data_3VBP
#
_model_server_result.job_id            BoFzl0NRBJ18xVtGP9oVdA 
_model_server_result.datetime_utc      '2024-10-12 01:28:43' 
_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          3vbp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":301}' 
#
_entry.id    3VBP 
#
_exptl.entry_id    3VBP 
_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    3 
_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            3VBP 
_cell.length_a            71.339 
_cell.length_b            71.339 
_cell.length_c            138.184 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VBP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 3 E N N 
? 3 H N N 
? 3 J N N 
#
_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 420 n n 
PA O2A TYD sing 421 n n 
PA O3A TYD sing 422 n n 
PA O5' TYD sing 423 n n 
O2A HOA2 TYD sing 424 n n 
O3A PB TYD sing 425 n n 
PB O1B TYD doub 426 n n 
PB O2B TYD sing 427 n n 
PB O3B TYD sing 428 n n 
O2B HOB2 TYD sing 429 n n 
O3B HOB3 TYD sing 430 n n 
O5' C5' TYD sing 431 n n 
C5' C4' TYD sing 432 n n 
C5' "H5'1" TYD sing 433 n n 
C5' "H5'2" TYD sing 434 n n 
C4' O4' TYD sing 435 n n 
C4' C3' TYD sing 436 n n 
C4' H4' TYD sing 437 n n 
O4' C1' TYD sing 438 n n 
C3' O3' TYD sing 439 n n 
C3' C2' TYD sing 440 n n 
C3' H3' TYD sing 441 n n 
O3' HO3' TYD sing 442 n n 
C2' C1' TYD sing 443 n n 
C2' "H2'1" TYD sing 444 n n 
C2' "H2'2" TYD sing 445 n n 
C1' N1 TYD sing 446 n n 
C1' H1' TYD sing 447 n n 
N1 C2 TYD sing 448 n y 
N1 C6 TYD sing 449 n y 
C2 O2 TYD doub 450 n n 
C2 N3 TYD sing 451 n y 
N3 C4 TYD sing 452 n y 
N3 HN3 TYD sing 453 n n 
C4 O4 TYD doub 454 n n 
C4 C5 TYD sing 455 n y 
C5 C5M TYD sing 456 n n 
C5 C6 TYD doub 457 n y 
C5M H51 TYD sing 458 n n 
C5M H52 TYD sing 459 n n 
C5M H53 TYD sing 460 n n 
C6 H6 TYD sing 461 n n 
#
_atom_sites.entry_id                     3VBP 
_atom_sites.fract_transf_matrix[1][1]    0.014018 
_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]    0.014018 
_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]    0.007237 
_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
D 2 COA A 1 189 1 COA COA . 
E 3 TYD A 1 301 301 TYD TYD . 
F 2 COA C 1 189 1 COA COA . 
G 4 CL C 1 190 1 CL CL . 
H 3 TYD C 1 301 301 TYD TYD . 
I 2 COA E 1 189 1 COA COA . 
J 3 TYD E 1 301 301 TYD TYD . 
K 5 HOH A 1 190 2 HOH HOH . 
K 5 HOH A 2 191 4 HOH HOH . 
K 5 HOH A 3 192 5 HOH HOH . 
K 5 HOH A 4 193 6 HOH HOH . 
K 5 HOH A 5 194 7 HOH HOH . 
K 5 HOH A 6 195 8 HOH HOH . 
K 5 HOH A 7 196 9 HOH HOH . 
K 5 HOH A 8 197 11 HOH HOH . 
K 5 HOH A 9 198 12 HOH HOH . 
K 5 HOH A 10 199 13 HOH HOH . 
K 5 HOH A 11 200 14 HOH HOH . 
K 5 HOH A 12 201 15 HOH HOH . 
K 5 HOH A 13 202 17 HOH HOH . 
K 5 HOH A 14 203 18 HOH HOH . 
K 5 HOH A 15 204 35 HOH HOH . 
K 5 HOH A 16 205 43 HOH HOH . 
K 5 HOH A 17 206 44 HOH HOH . 
K 5 HOH A 18 207 45 HOH HOH . 
K 5 HOH A 19 208 46 HOH HOH . 
K 5 HOH A 20 209 53 HOH HOH . 
K 5 HOH A 21 210 54 HOH HOH . 
K 5 HOH A 22 211 55 HOH HOH . 
K 5 HOH A 23 212 57 HOH HOH . 
K 5 HOH A 24 213 60 HOH HOH . 
K 5 HOH A 25 214 62 HOH HOH . 
K 5 HOH A 26 215 63 HOH HOH . 
K 5 HOH A 27 216 64 HOH HOH . 
K 5 HOH A 28 217 65 HOH HOH . 
K 5 HOH A 29 218 66 HOH HOH . 
