data_3VBN
#
_model_server_result.job_id            JWoG3PX1N3MATQUKFsd67g 
_model_server_result.datetime_utc      '2024-10-12 01:27:51' 
_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          3vbn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":301}' 
#
_entry.id    3VBN 
#
_exptl.entry_id    3VBN 
_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            3VBN 
_cell.length_a            71.076 
_cell.length_b            71.076 
_cell.length_c            137.749 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VBN 
_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                     3VBN 
_atom_sites.fract_transf_matrix[1][1]    0.014069 
_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]    0.014069 
_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]    0.00726 
_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 4 CL A 1 190 1 CL CL . 
G 2 COA C 1 189 1 COA COA . 
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 1 191 1 HOH HOH . 
K 5 HOH A 2 192 2 HOH HOH . 
K 5 HOH A 3 193 3 HOH HOH . 
K 5 HOH A 4 194 5 HOH HOH . 
K 5 HOH A 5 195 7 HOH HOH . 
K 5 HOH A 6 196 8 HOH HOH . 
K 5 HOH A 7 197 9 HOH HOH . 
K 5 HOH A 8 198 28 HOH HOH . 
K 5 HOH A 9 199 29 HOH HOH . 
K 5 HOH A 10 200 30 HOH HOH . 
K 5 HOH A 11 201 31 HOH HOH . 
K 5 HOH A 12 202 33 HOH HOH . 
K 5 HOH A 13 203 34 HOH HOH . 
K 5 HOH A 14 204 35 HOH HOH . 
K 5 HOH A 15 205 36 HOH HOH . 
K 5 HOH A 16 206 43 HOH HOH . 
K 5 HOH A 17 207 53 HOH HOH . 
K 5 HOH A 18 208 59 HOH HOH . 
K 5 HOH A 19 209 62 HOH HOH . 
K 5 HOH A 20 210 63 HOH HOH . 
K 5 HOH A 21 211 67 HOH HOH . 
L 5 HOH C 1 190 4 HOH HOH . 
L 5 HOH C 2 191 11 HOH HOH . 
L 5 HOH C 3 192 12 HOH HOH . 
L 5 HOH C 4 193 14 HOH HOH . 
L 5 HOH C 5 194 15 HOH HOH . 
L 5 HOH C 6 195 16 HOH HOH . 
L 5 HOH C 7 196 17 HOH HOH . 
L 5 HOH C 8 197 18 HOH HOH . 
L 5 HOH C 9 198 19 HOH HOH . 
L 5 HOH C 10 199 20 HOH HOH . 
L 5 HOH C 11 200 21 HOH HOH . 
L 5 HOH C 12 201 46 HOH HOH . 
L 5 HOH C 13 202 47 HOH HOH . 
L 5 HOH C 14 203 48 HOH HOH . 
L 5 HOH C 15 204 49 HOH HOH . 
L 5 HOH C 16 205 50 HOH HOH . 
L 5 HOH C 17 206 64 HOH HOH . 
L 5 HOH C 18 207 65 HOH HOH . 
M 5 HOH E 1 190 13 HOH HOH . 
M 5 HOH E 2 191 22 HOH HOH . 
M 5 HOH E 3 192 23 HOH HOH . 
M 5 HOH E 4 193 24 HOH HOH . 
M 5 HOH E 5 194 25 HOH HOH . 
M 5 HOH E 6 195 26 HOH HOH . 
M 5 HOH E 7 196 37 HOH HOH . 
M 5 HOH E 8 197 38 HOH HOH . 
M 5 HOH E 9 198 39 HOH HOH . 
M 5 HOH E 10 199 40 HOH HOH . 
M 5 HOH E 11 200 41 HOH HOH . 
M 5 HOH E 12 201 42 HOH HOH . 
M 5 HOH E 13 202 44 HOH HOH . 
M 5 HOH E 14 203 51 HOH HOH . 
M 5 HOH E 15 204 52 HOH HOH . 
