data_1G3L
#
_model_server_result.job_id            QQmDJjChxDRpc0-4IHzE-w 
_model_server_result.datetime_utc      '2024-10-12 10:21:03' 
_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":"G","auth_seq_id":501}' 
#
_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 . . . G 3 -4.686 67.593 10.344 1 7.85 ? O4P TRH 501 A 1 
HETATM 2 P P2 TRH . . . G 3 -4.714 68.743 9.224 1 9.84 ? P2 TRH 501 A 1 
HETATM 3 O O3P TRH . . . G 3 -3.472 69.725 9.058 1 12.95 ? O3P TRH 501 A 1 
HETATM 4 O O1 TRH . . . G 3 -5.026 68.073 7.854 1 13.32 ? O1 TRH 501 A 1 
HETATM 5 C C1 TRH . . . G 3 -4.492 68.515 6.652 1 15.6 ? C1 TRH 501 A 1 
HETATM 6 C C2 TRH . . . G 3 -5.672 68.637 5.729 1 17.67 ? C2 TRH 501 A 1 
HETATM 7 O O2 TRH . . . G 3 -6.408 67.395 5.769 1 15.02 ? O2 TRH 501 A 1 
HETATM 8 C C3 TRH . . . G 3 -5.175 68.84 4.309 1 17.86 ? C3 TRH 501 A 1 
HETATM 9 O O3 TRH . . . G 3 -6.212 68.658 3.367 1 17.96 ? O3 TRH 501 A 1 
HETATM 10 C C4 TRH . . . G 3 -4.145 67.789 4.042 1 17.45 ? C4 TRH 501 A 1 
HETATM 11 O O4 TRH . . . G 3 -3.466 68.194 2.845 1 19.65 ? O4 TRH 501 A 1 
HETATM 12 C C5 TRH . . . G 3 -3.207 67.668 5.242 1 15.86 ? C5 TRH 501 A 1 
HETATM 13 O O5 TRH . . . G 3 -3.886 67.276 6.468 1 17.54 ? O5 TRH 501 A 1 
HETATM 14 C C6 TRH . . . G 3 -2.171 66.665 4.801 1 18.53 ? C6 TRH 501 A 1 
HETATM 15 O OPP TRH . . . G 3 -6.03 69.625 9.462 1 9.05 ? OPP TRH 501 A 1 
HETATM 16 P P TRH . . . G 3 -6.034 71.234 9.701 1 8.49 ? P TRH 501 A 1 
HETATM 17 O O1P TRH . . . G 3 -7.535 71.624 9.98 1 9.54 ? O1P TRH 501 A 1 
HETATM 18 O O2P TRH . . . G 3 -5.172 72 8.591 1 11.47 ? O2P TRH 501 A 1 
HETATM 19 O O5' TRH . . . G 3 -5.254 71.542 11.026 1 7.36 ? O5' TRH 501 A 1 
HETATM 20 C C5' TRH . . . G 3 -5.087 70.561 12.003 1 7.91 ? C5' TRH 501 A 1 
HETATM 21 C C4' TRH . . . G 3 -5.227 71.272 13.321 1 9.55 ? C4' TRH 501 A 1 
HETATM 22 O O4' TRH . . . G 3 -4.036 72.003 13.397 1 9.15 ? O4' TRH 501 A 1 
HETATM 23 C C3' TRH . . . G 3 -6.21 72.363 13.406 1 10.54 ? C3' TRH 501 A 1 
HETATM 24 O O3' TRH . . . G 3 -6.661 72.354 14.761 1 12.07 ? O3' TRH 501 A 1 
HETATM 25 C C2' TRH . . . G 3 -5.396 73.601 13.083 1 10.74 ? C2' TRH 501 A 1 
HETATM 26 C C1' TRH . . . G 3 -3.987 73.391 13.608 1 8.35 ? C1' TRH 501 A 1 
HETATM 27 N N11 TRH . . . G 3 -2.921 74.112 12.901 1 9.41 ? N11 TRH 501 A 1 
HETATM 28 C C21 TRH . . . G 3 -2.019 74.86 13.618 1 10.1 ? C21 TRH 501 A 1 
HETATM 29 O O21 TRH . . . G 3 -2.119 75.026 14.929 1 8.93 ? O21 TRH 501 A 1 
HETATM 30 N N31 TRH . . . G 3 -0.996 75.479 13.037 1 10.19 ? N31 TRH 501 A 1 
HETATM 31 C C41 TRH . . . G 3 -0.807 75.364 11.729 1 10.29 ? C41 TRH 501 A 1 
HETATM 32 O O41 TRH . . . G 3 0.189 75.983 11.115 1 10.43 ? O41 TRH 501 A 1 
HETATM 33 C C51 TRH . . . G 3 -1.676 74.612 10.983 1 9.12 ? C51 TRH 501 A 1 
HETATM 34 C C5A TRH . . . G 3 -1.411 74.537 9.522 1 8.73 ? C5A TRH 501 A 1 
HETATM 35 C C61 TRH . . . G 3 -2.742 73.964 11.584 1 7.8 ? C61 TRH 501 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           35 
#