data_3G2X
#
_model_server_result.job_id            1XB6nWBphXtI0BQWfu10rQ 
_model_server_result.datetime_utc      '2024-11-13 06:19:36' 
_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          3g2x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":201}' 
#
_entry.id    3G2X 
#
_exptl.entry_id    3G2X 
_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            3G2X 
_cell.length_a            84.371 
_cell.length_b            151.492 
_cell.length_c            181.723 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3G2X 
_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,B,C,G,H,I,J,K,L,S,T,U 1 1,2 
D,E,F,M,N,O,P,Q,R,V,W,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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 84.371 0 90.8615 
3 'crystal symmetry operation' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 151.492 0 
#
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 
#
_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                     3G2X 
_atom_sites.fract_transf_matrix[1][1]    0.011852 
_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]    0.006601 
_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]    0.005503 
_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 1 202 202 MG MG . 
H 3 TYD A 1 201 201 TYD TYD . 
I 2 MG B 1 202 202 MG MG . 
J 3 TYD B 1 201 201 TYD TYD . 
K 2 MG C 1 202 202 MG MG . 
L 3 TYD C 1 201 201 TYD TYD . 
M 2 MG D 1 202 202 MG MG . 
N 3 TYD D 1 201 201 TYD TYD . 
O 2 MG E 1 202 202 MG MG . 
P 3 TYD E 1 201 201 TYD TYD . 
Q 2 MG F 1 202 202 MG MG . 
R 3 TYD F 1 201 201 TYD TYD . 
S 4 HOH A 1 142 5 HOH HOH . 
S 4 HOH A 2 143 6 HOH HOH . 
S 4 HOH A 3 144 14 HOH HOH . 
S 4 HOH A 4 145 19 HOH HOH . 
S 4 HOH A 5 146 32 HOH HOH . 
S 4 HOH A 6 147 45 HOH HOH . 
S 4 HOH A 7 148 57 HOH HOH . 
S 4 HOH A 8 149 59 HOH HOH . 
S 4 HOH A 9 150 60 HOH HOH . 
S 4 HOH A 10 151 64 HOH HOH . 
T 4 HOH B 1 142 12 HOH HOH . 
T 4 HOH B 2 143 25 HOH HOH . 
T 4 HOH B 3 144 36 HOH HOH . 
T 4 HOH B 4 145 39 HOH HOH . 
T 4 HOH B 5 146 43 HOH HOH . 
T 4 HOH B 6 147 62 HOH HOH . 
T 4 HOH B 7 148 70 HOH HOH . 
U 4 HOH C 1 142 8 HOH HOH . 
U 4 HOH C 2 143 22 HOH HOH . 
U 4 HOH C 3 144 23 HOH HOH . 
U 4 HOH C 4 145 29 HOH HOH . 
U 4 HOH C 5 146 35 HOH HOH . 
U 4 HOH C 6 147 41 HOH HOH . 
U 4 HOH C 7 148 47 HOH HOH . 
U 4 HOH C 8 149 49 HOH HOH . 
U 4 HOH C 9 150 58 HOH HOH . 
U 4 HOH C 10 151 63 HOH HOH . 
V 4 HOH D 1 142 13 HOH HOH . 
V 4 HOH D 2 143 17 HOH HOH . 
V 4 HOH D 3 144 18 HOH HOH . 
V 4 HOH D 4 145 26 HOH HOH . 
V 4 HOH D 5 146 30 HOH HOH . 
V 4 HOH D 6 147 33 HOH HOH . 
V 4 HOH D 7 148 40 HOH HOH . 
V 4 HOH D 8 149 44 HOH HOH . 
V 4 HOH D 9 150 51 HOH HOH . 
V 4 HOH D 10 151 52 HOH HOH . 
V 4 HOH D 11 152 54 HOH HOH . 
V 4 HOH D 12 153 55 HOH HOH . 
V 4 HOH D 13 154 56 HOH HOH . 
V 4 HOH D 14 155 65 HOH HOH . 
V 4 HOH D 15 156 67 HOH HOH . 
V 4 HOH D 16 157 68 HOH HOH . 
W 4 HOH E 1 142 3 HOH HOH . 
