data_3FBF
#
_model_server_result.job_id            oj4kerqd_O3uqk7XjYbwLg 
_model_server_result.datetime_utc      '2024-11-16 21:51:59' 
_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          3fbf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":138}' 
#
_entry.id    3FBF 
#
_exptl.entry_id    3FBF 
_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            3FBF 
_cell.length_a            80.241 
_cell.length_b            152.68 
_cell.length_c            185.248 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3FBF 
_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,K,L,O,P,S,U,W 1 1,2 
B,D,F,I,J,M,N,Q,R,T,V,X 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 -1 160.482 0 92.624 
#
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 J N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 R N N 
#
_struct_conn.conn_type_id                   metalc 
_struct_conn.details                        ? 
_struct_conn.id                             metalc1 
_struct_conn.ptnr1_label_asym_id            P 
_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             E 
_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            O 
_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             E 
_struct_conn.ptnr2_auth_comp_id             MG 
_struct_conn.ptnr2_auth_seq_id              164 
_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                2.463 
_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 334 n n 
PA O2A TYD sing 335 n n 
PA O3A TYD sing 336 n n 
PA O5' TYD sing 337 n n 
O2A HOA2 TYD sing 338 n n 
O3A PB TYD sing 339 n n 
PB O1B TYD doub 340 n n 
PB O2B TYD sing 341 n n 
PB O3B TYD sing 342 n n 
O2B HOB2 TYD sing 343 n n 
O3B HOB3 TYD sing 344 n n 
O5' C5' TYD sing 345 n n 
C5' C4' TYD sing 346 n n 
C5' "H5'1" TYD sing 347 n n 
C5' "H5'2" TYD sing 348 n n 
C4' O4' TYD sing 349 n n 
C4' C3' TYD sing 350 n n 
C4' H4' TYD sing 351 n n 
O4' C1' TYD sing 352 n n 
C3' O3' TYD sing 353 n n 
C3' C2' TYD sing 354 n n 
C3' H3' TYD sing 355 n n 
O3' HO3' TYD sing 356 n n 
C2' C1' TYD sing 357 n n 
C2' "H2'1" TYD sing 358 n n 
C2' "H2'2" TYD sing 359 n n 
C1' N1 TYD sing 360 n n 
C1' H1' TYD sing 361 n n 
N1 C2 TYD sing 362 n y 
N1 C6 TYD sing 363 n y 
C2 O2 TYD doub 364 n n 
C2 N3 TYD sing 365 n y 
N3 C4 TYD sing 366 n y 
N3 HN3 TYD sing 367 n n 
C4 O4 TYD doub 368 n n 
C4 C5 TYD sing 369 n y 
C5 C5M TYD sing 370 n n 
C5 C6 TYD doub 371 n y 
C5M H51 TYD sing 372 n n 
C5M H52 TYD sing 373 n n 
C5M H53 TYD sing 374 n n 
C6 H6 TYD sing 375 n n 
#
_atom_sites.entry_id                     3FBF 
_atom_sites.fract_transf_matrix[1][1]    0.012462 
_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]    0.00655 
_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]    0.005398 
_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 2 MG B 1 161 161 MG MG . 
J 3 TYD B 1 138 161 TYD TYD . 
K 2 MG C 1 162 162 MG MG . 
L 3 TYD C 1 138 162 TYD TYD . 
M 2 MG D 1 163 163 MG MG . 
N 3 TYD D 1 138 163 TYD TYD . 
O 2 MG E 1 164 164 MG MG . 
P 3 TYD E 1 138 164 TYD TYD . 
Q 2 MG F 1 165 165 MG MG . 
R 3 TYD F 1 138 165 TYD TYD . 
S 4 HOH A 1 139 139 HOH HOH . 
S 4 HOH A 2 140 3 HOH HOH . 
S 4 HOH A 3 141 5 HOH HOH . 
S 4 HOH A 4 142 142 HOH HOH . 
