data_3FBC
#
_model_server_result.job_id            B8qDvJs1jV-p_ouxfynfiw 
_model_server_result.datetime_utc      '2024-11-13 06:19:20' 
_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          3fbc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":138}' 
#
_entry.id    3FBC 
#
_exptl.entry_id    3FBC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_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            3FBC 
_cell.length_a            80.387 
_cell.length_b            153.337 
_cell.length_c            185.384 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3FBC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? hexameric 6 author_defined_assembly 1 
? hexameric 6 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,G,H,I,M,N,O,S,T,U,Y,AA,CA 1 1,2 
B,D,F,J,K,L,P,Q,R,V,W,X,Z,BA,DA 2 1,3 
#
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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
3 'crystal symmetry operation' 3_755 -x+2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 160.774 0 92.692 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 H N N 
? 3 K N N 
? 3 N N N 
? 3 Q N N 
? 3 T N N 
? 3 W N N 
#
_struct_conn.conn_type_id                   metalc 
_struct_conn.details                        ? 
_struct_conn.id                             metalc1 
_struct_conn.ptnr1_label_asym_id            N 
_struct_conn.ptnr1_label_atom_id            O2B 
_struct_conn.ptnr1_label_comp_id            TYD 
_struct_conn.ptnr1_label_seq_id             . 
_struct_conn.ptnr1_auth_asym_id             C 
_struct_conn.ptnr1_auth_comp_id             TYD 
_struct_conn.ptnr1_auth_seq_id              138 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            M 
_struct_conn.ptnr2_label_atom_id            MG 
_struct_conn.ptnr2_label_comp_id            MG 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             C 
_struct_conn.ptnr2_auth_comp_id             MG 
_struct_conn.ptnr2_auth_seq_id              162 
_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                2.275 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                TYD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-5'-DIPHOSPHATE" 
_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
PA O1A TYD doub 338 n n 
PA O2A TYD sing 339 n n 
PA O3A TYD sing 340 n n 
PA O5' TYD sing 341 n n 
O2A HOA2 TYD sing 342 n n 
O3A PB TYD sing 343 n n 
PB O1B TYD doub 344 n n 
PB O2B TYD sing 345 n n 
PB O3B TYD sing 346 n n 
O2B HOB2 TYD sing 347 n n 
O3B HOB3 TYD sing 348 n n 
O5' C5' TYD sing 349 n n 
C5' C4' TYD sing 350 n n 
C5' "H5'1" TYD sing 351 n n 
C5' "H5'2" TYD sing 352 n n 
C4' O4' TYD sing 353 n n 
C4' C3' TYD sing 354 n n 
C4' H4' TYD sing 355 n n 
O4' C1' TYD sing 356 n n 
C3' O3' TYD sing 357 n n 
C3' C2' TYD sing 358 n n 
C3' H3' TYD sing 359 n n 
O3' HO3' TYD sing 360 n n 
C2' C1' TYD sing 361 n n 
C2' "H2'1" TYD sing 362 n n 
C2' "H2'2" TYD sing 363 n n 
C1' N1 TYD sing 364 n n 
C1' H1' TYD sing 365 n n 
N1 C2 TYD sing 366 n y 
N1 C6 TYD sing 367 n y 
C2 O2 TYD doub 368 n n 
C2 N3 TYD sing 369 n y 
N3 C4 TYD sing 370 n y 
N3 HN3 TYD sing 371 n n 
C4 O4 TYD doub 372 n n 
C4 C5 TYD sing 373 n y 
C5 C5M TYD sing 374 n n 
C5 C6 TYD doub 375 n y 
C5M H51 TYD sing 376 n n 
C5M H52 TYD sing 377 n n 
C5M H53 TYD sing 378 n n 
C6 H6 TYD sing 379 n n 
#
_atom_sites.entry_id                     3FBC 
_atom_sites.fract_transf_matrix[1][1]    0.01244 
_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]    0.006522 
_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]    0.005394 
_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 2 MG A 1 160 160 MG MG . 
H 3 TYD A 1 138 160 TYD TYD . 
I 4 PO4 A 1 139 2 PO4 PO4 . 
J 2 MG B 1 161 161 MG MG . 
K 3 TYD B 1 138 161 TYD TYD . 
L 4 PO4 B 1 139 3 PO4 PO4 . 
M 2 MG C 1 162 162 MG MG . 
N 3 TYD C 1 138 162 TYD TYD . 
O 4 PO4 C 1 139 4 PO4 PO4 . 
P 2 MG D 1 163 163 MG MG . 
Q 3 TYD D 1 138 163 TYD TYD . 
R 4 PO4 D 1 139 5 PO4 PO4 . 
S 2 MG E 1 164 164 MG MG . 
T 3 TYD E 1 138 164 TYD TYD . 
U 4 PO4 E 1 139 1 PO4 PO4 . 
V 2 MG F 1 165 165 MG MG . 
W 3 TYD F 1 138 165 TYD TYD . 
X 4 PO4 F 1 139 6 PO4 PO4 . 
Y 5 HOH A 1 140 3 HOH HOH . 
