data_3EVW
#
_model_server_result.job_id            2oryNlCwseCRzJd2CebJOA 
_model_server_result.datetime_utc      '2024-11-24 08:54:59' 
_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          3evw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":138}' 
#
_entry.id    3EVW 
#
_exptl.entry_id    3EVW 
_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            3EVW 
_cell.length_a            80.69 
_cell.length_b            151.038 
_cell.length_c            184.874 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EVW 
_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 -1 161.38 0 92.437 
#
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 
#
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 H O2B TYD . A TYD 138 1_555 G MG MG . A MG 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc2 J O2B TYD . B TYD 138 1_555 I MG MG . B MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc3 L O1A TYD . C TYD 138 1_555 K MG MG . C MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? 
metalc ? metalc4 L O2B TYD . C TYD 138 1_555 K MG MG . C MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc5 N O2B TYD . D TYD 138 1_555 M MG MG . D MG 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc6 P O2B TYD . E TYD 138 1_555 O MG MG . E MG 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc7 P O1A TYD . E TYD 138 1_555 O MG MG . E MG 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc8 R O2B TYD . F TYD 138 1_555 Q MG MG . F MG 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? 
#
_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                     3EVW 
_atom_sites.fract_transf_matrix[1][1]    0.012393 
_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]    0.006621 
_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]    0.005409 
_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 10 HOH HOH . 
S 4 HOH A 2 140 11 HOH HOH . 
S 4 HOH A 3 141 16 HOH HOH . 
S 4 HOH A 4 142 24 HOH HOH . 
S 4 HOH A 5 143 26 HOH HOH . 
T 4 HOH B 1 139 13 HOH HOH . 
T 4 HOH B 2 140 17 HOH HOH . 
T 4 HOH B 3 141 32 HOH HOH . 
T 4 HOH B 4 142 33 HOH HOH . 
U 4 HOH C 1 139 2 HOH HOH . 
U 4 HOH C 2 140 3 HOH HOH . 
U 4 HOH C 3 141 4 HOH HOH . 
U 4 HOH C 4 142 5 HOH HOH . 
U 4 HOH C 5 143 7 HOH HOH . 
U 4 HOH C 6 144 8 HOH HOH . 
U 4 HOH C 7 145 9 HOH HOH . 
U 4 HOH C 8 146 14 HOH HOH . 
U 4 HOH C 9 147 20 HOH HOH . 
U 4 HOH C 10 148 23 HOH HOH . 
V 4 HOH D 1 139 15 HOH HOH . 
V 4 HOH D 2 140 18 HOH HOH . 
V 4 HOH D 3 141 25 HOH HOH . 
V 4 HOH D 4 142 28 HOH HOH . 
V 4 HOH D 5 143 29 HOH HOH . 
V 4 HOH D 6 144 30 HOH HOH . 
V 4 HOH D 7 145 31 HOH HOH . 
W 4 HOH E 1 139 12 HOH HOH . 
W 4 HOH E 2 140 19 HOH HOH . 
W 4 HOH E 3 141 21 HOH HOH . 
W 4 HOH E 4 142 22 HOH HOH . 
W 4 HOH E 5 143 27 HOH HOH . 
X 4 HOH F 1 139 1 HOH HOH . 
X 4 HOH F 2 140 6 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 -11.315 16.119 17.781 1 60.44 ? PA TYD 138 A 1 
HETATM 2 O O1A TYD . . . H 3 -10.752 16.026 19.19 1 61.14 ? O1A TYD 138 A 1 
HETATM 3 O O2A TYD . . . H 3 -11.519 17.462 17.12 1 52.62 ? O2A TYD 138 A 1 
HETATM 4 O O3A TYD . . . H 3 -10.433 15.203 16.775 1 60.74 ? O3A TYD 138 A 1 
HETATM 5 P PB TYD . . . H 3 -9.122 14.389 17.27 1 56.15 ? PB TYD 138 A 1 
HETATM 6 O O1B TYD . . . H 3 -9.491 12.935 17.087 1 54.38 ? O1B TYD 138 A 1 
HETATM 7 O O2B TYD . . . H 3 -8.942 14.754 18.728 1 61.7 ? O2B TYD 138 A 1 
HETATM 8 O O3B TYD . . . H 3 -8.103 14.962 16.305 1 55.78 ? O3B TYD 138 A 1 
HETATM 9 O O5' TYD . . . H 3 -12.693 15.309 17.657 1 57.72 ? O5' TYD 138 A 1 
HETATM 10 C C5' TYD . . . H 3 -12.784 14.017 18.252 1 58.67 ? C5' TYD 138 A 1 
HETATM 11 C C4' TYD . . . H 3 -13.446 13.116 17.21 1 61.63 ? C4' TYD 138 A 1 
HETATM 12 O O4' TYD . . . H 3 -14.745 13.627 16.914 1 62.73 ? O4' TYD 138 A 1 
HETATM 13 C C3' TYD . . . H 3 -12.73 13.108 15.862 1 62.56 ? C3' TYD 138 A 1 
HETATM 14 O O3' TYD . . . H 3 -11.765 12.051 15.804 1 64.79 ? O3' TYD 138 A 1 
HETATM 15 C C2' TYD . . . H 3 -13.836 12.921 14.828 1 58.94 ? C2' TYD 138 A 1 
HETATM 16 C C1' TYD . . . H 3 -15.075 13.441 15.542 1 55.14 ? C1' TYD 138 A 1 
HETATM 17 N N1 TYD . . . H 3 -15.43 14.74 15.001 1 55.21 ? N1 TYD 138 A 1 
HETATM 18 C C2 TYD . . . H 3 -16.491 14.824 14.073 1 56.5 ? C2 TYD 138 A 1 
HETATM 19 O O2 TYD . . . H 3 -17.096 13.784 13.743 1 59.45 ? O2 TYD 138 A 1 
HETATM 20 N N3 TYD . . . H 3 -16.87 15.987 13.54 1 53.72 ? N3 TYD 138 A 1 
HETATM 21 C C4 TYD . . . H 3 -16.244 17.113 13.882 1 58.33 ? C4 TYD 138 A 1 
HETATM 22 O O4 TYD . . . H 3 -16.593 18.214 13.388 1 66.53 ? O4 TYD 138 A 1 
HETATM 23 C C5 TYD . . . H 3 -15.127 17.057 14.857 1 55.9 ? C5 TYD 138 A 1 
HETATM 24 C C5M TYD . . . H 3 -14.435 18.346 15.221 1 50.68 ? C5M TYD 138 A 1 
HETATM 25 C C6 TYD . . . H 3 -14.765 15.828 15.408 1 49.46 ? C6 TYD 138 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           223 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#