data_2TSR
#
_model_server_result.job_id            KDJEMyyUNhG5tGH9EETBww 
_model_server_result.datetime_utc      '2024-11-24 01:15:22' 
_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          2tsr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":608}' 
#
_entry.id    2TSR 
#
_exptl.entry_id    2TSR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          101.4 
_cell.angle_gamma         90 
_cell.entry_id            2TSR 
_cell.length_a            99.7 
_cell.length_b            101.6 
_cell.length_c            140.8 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2TSR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_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,E,F,G,H,M,N 1 1 
C,D,I,J,K,L,O,P 2 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
? 2 E N N 
? 2 G N N 
? 2 I N N 
? 2 K N N 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
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
N1 C2 UMP sing 414 n n 
N1 C6 UMP sing 415 n n 
N1 C1' UMP sing 416 n n 
C2 N3 UMP sing 417 n n 
C2 O2 UMP doub 418 n n 
N3 C4 UMP sing 419 n n 
N3 HN3 UMP sing 420 n n 
C4 C5 UMP sing 421 n n 
C4 O4 UMP doub 422 n n 
C5 C6 UMP doub 423 n n 
C5 H5 UMP sing 424 n n 
C6 H6 UMP sing 425 n n 
C1' C2' UMP sing 426 n n 
C1' O4' UMP sing 427 n n 
C1' H1' UMP sing 428 n n 
C2' C3' UMP sing 429 n n 
C2' H2' UMP sing 430 n n 
C2' "H2''" UMP sing 431 n n 
C3' C4' UMP sing 432 n n 
C3' O3' UMP sing 433 n n 
C3' H3' UMP sing 434 n n 
C4' O4' UMP sing 435 n n 
C4' C5' UMP sing 436 n n 
C4' H4' UMP sing 437 n n 
O3' HO3' UMP sing 438 n n 
C5' O5' UMP sing 439 n n 
C5' H5' UMP sing 440 n n 
C5' "H5''" UMP sing 441 n n 
O5' P UMP sing 442 n n 
P OP1 UMP doub 443 n n 
P OP2 UMP sing 444 n n 
P OP3 UMP sing 445 n n 
OP2 HOP2 UMP sing 446 n n 
OP3 HOP3 UMP sing 447 n n 
#
_atom_sites.entry_id                     2TSR 
_atom_sites.fract_transf_matrix[1][1]    0.01003 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002022 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009843 
_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]    0.007245 
_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 UMP A 1 308 308 UMP UMP . 
F 3 D16 A 1 309 309 D16 D16 . 
G 2 UMP B 1 408 408 UMP UMP . 
H 3 D16 B 1 409 409 D16 D16 . 
I 2 UMP C 1 508 508 UMP UMP . 
J 3 D16 C 1 509 509 D16 D16 . 
K 2 UMP D 1 608 608 UMP UMP . 
L 3 D16 D 1 609 609 D16 D16 . 
M 4 HOH A 1 310 4 HOH HOH . 
M 4 HOH A 2 311 6 HOH HOH . 
M 4 HOH A 3 312 8 HOH HOH . 
M 4 HOH A 4 313 9 HOH HOH . 
M 4 HOH A 5 314 11 HOH HOH . 
M 4 HOH A 6 315 12 HOH HOH . 
M 4 HOH A 7 316 13 HOH HOH . 
M 4 HOH A 8 317 14 HOH HOH . 
M 4 HOH A 9 318 15 HOH HOH . 
M 4 HOH A 10 319 16 HOH HOH . 
M 4 HOH A 11 320 18 HOH HOH . 
M 4 HOH A 12 321 23 HOH HOH . 
M 4 HOH A 13 322 24 HOH HOH . 
M 4 HOH A 14 323 25 HOH HOH . 
M 4 HOH A 15 324 26 HOH HOH . 
M 4 HOH A 16 325 27 HOH HOH . 
M 4 HOH A 17 326 28 HOH HOH . 
M 4 HOH A 18 327 29 HOH HOH . 
M 4 HOH A 19 328 32 HOH HOH . 
M 4 HOH A 20 329 35 HOH HOH . 
M 4 HOH A 21 330 36 HOH HOH . 
M 4 HOH A 22 331 41 HOH HOH . 
M 4 HOH A 23 332 43 HOH HOH . 
M 4 HOH A 24 333 46 HOH HOH . 
N 4 HOH B 1 410 1 HOH HOH . 
N 4 HOH B 2 411 3 HOH HOH . 
N 4 HOH B 3 412 5 HOH HOH . 
N 4 HOH B 4 413 7 HOH HOH . 
N 4 HOH B 5 414 10 HOH HOH . 
N 4 HOH B 6 415 17 HOH HOH . 
N 4 HOH B 7 416 19 HOH HOH . 
N 4 HOH B 8 417 20 HOH HOH . 
N 4 HOH B 9 418 21 HOH HOH . 
N 4 HOH B 10 419 22 HOH HOH . 
N 4 HOH B 11 420 30 HOH HOH . 
N 4 HOH B 12 421 31 HOH HOH . 
N 4 HOH B 13 422 33 HOH HOH . 