K 5 HOH A 30 219 67 HOH HOH . 
K 5 HOH A 31 220 68 HOH HOH . 
K 5 HOH A 32 221 69 HOH HOH . 
K 5 HOH A 33 222 70 HOH HOH . 
K 5 HOH A 34 223 73 HOH HOH . 
K 5 HOH A 35 224 74 HOH HOH . 
K 5 HOH A 36 225 75 HOH HOH . 
K 5 HOH A 37 226 76 HOH HOH . 
K 5 HOH A 38 227 77 HOH HOH . 
K 5 HOH A 39 228 78 HOH HOH . 
K 5 HOH A 40 229 79 HOH HOH . 
K 5 HOH A 41 230 80 HOH HOH . 
K 5 HOH A 42 232 82 HOH HOH . 
K 5 HOH A 43 233 83 HOH HOH . 
K 5 HOH A 44 234 108 HOH HOH . 
K 5 HOH A 45 235 109 HOH HOH . 
K 5 HOH A 46 236 110 HOH HOH . 
K 5 HOH A 47 237 111 HOH HOH . 
K 5 HOH A 48 238 113 HOH HOH . 
K 5 HOH A 49 239 114 HOH HOH . 
K 5 HOH A 50 240 116 HOH HOH . 
K 5 HOH A 51 241 117 HOH HOH . 
K 5 HOH A 52 242 128 HOH HOH . 
K 5 HOH A 53 243 136 HOH HOH . 
K 5 HOH A 54 244 137 HOH HOH . 
K 5 HOH A 55 245 138 HOH HOH . 
K 5 HOH A 56 246 139 HOH HOH . 
L 5 HOH C 1 191 3 HOH HOH . 
L 5 HOH C 2 192 10 HOH HOH . 
L 5 HOH C 3 193 19 HOH HOH . 
L 5 HOH C 4 194 20 HOH HOH . 
L 5 HOH C 5 195 22 HOH HOH . 
L 5 HOH C 6 196 23 HOH HOH . 
L 5 HOH C 7 197 24 HOH HOH . 
L 5 HOH C 8 198 25 HOH HOH . 
L 5 HOH C 9 199 26 HOH HOH . 
L 5 HOH C 10 200 40 HOH HOH . 
L 5 HOH C 11 201 41 HOH HOH . 
L 5 HOH C 12 202 42 HOH HOH . 
L 5 HOH C 13 203 47 HOH HOH . 
L 5 HOH C 14 204 48 HOH HOH . 
L 5 HOH C 15 205 50 HOH HOH . 
L 5 HOH C 16 206 51 HOH HOH . 
L 5 HOH C 17 207 84 HOH HOH . 
L 5 HOH C 18 208 85 HOH HOH . 
L 5 HOH C 19 209 86 HOH HOH . 
L 5 HOH C 20 210 87 HOH HOH . 
L 5 HOH C 21 211 88 HOH HOH . 
L 5 HOH C 22 212 89 HOH HOH . 
L 5 HOH C 23 213 90 HOH HOH . 
L 5 HOH C 24 214 91 HOH HOH . 
L 5 HOH C 25 215 92 HOH HOH . 
L 5 HOH C 26 216 118 HOH HOH . 
L 5 HOH C 27 217 120 HOH HOH . 
L 5 HOH C 28 218 121 HOH HOH . 
L 5 HOH C 29 219 122 HOH HOH . 
L 5 HOH C 30 220 125 HOH HOH . 
L 5 HOH C 31 221 130 HOH HOH . 
L 5 HOH C 32 222 133 HOH HOH . 
L 5 HOH C 33 223 134 HOH HOH . 
L 5 HOH C 34 224 141 HOH HOH . 
L 5 HOH C 35 225 142 HOH HOH . 
M 5 HOH E 1 190 21 HOH HOH . 
M 5 HOH E 2 191 27 HOH HOH . 
M 5 HOH E 3 192 28 HOH HOH . 
M 5 HOH E 4 193 29 HOH HOH . 
M 5 HOH E 5 194 31 HOH HOH . 
M 5 HOH E 6 195 32 HOH HOH . 
M 5 HOH E 7 196 33 HOH HOH . 
M 5 HOH E 8 197 34 HOH HOH . 
M 5 HOH E 9 198 36 HOH HOH . 
M 5 HOH E 10 199 37 HOH HOH . 
M 5 HOH E 11 200 38 HOH HOH . 
M 5 HOH E 12 201 39 HOH HOH . 
M 5 HOH E 13 202 49 HOH HOH . 
M 5 HOH E 14 203 52 HOH HOH . 
M 5 HOH E 15 204 56 HOH HOH . 
M 5 HOH E 16 205 58 HOH HOH . 