Y 5 HOH A 2 141 5 HOH HOH . 
Y 5 HOH A 3 142 7 HOH HOH . 
Y 5 HOH A 4 143 9 HOH HOH . 
Y 5 HOH A 5 144 10 HOH HOH . 
Y 5 HOH A 6 145 15 HOH HOH . 
Y 5 HOH A 7 146 23 HOH HOH . 
Y 5 HOH A 8 147 24 HOH HOH . 
Y 5 HOH A 9 148 25 HOH HOH . 
Y 5 HOH A 10 149 26 HOH HOH . 
Y 5 HOH A 11 150 39 HOH HOH . 
Y 5 HOH A 12 151 40 HOH HOH . 
Y 5 HOH A 13 152 57 HOH HOH . 
Y 5 HOH A 14 153 73 HOH HOH . 
Y 5 HOH A 15 154 85 HOH HOH . 
Y 5 HOH A 16 155 99 HOH HOH . 
Y 5 HOH A 17 156 102 HOH HOH . 
Y 5 HOH A 18 157 104 HOH HOH . 
Y 5 HOH A 19 158 105 HOH HOH . 
Z 5 HOH B 1 140 30 HOH HOH . 
Z 5 HOH B 2 141 31 HOH HOH . 
Z 5 HOH B 3 142 32 HOH HOH . 
Z 5 HOH B 4 143 42 HOH HOH . 
Z 5 HOH B 5 144 49 HOH HOH . 
Z 5 HOH B 6 145 56 HOH HOH . 
Z 5 HOH B 7 146 59 HOH HOH . 
Z 5 HOH B 8 147 62 HOH HOH . 
Z 5 HOH B 9 148 64 HOH HOH . 
Z 5 HOH B 10 149 92 HOH HOH . 
Z 5 HOH B 11 150 93 HOH HOH . 
Z 5 HOH B 12 151 98 HOH HOH . 
Z 5 HOH B 13 152 101 HOH HOH . 
AA 5 HOH C 1 140 4 HOH HOH . 
AA 5 HOH C 2 141 6 HOH HOH . 
AA 5 HOH C 3 142 8 HOH HOH . 
AA 5 HOH C 4 143 11 HOH HOH . 
AA 5 HOH C 5 144 12 HOH HOH . 
AA 5 HOH C 6 145 14 HOH HOH . 
AA 5 HOH C 7 146 17 HOH HOH . 
AA 5 HOH C 8 147 18 HOH HOH . 
AA 5 HOH C 9 148 21 HOH HOH . 
AA 5 HOH C 10 149 22 HOH HOH . 
AA 5 HOH C 11 150 33 HOH HOH . 
AA 5 HOH C 12 151 34 HOH HOH . 
AA 5 HOH C 13 152 67 HOH HOH . 
AA 5 HOH C 14 153 68 HOH HOH . 
AA 5 HOH C 15 154 69 HOH HOH . 
AA 5 HOH C 16 155 70 HOH HOH . 
AA 5 HOH C 17 156 71 HOH HOH . 
AA 5 HOH C 18 157 72 HOH HOH . 
AA 5 HOH C 19 158 74 HOH HOH . 
AA 5 HOH C 20 159 81 HOH HOH . 
AA 5 HOH C 21 160 84 HOH HOH . 
AA 5 HOH C 22 161 87 HOH HOH . 
AA 5 HOH C 23 163 89 HOH HOH . 
AA 5 HOH C 24 164 95 HOH HOH . 
BA 5 HOH D 1 140 37 HOH HOH . 
BA 5 HOH D 2 141 38 HOH HOH . 
BA 5 HOH D 3 142 41 HOH HOH . 
BA 5 HOH D 4 143 43 HOH HOH . 
BA 5 HOH D 5 144 45 HOH HOH . 
BA 5 HOH D 6 145 52 HOH HOH . 
BA 5 HOH D 7 146 53 HOH HOH . 
BA 5 HOH D 8 147 58 HOH HOH . 
BA 5 HOH D 9 148 75 HOH HOH . 
BA 5 HOH D 10 149 76 HOH HOH . 
BA 5 HOH D 11 150 77 HOH HOH . 
BA 5 HOH D 12 151 78 HOH HOH . 
BA 5 HOH D 13 152 79 HOH HOH . 
BA 5 HOH D 14 153 80 HOH HOH . 
BA 5 HOH D 15 154 88 HOH HOH . 
BA 5 HOH D 16 155 90 HOH HOH . 
BA 5 HOH D 17 156 100 HOH HOH . 
BA 5 HOH D 18 157 103 HOH HOH . 
CA 5 HOH E 1 140 1 HOH HOH . 
CA 5 HOH E 2 141 16 HOH HOH . 
CA 5 HOH E 3 142 19 HOH HOH . 
CA 5 HOH E 4 143 28 HOH HOH . 
CA 5 HOH E 5 144 29 HOH HOH . 
CA 5 HOH E 6 145 35 HOH HOH . 
CA 5 HOH E 7 146 36 HOH HOH . 
CA 5 HOH E 8 147 47 HOH HOH . 