S 4 HOH A 5 143 8 HOH HOH . 
S 4 HOH A 6 144 9 HOH HOH . 
S 4 HOH A 7 145 17 HOH HOH . 
S 4 HOH A 8 146 20 HOH HOH . 
S 4 HOH A 9 147 21 HOH HOH . 
S 4 HOH A 10 148 22 HOH HOH . 
S 4 HOH A 11 149 24 HOH HOH . 
S 4 HOH A 12 150 42 HOH HOH . 
S 4 HOH A 13 151 43 HOH HOH . 
S 4 HOH A 14 152 75 HOH HOH . 
S 4 HOH A 15 153 76 HOH HOH . 
S 4 HOH A 16 154 78 HOH HOH . 
S 4 HOH A 17 155 89 HOH HOH . 
S 4 HOH A 18 156 96 HOH HOH . 
S 4 HOH A 19 157 97 HOH HOH . 
S 4 HOH A 20 158 111 HOH HOH . 
S 4 HOH A 21 159 114 HOH HOH . 
S 4 HOH A 22 161 117 HOH HOH . 
S 4 HOH A 23 162 120 HOH HOH . 
S 4 HOH A 24 163 123 HOH HOH . 
S 4 HOH A 25 164 124 HOH HOH . 
S 4 HOH A 26 165 126 HOH HOH . 
S 4 HOH A 27 166 128 HOH HOH . 
S 4 HOH A 28 167 129 HOH HOH . 
S 4 HOH A 29 168 132 HOH HOH . 
S 4 HOH A 30 169 133 HOH HOH . 
T 4 HOH B 1 139 18 HOH HOH . 
T 4 HOH B 2 140 27 HOH HOH . 
T 4 HOH B 3 141 29 HOH HOH . 
T 4 HOH B 4 142 30 HOH HOH . 
T 4 HOH B 5 143 31 HOH HOH . 
T 4 HOH B 6 144 46 HOH HOH . 
T 4 HOH B 7 145 50 HOH HOH . 
T 4 HOH B 8 146 56 HOH HOH . 
T 4 HOH B 9 147 59 HOH HOH . 
T 4 HOH B 10 148 62 HOH HOH . 
T 4 HOH B 11 149 64 HOH HOH . 
T 4 HOH B 12 150 66 HOH HOH . 
T 4 HOH B 13 151 85 HOH HOH . 
T 4 HOH B 14 152 87 HOH HOH . 
T 4 HOH B 15 153 100 HOH HOH . 
T 4 HOH B 16 154 103 HOH HOH . 
T 4 HOH B 17 155 108 HOH HOH . 
T 4 HOH B 18 156 113 HOH HOH . 
U 4 HOH C 1 139 4 HOH HOH . 
U 4 HOH C 2 140 6 HOH HOH . 
U 4 HOH C 3 141 7 HOH HOH . 
U 4 HOH C 4 142 10 HOH HOH . 
U 4 HOH C 5 143 143 HOH HOH . 
U 4 HOH C 6 144 12 HOH HOH . 
U 4 HOH C 7 145 14 HOH HOH . 
U 4 HOH C 8 146 16 HOH HOH . 
U 4 HOH C 9 147 19 HOH HOH . 
U 4 HOH C 10 148 32 HOH HOH . 
U 4 HOH C 11 149 34 HOH HOH . 
U 4 HOH C 12 150 37 HOH HOH . 
U 4 HOH C 13 151 40 HOH HOH . 
U 4 HOH C 14 152 61 HOH HOH . 
U 4 HOH C 15 153 67 HOH HOH . 
U 4 HOH C 16 154 68 HOH HOH . 
U 4 HOH C 17 155 69 HOH HOH . 
U 4 HOH C 18 156 70 HOH HOH . 
U 4 HOH C 19 157 74 HOH HOH . 
U 4 HOH C 20 158 77 HOH HOH . 
U 4 HOH C 21 159 79 HOH HOH . 
