data_3H6D
#
_model_server_result.job_id            Wmir_m0KF9xybHTvybFaqw 
_model_server_result.datetime_utc      '2024-11-17 03:43:39' 
_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          3h6d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    3H6D 
#
_exptl.entry_id    3H6D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.157 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" 
_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         120 
_cell.entry_id            3H6D 
_cell.length_a            55.228 
_cell.length_b            55.228 
_cell.length_c            83.65 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3H6D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? trimeric 3 author_defined_assembly 1 
PISA monomeric 1 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,C,D,E,F 1 1,2,3 
A,B,C,D,E,F 2 1 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 27.614 -47.828851 0 
3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 55.228 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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
metalc ? metalc1 B MG MG . A MG 200 1_555 C O1B DUP . A DUP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc2 B MG MG . A MG 200 1_555 C O1A DUP . A DUP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc3 B MG MG . A MG 200 1_555 C O2G DUP . A DUP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
#
_chem_comp.formula           'C9 H16 N3 O13 P3' 
_chem_comp.formula_weight    467.157 
_chem_comp.id                DUP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-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
O4 C4 DUP doub 70 n n 
C4 C5 DUP sing 71 n y 
C4 N3 DUP sing 72 n y 
C5 C6 DUP doub 73 n y 
C5 H5 DUP sing 74 n n 
C6 N1 DUP sing 75 n y 
C6 H6 DUP sing 76 n n 
N3 C2 DUP sing 77 n y 
N3 HN3 DUP sing 78 n n 
C2 O2 DUP doub 79 n n 
C2 N1 DUP sing 80 n y 
N1 C1' DUP sing 81 n n 
C1' C2' DUP sing 82 n n 
C1' O4' DUP sing 83 n n 
C1' H1' DUP sing 84 n n 
C2' C3' DUP sing 85 n n 
C2' "H2'1" DUP sing 86 n n 
C2' "H2'2" DUP sing 87 n n 
C3' O3' DUP sing 88 n n 
C3' C4' DUP sing 89 n n 
C3' H1 DUP sing 90 n n 
O3' H3' DUP sing 91 n n 
O4' C4' DUP sing 92 n n 
C4' C5' DUP sing 93 n n 
C4' H4' DUP sing 94 n n 
C5' O5' DUP sing 95 n n 
C5' "H5'1" DUP sing 96 n n 
C5' "H5'2" DUP sing 97 n n 
O5' PA DUP sing 98 n n 
PA O1A DUP doub 99 n n 
PA O2A DUP sing 100 n n 
PA N3A DUP sing 101 n n 
O2A H2A DUP sing 102 n n 
N3A PB DUP sing 103 n n 
N3A H3A DUP sing 104 n n 
PB O1B DUP doub 105 n n 
PB O2B DUP sing 106 n n 
PB O3B DUP sing 107 n n 
O2B H2B DUP sing 108 n n 
O3B PG DUP sing 109 n n 
PG O2G DUP doub 110 n n 
PG O1G DUP sing 111 n n 
PG O3G DUP sing 112 n n 
O1G H1G DUP sing 113 n n 
O3G H3G DUP sing 114 n n 
#
_atom_sites.entry_id                     3H6D 
_atom_sites.fract_transf_matrix[1][1]    0.018107 
_atom_sites.fract_transf_matrix[1][2]    0.010454 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020908 
_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]    0.011955 
_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 MG A 1 200 200 MG MG . 
C 3 DUP A 1 201 201 DUP DUP . 
D 4 TRS A 1 202 202 TRS TRS . 
E 4 TRS A 1 203 203 TRS TRS . 
F 5 HOH A 1 175 175 HOH HOH . 
F 5 HOH A 2 176 176 HOH HOH . 
F 5 HOH A 3 177 177 HOH HOH . 
F 5 HOH A 4 178 178 HOH HOH . 
F 5 HOH A 5 179 179 HOH HOH . 
F 5 HOH A 6 180 180 HOH HOH . 
F 5 HOH A 7 181 181 HOH HOH . 
F 5 HOH A 8 182 182 HOH HOH . 
F 5 HOH A 9 183 183 HOH HOH . 
F 5 HOH A 10 184 184 HOH HOH . 
F 5 HOH A 11 185 185 HOH HOH . 
F 5 HOH A 12 186 186 HOH HOH . 