CA 5 HOH E 9 148 48 HOH HOH . 
CA 5 HOH E 10 149 50 HOH HOH . 
CA 5 HOH E 11 150 51 HOH HOH . 
CA 5 HOH E 12 151 55 HOH HOH . 
CA 5 HOH E 13 152 60 HOH HOH . 
CA 5 HOH E 14 153 65 HOH HOH . 
CA 5 HOH E 15 154 66 HOH HOH . 
CA 5 HOH E 16 155 91 HOH HOH . 
CA 5 HOH E 17 156 96 HOH HOH . 
CA 5 HOH E 18 157 106 HOH HOH . 
DA 5 HOH F 1 140 2 HOH HOH . 
DA 5 HOH F 2 141 13 HOH HOH . 
DA 5 HOH F 3 142 20 HOH HOH . 
DA 5 HOH F 4 143 27 HOH HOH . 
DA 5 HOH F 5 144 44 HOH HOH . 
DA 5 HOH F 6 145 46 HOH HOH . 
DA 5 HOH F 7 146 54 HOH HOH . 
DA 5 HOH F 8 147 61 HOH HOH . 
DA 5 HOH F 9 148 63 HOH HOH . 
DA 5 HOH F 10 149 82 HOH HOH . 
DA 5 HOH F 11 150 83 HOH HOH . 
DA 5 HOH F 12 151 86 HOH HOH . 
DA 5 HOH F 13 152 94 HOH HOH . 
DA 5 HOH F 14 153 97 HOH HOH . 
DA 5 HOH F 15 154 107 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 P PA TYD . . . N 3 4.789 28.182 -8.994 1 96.78 ? PA TYD 138 C 1 
HETATM 2 O O1A TYD . . . N 3 3.447 28.851 -9.216 1 82.99 ? O1A TYD 138 C 1 
HETATM 3 O O2A TYD . . . N 3 5.893 28.894 -8.24 1 87.25 ? O2A TYD 138 C 1 
HETATM 4 O O3A TYD . . . N 3 4.638 26.705 -8.336 1 88.09 ? O3A TYD 138 C 1 
HETATM 5 P PB TYD . . . N 3 3.272 25.856 -8.132 1 86.26 ? PB TYD 138 C 1 
HETATM 6 O O1B TYD . . . N 3 3.302 24.785 -9.203 1 71.91 ? O1B TYD 138 C 1 
HETATM 7 O O2B TYD . . . N 3 2.157 26.842 -8.345 1 90.41 ? O2B TYD 138 C 1 
HETATM 8 O O3B TYD . . . N 3 3.413 25.345 -6.711 1 69.77 ? O3B TYD 138 C 1 
HETATM 9 O O5' TYD . . . N 3 5.386 27.759 -10.423 1 83.56 ? O5' TYD 138 C 1 
HETATM 10 C C5' TYD . . . N 3 4.488 27.204 -11.385 1 75.97 ? C5' TYD 138 C 1 
HETATM 11 C C4' TYD . . . N 3 5.166 26.033 -12.098 1 76.78 ? C4' TYD 138 C 1 
HETATM 12 O O4' TYD . . . N 3 6.161 26.562 -12.981 1 76.6 ? O4' TYD 138 C 1 
HETATM 13 C C3' TYD . . . N 3 5.857 25.064 -11.134 1 70.05 ? C3' TYD 138 C 1 
HETATM 14 O O3' TYD . . . N 3 5.087 23.866 -11.011 1 68.57 ? O3' TYD 138 C 1 
HETATM 15 C C2' TYD . . . N 3 7.207 24.762 -11.761 1 69.3 ? C2' TYD 138 C 1 
HETATM 16 C C1' TYD . . . N 3 7.411 25.909 -12.755 1 75.03 ? C1' TYD 138 C 1 
HETATM 17 N N1 TYD . . . N 3 8.336 26.927 -12.259 1 73.09 ? N1 TYD 138 C 1 
HETATM 18 C C2 TYD . . . N 3 9.549 27.089 -12.953 1 73.57 ? C2 TYD 138 C 1 
HETATM 19 O O2 TYD . . . N 3 9.778 26.338 -13.935 1 71.75 ? O2 TYD 138 C 1 
HETATM 20 N N3 TYD . . . N 3 10.44 28.013 -12.561 1 73.24 ? N3 TYD 138 C 1 
HETATM 21 C C4 TYD . . . N 3 10.19 28.81 -11.512 1 76.74 ? C4 TYD 138 C 1 
HETATM 22 O O4 TYD . . . N 3 11.035 29.666 -11.164 1 81.67 ? O4 TYD 138 C 1 
HETATM 23 C C5 TYD . . . N 3 8.904 28.665 -10.772 1 79.27 ? C5 TYD 138 C 1 
HETATM 24 C C5M TYD . . . N 3 8.586 29.543 -9.588 1 74.27 ? C5M TYD 138 C 1 
HETATM 25 C C6 TYD . . . N 3 8.004 27.7 -11.209 1 74.63 ? C6 TYD 138 C 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#