W 4 HOH E 2 143 16 HOH HOH . 
W 4 HOH E 3 144 31 HOH HOH . 
W 4 HOH E 4 145 37 HOH HOH . 
W 4 HOH E 5 146 38 HOH HOH . 
W 4 HOH E 6 147 42 HOH HOH . 
W 4 HOH E 7 148 46 HOH HOH . 
W 4 HOH E 8 149 48 HOH HOH . 
W 4 HOH E 9 150 61 HOH HOH . 
W 4 HOH E 10 151 66 HOH HOH . 
X 4 HOH F 1 142 24 HOH HOH . 
X 4 HOH F 2 143 34 HOH HOH . 
X 4 HOH F 3 144 50 HOH HOH . 
X 4 HOH F 4 145 69 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 33.803 67.609 67.065 1 54.38 ? PA TYD 201 B 1 
HETATM 2 O O1A TYD . . . J 3 33.087 66.955 68.221 1 54.44 ? O1A TYD 201 B 1 
HETATM 3 O O2A TYD . . . J 3 33.149 68.706 66.259 1 52.65 ? O2A TYD 201 B 1 
HETATM 4 O O3A TYD . . . J 3 34.289 66.394 66.118 1 55.96 ? O3A TYD 201 B 1 
HETATM 5 P PB TYD . . . J 3 33.968 66.313 64.543 1 54.41 ? PB TYD 201 B 1 
HETATM 6 O O1B TYD . . . J 3 35.33 66.543 63.943 1 44.62 ? O1B TYD 201 B 1 
HETATM 7 O O2B TYD . . . J 3 33.032 67.464 64.244 1 59.76 ? O2B TYD 201 B 1 
HETATM 8 O O3B TYD . . . J 3 33.335 64.943 64.41 1 47.4 ? O3B TYD 201 B 1 
HETATM 9 O O5' TYD . . . J 3 35.236 68.103 67.555 1 46.67 ? O5' TYD 201 B 1 
HETATM 10 C C5' TYD . . . J 3 35.944 69.051 66.779 1 49.15 ? C5' TYD 201 B 1 
HETATM 11 C C4' TYD . . . J 3 37.395 68.584 66.707 1 51.65 ? C4' TYD 201 B 1 
HETATM 12 O O4' TYD . . . J 3 38.021 68.727 67.984 1 50.46 ? O4' TYD 201 B 1 
HETATM 13 C C3' TYD . . . J 3 37.503 67.103 66.377 1 49.69 ? C3' TYD 201 B 1 
HETATM 14 O O3' TYD . . . J 3 37.593 66.9 64.978 1 51.08 ? O3' TYD 201 B 1 
HETATM 15 C C2' TYD . . . J 3 38.794 66.677 67.036 1 49.57 ? C2' TYD 201 B 1 
HETATM 16 C C1' TYD . . . J 3 38.905 67.628 68.223 1 50.43 ? C1' TYD 201 B 1 
HETATM 17 N N1 TYD . . . J 3 38.573 66.95 69.483 1 46.57 ? N1 TYD 201 B 1 
HETATM 18 C C2 TYD . . . J 3 39.616 66.648 70.385 1 49.11 ? C2 TYD 201 B 1 
HETATM 19 O O2 TYD . . . J 3 40.808 66.944 70.105 1 48.58 ? O2 TYD 201 B 1 
HETATM 20 N N3 TYD . . . J 3 39.356 66.042 71.551 1 51.75 ? N3 TYD 201 B 1 
HETATM 21 C C4 TYD . . . J 3 38.113 65.705 71.899 1 51 ? C4 TYD 201 B 1 
HETATM 22 O O4 TYD . . . J 3 37.923 65.136 72.991 1 51.03 ? O4 TYD 201 B 1 
HETATM 23 C C5 TYD . . . J 3 36.992 66.014 70.972 1 51.85 ? C5 TYD 201 B 1 
HETATM 24 C C5M TYD . . . J 3 35.568 65.651 71.315 1 46.3 ? C5M TYD 201 B 1 
HETATM 25 C C6 TYD . . . J 3 37.301 66.652 69.775 1 49.72 ? C6 TYD 201 B 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           259 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#