F 5 HOH A 13 187 187 HOH HOH . 
F 5 HOH A 14 188 188 HOH HOH . 
F 5 HOH A 15 189 189 HOH HOH . 
F 5 HOH A 16 190 190 HOH HOH . 
F 5 HOH A 17 191 191 HOH HOH . 
F 5 HOH A 18 192 192 HOH HOH . 
F 5 HOH A 19 193 193 HOH HOH . 
F 5 HOH A 20 194 194 HOH HOH . 
F 5 HOH A 21 195 195 HOH HOH . 
F 5 HOH A 22 196 196 HOH HOH . 
F 5 HOH A 23 197 197 HOH HOH . 
F 5 HOH A 24 198 198 HOH HOH . 
F 5 HOH A 25 199 199 HOH HOH . 
F 5 HOH A 26 204 204 HOH HOH . 
F 5 HOH A 27 205 205 HOH HOH . 
F 5 HOH A 28 206 206 HOH HOH . 
F 5 HOH A 29 207 207 HOH HOH . 
F 5 HOH A 30 208 208 HOH HOH . 
F 5 HOH A 31 209 209 HOH HOH . 
F 5 HOH A 32 210 210 HOH HOH . 
F 5 HOH A 33 211 211 HOH HOH . 
F 5 HOH A 34 212 212 HOH HOH . 
F 5 HOH A 35 213 213 HOH HOH . 
F 5 HOH A 36 214 214 HOH HOH . 
F 5 HOH A 37 215 215 HOH HOH . 
F 5 HOH A 38 216 216 HOH HOH . 
F 5 HOH A 39 217 217 HOH HOH . 
F 5 HOH A 40 218 218 HOH HOH . 
F 5 HOH A 41 219 219 HOH HOH . 
F 5 HOH A 42 220 220 HOH HOH . 
F 5 HOH A 43 221 221 HOH HOH . 
F 5 HOH A 44 222 222 HOH HOH . 
F 5 HOH A 45 223 223 HOH HOH . 
F 5 HOH A 46 224 224 HOH HOH . 
F 5 HOH A 47 225 225 HOH HOH . 
F 5 HOH A 48 226 226 HOH HOH . 
F 5 HOH A 49 227 227 HOH HOH . 
F 5 HOH A 50 228 228 HOH HOH . 
F 5 HOH A 51 229 229 HOH HOH . 
F 5 HOH A 52 230 230 HOH HOH . 
F 5 HOH A 53 231 231 HOH HOH . 
F 5 HOH A 54 232 232 HOH HOH . 
F 5 HOH A 55 233 233 HOH HOH . 
F 5 HOH A 56 234 234 HOH HOH . 
F 5 HOH A 57 235 235 HOH HOH . 
F 5 HOH A 58 236 236 HOH HOH . 
F 5 HOH A 59 237 237 HOH HOH . 
F 5 HOH A 60 238 238 HOH HOH . 
F 5 HOH A 61 239 239 HOH HOH . 
F 5 HOH A 62 240 240 HOH HOH . 
F 5 HOH A 63 241 241 HOH HOH . 
F 5 HOH A 64 242 242 HOH HOH . 
F 5 HOH A 65 243 243 HOH HOH . 
F 5 HOH A 66 244 244 HOH HOH . 
F 5 HOH A 67 245 245 HOH HOH . 
F 5 HOH A 68 246 246 HOH HOH . 
F 5 HOH A 69 247 247 HOH HOH . 
F 5 HOH A 70 248 248 HOH HOH . 
F 5 HOH A 71 250 250 HOH HOH . 
F 5 HOH A 72 251 251 HOH HOH . 
F 5 HOH A 73 252 252 HOH HOH . 
F 5 HOH A 74 253 253 HOH HOH . 
F 5 HOH A 75 254 254 HOH HOH . 
F 5 HOH A 76 255 255 HOH HOH . 
F 5 HOH A 77 257 257 HOH HOH . 
F 5 HOH A 78 258 258 HOH HOH . 
F 5 HOH A 79 259 259 HOH HOH . 
F 5 HOH A 80 260 260 HOH HOH . 
F 5 HOH A 81 261 261 HOH HOH . 
F 5 HOH A 82 262 262 HOH HOH . 
F 5 HOH A 83 263 263 HOH HOH . 
