . . . O 4 -36.562 -55.486 -32.361 1 137.3 ? O4' DCP 603 E 1 
HETATM 14 O O3' DCP . . . O 4 -38.769 -55.03 -35.099 1 142.36 ? O3' DCP 603 E 1 
HETATM 15 C C5' DCP . . . O 4 -35.667 -55.429 -34.61 1 148.92 ? C5' DCP 603 E 1 
HETATM 16 O O5' DCP . . . O 4 -35.131 -54.158 -34.463 1 149.11 ? O5' DCP 603 E 1 
HETATM 17 P PA DCP . . . O 4 -34.923 -53.223 -35.73 1 171.87 ? PA DCP 603 E 1 
HETATM 18 O O1A DCP . . . O 4 -34.005 -52.09 -35.319 1 155.44 ? O1A DCP 603 E 1 
HETATM 19 O O2A DCP . . . O 4 -34.234 -54.05 -36.79 1 172.65 ? O2A DCP 603 E 1 
HETATM 20 O O3A DCP . . . O 4 -36.319 -52.644 -36.231 1 156.48 ? O3A DCP 603 E 1 
HETATM 21 P PB DCP . . . O 4 -36.992 -53.036 -37.624 1 175.86 ? PB DCP 603 E 1 
HETATM 22 O O1B DCP . . . O 4 -38.455 -53.402 -37.397 1 158.59 ? O1B DCP 603 E 1 
HETATM 23 O O2B DCP . . . O 4 -36.305 -54.224 -38.271 1 159.67 ? O2B DCP 603 E 1 
HETATM 24 O O3B DCP . . . O 4 -36.875 -51.813 -38.627 1 177.14 ? O3B DCP 603 E 1 
HETATM 25 P PG DCP . . . O 4 -35.726 -51.677 -39.713 1 185.57 ? PG DCP 603 E 1 
HETATM 26 O O1G DCP . . . O 4 -35.209 -50.255 -39.725 1 173.49 ? O1G DCP 603 E 1 
HETATM 27 O O2G DCP . . . O 4 -34.61 -52.69 -39.506 1 162.12 ? O2G DCP 603 E 1 
HETATM 28 O O3G DCP . . . O 4 -36.388 -51.736 -41.078 1 185.14 ? O3G DCP 603 E 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#