M 5 HOH E 16 205 55 HOH HOH . 
M 5 HOH E 17 206 56 HOH HOH . 
M 5 HOH E 18 207 57 HOH HOH . 
M 5 HOH E 19 208 58 HOH HOH . 
M 5 HOH E 20 209 60 HOH HOH . 
M 5 HOH E 21 210 66 HOH HOH . 
M 5 HOH E 22 211 68 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 . . . H 3 -3.188 41.977 2.324 1 68 ? PA TYD 301 C 1 
HETATM 2 O O1A TYD . . . H 3 -1.77 41.479 2.448 1 67.76 ? O1A TYD 301 C 1 
HETATM 3 O O2A TYD . . . H 3 -4.041 41.349 1.252 1 66.49 ? O2A TYD 301 C 1 
HETATM 4 O O3A TYD . . . H 3 -3.875 41.89 3.788 1 73.58 ? O3A TYD 301 C 1 
HETATM 5 P PB TYD . . . H 3 -5.175 41.071 4.323 1 76.76 ? PB TYD 301 C 1 
HETATM 6 O O1B TYD . . . H 3 -5.617 41.887 5.524 1 76.77 ? O1B TYD 301 C 1 
HETATM 7 O O2B TYD . . . H 3 -4.67 39.678 4.656 1 76.28 ? O2B TYD 301 C 1 
HETATM 8 O O3B TYD . . . H 3 -6.201 41.074 3.207 1 77.12 ? O3B TYD 301 C 1 
HETATM 9 O O5' TYD . . . H 3 -3.256 43.573 2.1 1 67.52 ? O5' TYD 301 C 1 
HETATM 10 C C5' TYD . . . H 3 -2.774 44.613 2.955 1 66.92 ? C5' TYD 301 C 1 
HETATM 11 C C4' TYD . . . H 3 -3.294 45.941 2.398 1 67.14 ? C4' TYD 301 C 1 
HETATM 12 O O4' TYD . . . H 3 -2.763 46.226 1.102 1 66.01 ? O4' TYD 301 C 1 
HETATM 13 C C3' TYD . . . H 3 -4.808 45.917 2.233 1 67.72 ? C3' TYD 301 C 1 
HETATM 14 O O3' TYD . . . H 3 -5.397 46.78 3.214 1 69.05 ? O3' TYD 301 C 1 
HETATM 15 C C2' TYD . . . H 3 -5.096 46.352 0.8 1 66.81 ? C2' TYD 301 C 1 
HETATM 16 C C1' TYD . . . H 3 -3.752 46.394 0.073 1 65.74 ? C1' TYD 301 C 1 
HETATM 17 N N1 TYD . . . H 3 -3.649 45.449 -1.073 1 63.63 ? N1 TYD 301 C 1 
HETATM 18 C C2 TYD . . . H 3 -4.09 45.745 -2.316 1 62.05 ? C2 TYD 301 C 1 
HETATM 19 O O2 TYD . . . H 3 -4.623 46.846 -2.571 1 62.64 ? O2 TYD 301 C 1 
HETATM 20 N N3 TYD . . . H 3 -3.993 44.87 -3.355 1 62.08 ? N3 TYD 301 C 1 
HETATM 21 C C4 TYD . . . H 3 -3.446 43.633 -3.208 1 61.82 ? C4 TYD 301 C 1 
HETATM 22 O O4 TYD . . . H 3 -3.354 42.823 -4.156 1 58.77 ? O4 TYD 301 C 1 
HETATM 23 C C5 TYD . . . H 3 -2.973 43.285 -1.95 1 62.69 ? C5 TYD 301 C 1 
HETATM 24 C C5M TYD . . . H 3 -2.355 41.927 -1.726 1 61.06 ? C5M TYD 301 C 1 
HETATM 25 C C6 TYD . . . H 3 -3.093 44.228 -0.914 1 63.64 ? C6 TYD 301 C 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#