data_1G3L
#
_model_server_result.job_id            4MHay9fR08lYuNfnIzgkHw 
_model_server_result.datetime_utc      '2024-10-12 10:22:14' 
_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          1g3l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":503}' 
#
_entry.id    1G3L 
#
_exptl.entry_id    1G3L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              548.33 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" 
_entity.pdbx_number_of_molecules    8 
_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            1G3L 
_cell.length_a            71.087 
_cell.length_b            138.557 
_cell.length_c            139.676 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1G3L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,N,O,P,Q 
_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 F N N 
? 3 G N N 
? 3 J N N 
? 3 K N N 
? 3 M N N 
? 3 N N N 
? 3 P N N 
? 3 Q N N 
#
_chem_comp.formula           'C16 H26 N2 O15 P2' 
_chem_comp.formula_weight    548.33 
_chem_comp.id                TRH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" 
_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
O4P P2 TRH sing 308 n n 
O4P H4PO TRH sing 309 n n 
P2 O3P TRH doub 310 n n 
P2 O1 TRH sing 311 n n 
P2 OPP TRH sing 312 n n 
O1 C1 TRH sing 313 n n 
C1 C2 TRH sing 314 n n 
C1 O5 TRH sing 315 n n 
C1 HC1 TRH sing 316 n n 
C2 O2 TRH sing 317 n n 
C2 C3 TRH sing 318 n n 
C2 HC2 TRH sing 319 n n 
O2 HO2 TRH sing 320 n n 
C3 O3 TRH sing 321 n n 
C3 C4 TRH sing 322 n n 
C3 HC3 TRH sing 323 n n 
O3 HO3 TRH sing 324 n n 
C4 O4 TRH sing 325 n n 
C4 C5 TRH sing 326 n n 
C4 HC4 TRH sing 327 n n 
O4 HO4 TRH sing 328 n n 
C5 O5 TRH sing 329 n n 
C5 C6 TRH sing 330 n n 
C5 HC5 TRH sing 331 n n 
C6 HC61 TRH sing 332 n n 
C6 HC62 TRH sing 333 n n 
C6 HC63 TRH sing 334 n n 
OPP P TRH sing 335 n n 
P O1P TRH sing 336 n n 
P O2P TRH doub 337 n n 
P O5' TRH sing 338 n n 
O1P H1PO TRH sing 339 n n 
O5' C5' TRH sing 340 n n 
C5' C4' TRH sing 341 n n 
C5' "H5'1" TRH sing 342 n n 
C5' "H5'2" TRH sing 343 n n 
C4' O4' TRH sing 344 n n 
C4' C3' TRH sing 345 n n 
C4' "H4'C" TRH sing 346 n n 
O4' C1' TRH sing 347 n n 
C3' O3' TRH sing 348 n n 
C3' C2' TRH sing 349 n n 
C3' "H3'C" TRH sing 350 n n 
O3' "H3'O" TRH sing 351 n n 
C2' C1' TRH sing 352 n n 
C2' "H2'1" TRH sing 353 n n 
C2' "H2'2" TRH sing 354 n n 
C1' N11 TRH sing 355 n n 
C1' "H1'C" TRH sing 356 n n 
N11 C21 TRH sing 357 n n 
N11 C61 TRH sing 358 n n 
C21 O21 TRH doub 359 n n 
C21 N31 TRH sing 360 n n 
N31 C41 TRH sing 361 n n 
N31 H31N TRH sing 362 n n 
C41 O41 TRH doub 363 n n 
C41 C51 TRH sing 364 n n 
C51 C5A TRH sing 365 n n 
C51 C61 TRH doub 366 n n 
C5A HCA1 TRH sing 367 n n 
C5A HCA2 TRH sing 368 n n 
C5A HCA3 TRH sing 369 n n 
C61 H61C TRH sing 370 n n 
#
_atom_sites.entry_id                     1G3L 
_atom_sites.fract_transf_matrix[1][1]    0.014067 
_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]    0.007217 
_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]    0.007159 
_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
E 2 SO4 A 1 701 701 SO4 SO4 . 
F 3 TRH A 1 500 500 TRH TDR . 
G 3 TRH A 1 501 600 TRH TDR . 
H 2 SO4 B 1 700 700 SO4 SO4 . 
I 2 SO4 B 1 702 702 SO4 SO4 . 
J 3 TRH B 1 502 500 TRH TDR . 
K 3 TRH B 1 503 600 TRH TDR . 
L 2 SO4 C 1 703 703 SO4 SO4 . 
M 3 TRH C 1 504 500 TRH TDR . 
N 3 TRH C 1 505 600 TRH TDR . 
O 2 SO4 D 1 704 704 SO4 SO4 . 
P 3 TRH D 1 506 500 TRH TDR . 
Q 3 TRH D 1 507 600 TRH TDR . 