N 4 HOH B 14 423 34 HOH HOH . 
N 4 HOH B 15 424 37 HOH HOH . 
N 4 HOH B 16 425 38 HOH HOH . 
N 4 HOH B 17 426 39 HOH HOH . 
N 4 HOH B 18 427 40 HOH HOH . 
N 4 HOH B 19 428 42 HOH HOH . 
N 4 HOH B 20 429 44 HOH HOH . 
N 4 HOH B 21 430 45 HOH HOH . 
N 4 HOH B 22 431 47 HOH HOH . 
N 4 HOH B 23 432 48 HOH HOH . 
N 4 HOH B 24 433 50 HOH HOH . 
N 4 HOH B 25 434 55 HOH HOH . 
N 4 HOH B 26 435 57 HOH HOH . 
O 4 HOH C 1 510 2 HOH HOH . 
O 4 HOH C 2 511 61 HOH HOH . 
O 4 HOH C 3 512 64 HOH HOH . 
O 4 HOH C 4 513 67 HOH HOH . 
O 4 HOH C 5 514 68 HOH HOH . 
O 4 HOH C 6 515 69 HOH HOH . 
O 4 HOH C 7 516 71 HOH HOH . 
O 4 HOH C 8 517 72 HOH HOH . 
O 4 HOH C 9 518 74 HOH HOH . 
P 4 HOH D 1 610 49 HOH HOH . 
P 4 HOH D 2 611 51 HOH HOH . 
P 4 HOH D 3 612 52 HOH HOH . 
P 4 HOH D 4 613 53 HOH HOH . 
P 4 HOH D 5 614 54 HOH HOH . 
P 4 HOH D 6 615 56 HOH HOH . 
P 4 HOH D 7 616 58 HOH HOH . 
P 4 HOH D 8 617 59 HOH HOH . 
P 4 HOH D 9 618 60 HOH HOH . 
P 4 HOH D 10 619 62 HOH HOH . 
P 4 HOH D 11 620 63 HOH HOH . 
P 4 HOH D 12 621 65 HOH HOH . 
P 4 HOH D 13 622 66 HOH HOH . 
P 4 HOH D 14 623 70 HOH HOH . 
P 4 HOH D 15 624 73 HOH HOH . 
P 4 HOH D 16 625 75 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 N N1 UMP . . . K 2 -5.124 -15.766 47.482 1 56.57 ? N1 UMP 608 D 1 
HETATM 2 C C2 UMP . . . K 2 -3.924 -16.187 46.922 1 53.01 ? C2 UMP 608 D 1 
HETATM 3 N N3 UMP . . . K 2 -2.911 -15.262 46.987 1 53.01 ? N3 UMP 608 D 1 
HETATM 4 C C4 UMP . . . K 2 -2.966 -13.998 47.554 1 51.31 ? C4 UMP 608 D 1 
HETATM 5 C C5 UMP . . . K 2 -4.221 -13.662 48.143 1 52.64 ? C5 UMP 608 D 1 
HETATM 6 C C6 UMP . . . K 2 -5.228 -14.533 48.091 1 57.22 ? C6 UMP 608 D 1 
HETATM 7 O O2 UMP . . . K 2 -3.762 -17.288 46.41 1 51.65 ? O2 UMP 608 D 1 
HETATM 8 O O4 UMP . . . K 2 -1.992 -13.252 47.467 1 46.9 ? O4 UMP 608 D 1 
HETATM 9 C C1' UMP . . . K 2 -6.316 -16.629 47.393 1 60.56 ? C1' UMP 608 D 1 
HETATM 10 C C2' UMP . . . K 2 -6.186 -18.151 47.49 1 62.55 ? C2' UMP 608 D 1 
HETATM 11 C C3' UMP . . . K 2 -6.834 -18.459 48.839 1 62.68 ? C3' UMP 608 D 1 
HETATM 12 C C4' UMP . . . K 2 -7.792 -17.292 49.088 1 62.4 ? C4' UMP 608 D 1 
HETATM 13 O O3' UMP . . . K 2 -7.712 -19.585 48.68 1 60.81 ? O3' UMP 608 D 1 
HETATM 14 O O4' UMP . . . K 2 -7.254 -16.173 48.348 1 64.58 ? O4' UMP 608 D 1 
HETATM 15 C C5' UMP . . . K 2 -7.918 -16.855 50.543 1 65.55 ? C5' UMP 608 D 1 
HETATM 16 O O5' UMP . . . K 2 -8.602 -17.854 51.342 1 64.89 ? O5' UMP 608 D 1 
HETATM 17 P P UMP . . . K 2 -8.045 -18.294 52.817 1 48.88 ? P UMP 608 D 1 
HETATM 18 O OP1 UMP . . . K 2 -9.125 -19.167 53.423 1 49.38 ? OP1 UMP 608 D 1 
HETATM 19 O OP2 UMP . . . K 2 -6.765 -19.054 52.533 1 52.37 ? OP2 UMP 608 D 1 
HETATM 20 O OP3 UMP . . . K 2 -7.812 -17.032 53.632 1 46.67 ? OP3 UMP 608 D 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#