data_1G3L
#
_model_server_result.job_id            VkuWNTkYh7TMEtw4293HXA 
_model_server_result.datetime_utc      '2024-10-12 10:23:46' 
_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":"N","auth_seq_id":505}' 
#
_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 . . . N 3 -15.163 63.475 14.952 1 10.88 ? O4P TRH 505 C 1 
HETATM 2 P P2 TRH . . . N 3 -15.947 62.3 14.208 1 9.45 ? P2 TRH 505 C 1 
HETATM 3 O O3P TRH . . . N 3 -16.871 61.279 15.059 1 10.07 ? O3P TRH 505 C 1 
HETATM 4 O O1 TRH . . . N 3 -16.746 63.1 13.152 1 9.96 ? O1 TRH 505 C 1 
HETATM 5 C C1 TRH . . . N 3 -17.923 62.62 12.616 1 11.92 ? C1 TRH 505 C 1 
HETATM 6 C C2 TRH . . . N 3 -17.763 62.557 11.114 1 15.41 ? C2 TRH 505 C 1 
HETATM 7 O O2 TRH . . . N 3 -17.41 63.892 10.646 1 15.11 ? O2 TRH 505 C 1 
HETATM 8 C C3 TRH . . . N 3 -19.097 62.262 10.484 1 14.88 ? C3 TRH 505 C 1 
HETATM 9 O O3 TRH . . . N 3 -19.129 62.482 9.087 1 17.85 ? O3 TRH 505 C 1 
HETATM 10 C C4 TRH . . . N 3 -19.973 63.341 11.022 1 15.36 ? C4 TRH 505 C 1 
HETATM 11 O O4 TRH . . . N 3 -21.284 63.052 10.539 1 14.19 ? O4 TRH 505 C 1 
HETATM 12 C C5 TRH . . . N 3 -19.821 63.311 12.556 1 14.84 ? C5 TRH 505 C 1 
HETATM 13 O O5 TRH . . . N 3 -18.526 63.809 13.004 1 13.87 ? O5 TRH 505 C 1 
HETATM 14 C C6 TRH . . . N 3 -21.061 64.011 13.072 1 15.32 ? C6 TRH 505 C 1 
HETATM 15 O OPP TRH . . . N 3 -14.976 61.424 13.288 1 11.61 ? OPP TRH 505 C 1 
HETATM 16 P P TRH . . . N 3 -14.857 59.825 13.453 1 12.29 ? P TRH 505 C 1 
HETATM 17 O O1P TRH . . . N 3 -13.992 59.271 12.23 1 12.75 ? O1P TRH 505 C 1 
HETATM 18 O O2P TRH . . . N 3 -16.089 59.117 14.119 1 15.8 ? O2P TRH 505 C 1 
HETATM 19 O O5' TRH . . . N 3 -13.829 59.792 14.636 1 13.11 ? O5' TRH 505 C 1 
HETATM 20 C C5' TRH . . . N 3 -14.053 60.143 15.944 1 9.58 ? C5' TRH 505 C 1 
HETATM 21 C C4' TRH . . . N 3 -12.75 59.643 16.525 1 12.43 ? C4' TRH 505 C 1 
HETATM 22 O O4' TRH . . . N 3 -13.242 58.819 17.514 1 11.51 ? O4' TRH 505 C 1 
HETATM 23 C C3' TRH . . . N 3 -11.926 58.651 15.747 1 12.56 ? C3' TRH 505 C 1 
HETATM 24 O O3' TRH . . . N 3 -10.644 58.51 16.357 1 13.04 ? O3' TRH 505 C 1 
HETATM 25 C C2' TRH . . . N 3 -12.731 57.4 15.931 1 12.03 ? C2' TRH 505 C 1 
HETATM 26 C C1' TRH . . . N 3 -13.062 57.41 17.421 1 12.09 ? C1' TRH 505 C 1 
HETATM 27 N N11 TRH . . . N 3 -14.26 56.699 17.823 1 10.57 ? N11 TRH 505 C 1 
HETATM 28 C C21 TRH . . . N 3 -14.303 55.965 18.955 1 10.23 ? C21 TRH 505 C 1 
HETATM 29 O O21 TRH . . . N 3 -13.227 55.774 19.704 1 10.36 ? O21 TRH 505 C 1 
HETATM 30 N N31 TRH . . . N 3 -15.431 55.398 19.325 1 11.77 ? N31 TRH 505 C 1 
HETATM 31 C C41 TRH . . . N 3 -16.527 55.552 18.566 1 11.11 ? C41 TRH 505 C 1 
HETATM 32 O O41 TRH . . . N 3 -17.684 54.996 18.89 1 12.68 ? O41 TRH 505 C 1 
HETATM 33 C C51 TRH . . . N 3 -16.48 56.312 17.445 1 8.93 ? C51 TRH 505 C 1 
HETATM 34 C C5A TRH . . . N 3 -17.686 56.514 16.582 1 10.29 ? C5A TRH 505 C 1 
HETATM 35 C C61 TRH . . . N 3 -15.316 56.902 17.091 1 9.12 ? C61 TRH 505 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           35 
#