U 4 HOH C 22 160 88 HOH HOH . 
U 4 HOH C 23 161 93 HOH HOH . 
U 4 HOH C 24 163 94 HOH HOH . 
U 4 HOH C 25 164 118 HOH HOH . 
U 4 HOH C 26 165 125 HOH HOH . 
U 4 HOH C 27 166 130 HOH HOH . 
V 4 HOH D 1 139 25 HOH HOH . 
V 4 HOH D 2 140 39 HOH HOH . 
V 4 HOH D 3 141 141 HOH HOH . 
V 4 HOH D 4 142 41 HOH HOH . 
V 4 HOH D 5 143 44 HOH HOH . 
V 4 HOH D 6 144 45 HOH HOH . 
V 4 HOH D 7 145 47 HOH HOH . 
V 4 HOH D 8 146 48 HOH HOH . 
V 4 HOH D 9 147 53 HOH HOH . 
V 4 HOH D 10 148 54 HOH HOH . 
V 4 HOH D 11 149 57 HOH HOH . 
V 4 HOH D 12 150 58 HOH HOH . 
V 4 HOH D 13 151 72 HOH HOH . 
V 4 HOH D 14 152 73 HOH HOH . 
V 4 HOH D 15 153 80 HOH HOH . 
V 4 HOH D 16 154 81 HOH HOH . 
V 4 HOH D 17 155 82 HOH HOH . 
V 4 HOH D 18 156 83 HOH HOH . 
V 4 HOH D 19 157 91 HOH HOH . 
V 4 HOH D 20 158 92 HOH HOH . 
V 4 HOH D 21 159 101 HOH HOH . 
V 4 HOH D 22 160 102 HOH HOH . 
V 4 HOH D 23 161 110 HOH HOH . 
V 4 HOH D 24 162 115 HOH HOH . 
V 4 HOH D 25 164 119 HOH HOH . 
V 4 HOH D 26 165 127 HOH HOH . 
V 4 HOH D 27 166 131 HOH HOH . 
V 4 HOH D 28 167 134 HOH HOH . 
V 4 HOH D 29 168 137 HOH HOH . 
W 4 HOH E 1 139 1 HOH HOH . 
W 4 HOH E 2 140 140 HOH HOH . 
W 4 HOH E 3 141 13 HOH HOH . 
W 4 HOH E 4 142 23 HOH HOH . 
W 4 HOH E 5 143 26 HOH HOH . 
W 4 HOH E 6 144 33 HOH HOH . 
W 4 HOH E 7 145 35 HOH HOH . 
W 4 HOH E 8 146 36 HOH HOH . 
W 4 HOH E 9 147 38 HOH HOH . 
W 4 HOH E 10 148 51 HOH HOH . 
W 4 HOH E 11 149 52 HOH HOH . 
W 4 HOH E 12 150 55 HOH HOH . 
W 4 HOH E 13 151 60 HOH HOH . 
W 4 HOH E 14 152 65 HOH HOH . 
W 4 HOH E 15 153 71 HOH HOH . 
W 4 HOH E 16 154 84 HOH HOH . 
W 4 HOH E 17 155 95 HOH HOH . 
W 4 HOH E 18 156 98 HOH HOH . 
W 4 HOH E 19 157 105 HOH HOH . 
W 4 HOH E 20 158 106 HOH HOH . 
W 4 HOH E 21 159 109 HOH HOH . 
W 4 HOH E 22 160 112 HOH HOH . 
W 4 HOH E 23 161 121 HOH HOH . 
W 4 HOH E 24 162 135 HOH HOH . 
W 4 HOH E 25 163 136 HOH HOH . 
X 4 HOH F 1 139 2 HOH HOH . 
X 4 HOH F 2 140 11 HOH HOH . 
X 4 HOH F 3 141 15 HOH HOH . 
X 4 HOH F 4 142 28 HOH HOH . 
X 4 HOH F 5 143 49 HOH HOH . 