M 5 HOH E 17 206 59 HOH HOH . 
M 5 HOH E 18 207 61 HOH HOH . 
M 5 HOH E 19 208 93 HOH HOH . 
M 5 HOH E 20 209 94 HOH HOH . 
M 5 HOH E 21 210 95 HOH HOH . 
M 5 HOH E 22 211 96 HOH HOH . 
M 5 HOH E 23 212 98 HOH HOH . 
M 5 HOH E 24 213 99 HOH HOH . 
M 5 HOH E 25 214 100 HOH HOH . 
M 5 HOH E 26 215 101 HOH HOH . 
M 5 HOH E 27 216 102 HOH HOH . 
M 5 HOH E 28 217 103 HOH HOH . 
M 5 HOH E 29 218 105 HOH HOH . 
M 5 HOH E 30 219 106 HOH HOH . 
M 5 HOH E 31 220 107 HOH HOH . 
M 5 HOH E 32 221 123 HOH HOH . 
M 5 HOH E 33 222 126 HOH HOH . 
M 5 HOH E 34 223 127 HOH HOH . 
M 5 HOH E 35 224 132 HOH HOH . 
M 5 HOH E 36 225 140 HOH HOH . 
M 5 HOH E 37 231 81 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 16.585 39.954 -17.646 1 73.63 ? PA TYD 301 E 1 
HETATM 2 O O1A TYD . . . J 3 15.904 39.71 -18.968 1 74.75 ? O1A TYD 301 E 1 
HETATM 3 O O2A TYD . . . J 3 15.954 39.296 -16.437 1 71.98 ? O2A TYD 301 E 1 
HETATM 4 O O3A TYD . . . J 3 18.149 39.597 -17.833 1 77.44 ? O3A TYD 301 E 1 
HETATM 5 P PB TYD . . . J 3 19.185 39.124 -16.688 1 80.21 ? PB TYD 301 E 1 
HETATM 6 O O1B TYD . . . J 3 20.533 39.167 -17.372 1 82.07 ? O1B TYD 301 E 1 
HETATM 7 O O2B TYD . . . J 3 18.662 37.754 -16.315 1 81.53 ? O2B TYD 301 E 1 
HETATM 8 O O3B TYD . . . J 3 19.137 40.154 -15.584 1 82.77 ? O3B TYD 301 E 1 
HETATM 9 O O5' TYD . . . J 3 16.738 41.55 -17.488 1 73.16 ? O5' TYD 301 E 1 
HETATM 10 C C5' TYD . . . J 3 17.362 42.368 -18.483 1 69.69 ? C5' TYD 301 E 1 
HETATM 11 C C4' TYD . . . J 3 17.159 43.845 -18.159 1 67.63 ? C4' TYD 301 E 1 
HETATM 12 O O4' TYD . . . J 3 15.797 44.218 -18.38 1 66.16 ? O4' TYD 301 E 1 
HETATM 13 C C3' TYD . . . J 3 17.429 44.135 -16.687 1 65.61 ? C3' TYD 301 E 1 
HETATM 14 O O3' TYD . . . J 3 18.776 44.555 -16.48 1 65.32 ? O3' TYD 301 E 1 
HETATM 15 C C2' TYD . . . J 3 16.434 45.23 -16.338 1 65.11 ? C2' TYD 301 E 1 
HETATM 16 C C1' TYD . . . J 3 15.281 45.032 -17.321 1 64.27 ? C1' TYD 301 E 1 
HETATM 17 N N1 TYD . . . J 3 14.158 44.413 -16.6 1 62.91 ? N1 TYD 301 E 1 
HETATM 18 C C2 TYD . . . J 3 13.253 45.144 -15.915 1 62.3 ? C2 TYD 301 E 1 
HETATM 19 O O2 TYD . . . J 3 13.296 46.394 -15.838 1 61.11 ? O2 TYD 301 E 1 
HETATM 20 N N3 TYD . . . J 3 12.242 44.539 -15.245 1 60.56 ? N3 TYD 301 E 1 
HETATM 21 C C4 TYD . . . J 3 12.075 43.196 -15.216 1 58.24 ? C4 TYD 301 E 1 
HETATM 22 O O4 TYD . . . J 3 11.1 42.731 -14.577 1 54.99 ? O4 TYD 301 E 1 
HETATM 23 C C5 TYD . . . J 3 12.994 42.429 -15.931 1 58.86 ? C5 TYD 301 E 1 
HETATM 24 C C5M TYD . . . J 3 12.948 40.923 -16.014 1 56.77 ? C5M TYD 301 E 1 
HETATM 25 C C6 TYD . . . J 3 14.03 43.076 -16.603 1 59.27 ? C6 TYD 301 E 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           25 
#