F 5 HOH A 84 264 264 HOH HOH . 
F 5 HOH A 85 265 265 HOH HOH . 
F 5 HOH A 86 266 266 HOH HOH . 
F 5 HOH A 87 267 267 HOH HOH . 
F 5 HOH A 88 268 268 HOH HOH . 
F 5 HOH A 89 269 269 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 O4 DUP . . . C 3 21.6 -7.05 0.006 1 17.97 ? O4 DUP 201 A 1 
HETATM 2 C C4 DUP . . . C 3 20.442 -6.651 -0.557 1 18.85 ? C4 DUP 201 A 1 
HETATM 3 C C5 DUP . . . C 3 19.524 -7.548 -1.082 1 17.75 ? C5 DUP 201 A 1 
HETATM 4 C C6 DUP . . . C 3 18.362 -7.072 -1.64 1 17.55 ? C6 DUP 201 A 1 
HETATM 5 N N3 DUP . . . C 3 20.179 -5.343 -0.572 1 21.34 ? N3 DUP 201 A 1 
HETATM 6 C C2 DUP . . . C 3 19.031 -4.896 -1.127 1 19.45 ? C2 DUP 201 A 1 
HETATM 7 O O2 DUP . . . C 3 18.903 -3.583 -1.073 1 17.1 ? O2 DUP 201 A 1 
HETATM 8 N N1 DUP . . . C 3 18.119 -5.756 -1.637 1 21.79 ? N1 DUP 201 A 1 
HETATM 9 C C1' DUP . . . C 3 16.862 -5.362 -2.287 1 25.15 ? C1' DUP 201 A 1 
HETATM 10 C C2' DUP . . . C 3 17.053 -5.651 -3.787 1 22.49 ? C2' DUP 201 A 1 
HETATM 11 C C3' DUP . . . C 3 16.237 -6.912 -4.044 1 20.65 ? C3' DUP 201 A 1 
HETATM 12 O O3' DUP . . . C 3 15.705 -7.05 -5.382 1 16.03 ? O3' DUP 201 A 1 
HETATM 13 O O4' DUP . . . C 3 15.757 -6.183 -1.85 1 23.39 ? O4' DUP 201 A 1 
HETATM 14 C C4' DUP . . . C 3 15.126 -6.768 -3.002 1 25.4 ? C4' DUP 201 A 1 
HETATM 15 C C5' DUP . . . C 3 14.528 -8.103 -2.6 1 29.61 ? C5' DUP 201 A 1 
HETATM 16 O O5' DUP . . . C 3 15.634 -8.861 -2.066 1 38.09 ? O5' DUP 201 A 1 
HETATM 17 P PA DUP . . . C 3 15.54 -10.426 -1.623 1 43.27 ? PA DUP 201 A 1 
HETATM 18 O O1A DUP . . . C 3 14.754 -11.165 -2.68 1 45.66 ? O1A DUP 201 A 1 
HETATM 19 O O2A DUP . . . C 3 16.99 -10.814 -1.407 1 41.82 ? O2A DUP 201 A 1 
HETATM 20 N N3A DUP . . . C 3 14.692 -10.514 -0.138 1 43.89 ? N3A DUP 201 A 1 
HETATM 21 P PB DUP . . . C 3 13.082 -10.95 0.165 1 45.65 ? PB DUP 201 A 1 
HETATM 22 O O1B DUP . . . C 3 12.798 -12.229 -0.603 1 43.02 ? O1B DUP 201 A 1 
HETATM 23 O O2B DUP . . . C 3 12.855 -11.008 1.653 1 38.54 ? O2B DUP 201 A 1 
HETATM 24 O O3B DUP . . . C 3 12.14 -9.718 -0.362 1 49.61 ? O3B DUP 201 A 1 
HETATM 25 P PG DUP . . . C 3 11.195 -9.645 -1.696 1 53.53 ? PG DUP 201 A 1 
HETATM 26 O O2G DUP . . . C 3 11.921 -10.386 -2.804 1 51.01 ? O2G DUP 201 A 1 
HETATM 27 O O1G DUP . . . C 3 9.886 -10.293 -1.265 1 50.62 ? O1G DUP 201 A 1 
HETATM 28 O O3G DUP . . . C 3 11.125 -8.144 -1.986 1 49.2 ? O3G DUP 201 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#