#
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 O O4P TRH . . . K 3 4.553 67.519 57.066 1 14.12 ? O4P TRH 503 B 1 
HETATM 2 P P2 TRH . . . K 3 4.699 68.609 58.236 1 10.78 ? P2 TRH 503 B 1 
HETATM 3 O O3P TRH . . . K 3 3.465 69.527 58.547 1 12.72 ? O3P TRH 503 B 1 
HETATM 4 O O1 TRH . . . K 3 5.105 67.903 59.554 1 14.63 ? O1 TRH 503 B 1 
HETATM 5 C C1 TRH . . . K 3 4.618 68.361 60.776 1 13.43 ? C1 TRH 503 B 1 
HETATM 6 C C2 TRH . . . K 3 5.762 68.438 61.759 1 15.27 ? C2 TRH 503 B 1 
HETATM 7 O O2 TRH . . . K 3 6.352 67.135 61.827 1 12.56 ? O2 TRH 503 B 1 
HETATM 8 C C3 TRH . . . K 3 5.247 68.712 63.146 1 15.91 ? C3 TRH 503 B 1 
HETATM 9 O O3 TRH . . . K 3 6.264 68.627 64.144 1 15.32 ? O3 TRH 503 B 1 
HETATM 10 C C4 TRH . . . K 3 4.235 67.598 63.34 1 16.65 ? C4 TRH 503 B 1 
HETATM 11 O O4 TRH . . . K 3 3.451 67.812 64.527 1 14.32 ? O4 TRH 503 B 1 
HETATM 12 C C5 TRH . . . K 3 3.3 67.527 62.119 1 17.42 ? C5 TRH 503 B 1 
HETATM 13 O O5 TRH . . . K 3 3.966 67.144 60.888 1 15.87 ? O5 TRH 503 B 1 
HETATM 14 C C6 TRH . . . K 3 2.209 66.581 62.541 1 19.14 ? C6 TRH 503 B 1 
HETATM 15 O OPP TRH . . . K 3 6.004 69.507 57.957 1 10.01 ? OPP TRH 503 B 1 
HETATM 16 P P TRH . . . K 3 5.941 71.103 57.754 1 8.17 ? P TRH 503 B 1 
HETATM 17 O O1P TRH . . . K 3 7.425 71.531 57.446 1 11.02 ? O1P TRH 503 B 1 
HETATM 18 O O2P TRH . . . K 3 5.061 71.8 58.894 1 14.34 ? O2P TRH 503 B 1 
HETATM 19 O O5' TRH . . . K 3 5.004 71.4 56.548 1 9.54 ? O5' TRH 503 B 1 
HETATM 20 C C5' TRH . . . K 3 4.975 70.46 55.489 1 12.04 ? C5' TRH 503 B 1 
HETATM 21 C C4' TRH . . . K 3 5.252 71.224 54.211 1 12.28 ? C4' TRH 503 B 1 
HETATM 22 O O4' TRH . . . K 3 4.104 72.015 54.159 1 13.04 ? O4' TRH 503 B 1 
HETATM 23 C C3' TRH . . . K 3 6.278 72.272 54.228 1 12.25 ? C3' TRH 503 B 1 
HETATM 24 O O3' TRH . . . K 3 6.715 72.318 52.89 1 12.78 ? O3' TRH 503 B 1 
HETATM 25 C C2' TRH . . . K 3 5.464 73.483 54.614 1 13.17 ? C2' TRH 503 B 1 
HETATM 26 C C1' TRH . . . K 3 4.142 73.387 53.865 1 12.09 ? C1' TRH 503 B 1 
HETATM 27 N N11 TRH . . . K 3 3.048 74.166 54.448 1 12.7 ? N11 TRH 503 B 1 
HETATM 28 C C21 TRH . . . K 3 2.205 74.92 53.704 1 13.89 ? C21 TRH 503 B 1 
HETATM 29 O O21 TRH . . . K 3 2.379 75.022 52.407 1 13.83 ? O21 TRH 503 B 1 
HETATM 30 N N31 TRH . . . K 3 1.196 75.609 54.244 1 14.63 ? N31 TRH 503 B 1 
HETATM 31 C C41 TRH . . . K 3 0.97 75.526 55.554 1 14.77 ? C41 TRH 503 B 1 
HETATM 32 O O41 TRH . . . K 3 -0.022 76.149 56.15 1 15.11 ? O41 TRH 503 B 1 
HETATM 33 C C51 TRH . . . K 3 1.79 74.772 56.34 1 16.02 ? C51 TRH 503 B 1 
HETATM 34 C C5A TRH . . . K 3 1.543 74.705 57.838 1 15.12 ? C5A TRH 503 B 1 
HETATM 35 C C61 TRH . . . K 3 2.843 74.088 55.749 1 14.96 ? C61 TRH 503 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           35 
#