X 4 HOH F 6 144 63 HOH HOH . 
X 4 HOH F 7 145 86 HOH HOH . 
X 4 HOH F 8 146 90 HOH HOH . 
X 4 HOH F 9 147 99 HOH HOH . 
X 4 HOH F 10 148 104 HOH HOH . 
X 4 HOH F 11 149 107 HOH HOH . 
X 4 HOH F 12 150 116 HOH HOH . 
X 4 HOH F 13 151 122 HOH HOH . 
X 4 HOH F 14 152 138 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 . . . J 3 71.041 66.203 68.194 1 76.26 ? PA TYD 138 B 1 
HETATM 2 O O1A TYD . . . J 3 69.961 67.178 67.77 1 75.08 ? O1A TYD 138 B 1 
HETATM 3 O O2A TYD . . . J 3 70.854 65.342 69.424 1 70.36 ? O2A TYD 138 B 1 
HETATM 4 O O3A TYD . . . J 3 71.457 65.221 66.971 1 72.49 ? O3A TYD 138 B 1 
HETATM 5 P PB TYD . . . J 3 70.952 65.374 65.439 1 65.89 ? PB TYD 138 B 1 
HETATM 6 O O1B TYD . . . J 3 72.164 65.86 64.675 1 65.4 ? O1B TYD 138 B 1 
HETATM 7 O O2B TYD . . . J 3 69.831 66.382 65.464 1 70.91 ? O2B TYD 138 B 1 
HETATM 8 O O3B TYD . . . J 3 70.535 63.959 65.11 1 58.6 ? O3B TYD 138 B 1 
HETATM 9 O O5' TYD . . . J 3 72.422 66.983 68.453 1 71.93 ? O5' TYD 138 B 1 
HETATM 10 C C5' TYD . . . J 3 72.994 67.813 67.447 1 68.38 ? C5' TYD 138 B 1 
HETATM 11 C C4' TYD . . . J 3 74.482 67.481 67.379 1 69.98 ? C4' TYD 138 B 1 
HETATM 12 O O4' TYD . . . J 3 75.072 67.731 68.659 1 69.84 ? O4' TYD 138 B 1 
HETATM 13 C C3' TYD . . . J 3 74.749 66.008 67.071 1 67.91 ? C3' TYD 138 B 1 
HETATM 14 O O3' TYD . . . J 3 74.961 65.782 65.67 1 61.48 ? O3' TYD 138 B 1 
HETATM 15 C C2' TYD . . . J 3 75.99 65.663 67.878 1 61.86 ? C2' TYD 138 B 1 
HETATM 16 C C1' TYD . . . J 3 76.058 66.738 68.961 1 63.56 ? C1' TYD 138 B 1 
HETATM 17 N N1 TYD . . . J 3 75.824 66.173 70.294 1 62.18 ? N1 TYD 138 B 1 
HETATM 18 C C2 TYD . . . J 3 76.901 66.112 71.21 1 61.49 ? C2 TYD 138 B 1 
HETATM 19 O O2 TYD . . . J 3 78.031 66.525 70.868 1 62.5 ? O2 TYD 138 B 1 
HETATM 20 N N3 TYD . . . J 3 76.736 65.615 72.44 1 65.21 ? N3 TYD 138 B 1 
HETATM 21 C C4 TYD . . . J 3 75.539 65.166 72.838 1 71.33 ? C4 TYD 138 B 1 
HETATM 22 O O4 TYD . . . J 3 75.412 64.705 73.994 1 72.98 ? O4 TYD 138 B 1 
HETATM 23 C C5 TYD . . . J 3 74.383 65.223 71.902 1 67.13 ? C5 TYD 138 B 1 
HETATM 24 C C5M TYD . . . J 3 73.021 64.727 72.315 1 62.44 ? C5M TYD 138 B 1 
HETATM 25 C C6 TYD . . . J 3 74.597 65.753 70.637 1 64.61 ? C6 TYD 138 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           362 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           25 
#