data_4XSD
#
_model_server_result.job_id            Jef7Y5Dxa-jJdqvbVG-95A 
_model_server_result.datetime_utc      '2024-11-13 13:59:45' 
_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          4xsd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1001}' 
#
_entry.id    4XSD 
#
_exptl.entry_id    4XSD 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            4XSD 
_cell.length_a            150.17 
_cell.length_b            150.17 
_cell.length_c            89.16 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XSD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32' 
#
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,I,J 1 1 
C,D,G,H,K,L 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 F N N 
? 2 G N N 
? 2 H 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 358 n n 
N1 C6 UMP sing 359 n n 
N1 C1' UMP sing 360 n n 
C2 N3 UMP sing 361 n n 
C2 O2 UMP doub 362 n n 
N3 C4 UMP sing 363 n n 
N3 HN3 UMP sing 364 n n 
C4 C5 UMP sing 365 n n 
C4 O4 UMP doub 366 n n 
C5 C6 UMP doub 367 n n 
C5 H5 UMP sing 368 n n 
C6 H6 UMP sing 369 n n 
C1' C2' UMP sing 370 n n 
C1' O4' UMP sing 371 n n 
C1' H1' UMP sing 372 n n 
C2' C3' UMP sing 373 n n 
C2' H2' UMP sing 374 n n 
C2' "H2''" UMP sing 375 n n 
C3' C4' UMP sing 376 n n 
C3' O3' UMP sing 377 n n 
C3' H3' UMP sing 378 n n 
C4' O4' UMP sing 379 n n 
C4' C5' UMP sing 380 n n 
C4' H4' UMP sing 381 n n 
O3' HO3' UMP sing 382 n n 
C5' O5' UMP sing 383 n n 
C5' H5' UMP sing 384 n n 
C5' "H5''" UMP sing 385 n n 
O5' P UMP sing 386 n n 
P OP1 UMP doub 387 n n 
P OP2 UMP sing 388 n n 
P OP3 UMP sing 389 n n 
OP2 HOP2 UMP sing 390 n n 
OP3 HOP3 UMP sing 391 n n 
#
_atom_sites.entry_id                     4XSD 
_atom_sites.fract_transf_matrix[1][1]    0.006659 
_atom_sites.fract_transf_matrix[1][2]    0.003845 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007689 
_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]    0.011216 
_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 1001 1001 UMP UMP . 
F 2 UMP B 1 1001 1001 UMP UMP . 
G 2 UMP C 1 1001 1001 UMP UMP . 
H 2 UMP D 1 1001 1001 UMP UMP . 
I 3 HOH A 1 1101 7 HOH HOH . 
I 3 HOH A 2 1102 8 HOH HOH . 
J 3 HOH B 1 1101 1 HOH HOH . 
J 3 HOH B 2 1102 2 HOH HOH . 
J 3 HOH B 3 1103 4 HOH HOH . 
J 3 HOH B 4 1104 3 HOH HOH . 
K 3 HOH C 1 1101 5 HOH HOH . 
K 3 HOH C 2 1102 6 HOH HOH . 
L 3 HOH D 1 1101 9 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 . . . G 2 0.446 14.156 2.249 1 52.95 ? N1 UMP 1001 C 1 
HETATM 2 C C2 UMP . . . G 2 1.702 13.618 2.824 1 43.43 ? C2 UMP 1001 C 1 
HETATM 3 N N3 UMP . . . G 2 2.96 14.378 2.685 1 49.28 ? N3 UMP 1001 C 1 
HETATM 4 C C4 UMP . . . G 2 2.967 15.629 1.994 1 65.73 ? C4 UMP 1001 C 1 
HETATM 5 C C5 UMP . . . G 2 1.732 16.157 1.426 1 38.66 ? C5 UMP 1001 C 1 
HETATM 6 C C6 UMP . . . G 2 0.483 15.398 1.565 1 28.68 ? C6 UMP 1001 C 1 
HETATM 7 O O2 UMP . . . G 2 1.741 12.574 3.406 1 40.4 ? O2 UMP 1001 C 1 
HETATM 8 O O4 UMP . . . G 2 4.008 16.258 1.874 1 50.81 ? O4 UMP 1001 C 1 
HETATM 9 C C1' UMP . . . G 2 -0.824 13.469 2.341 1 66.16 ? C1' UMP 1001 C 1 
HETATM 10 C C2' UMP . . . G 2 -1.01 12.652 3.669 1 34.19 ? C2' UMP 1001 C 1 
HETATM 11 C C3' UMP . . . G 2 -2.493 12.527 3.733 1 48.6 ? C3' UMP 1001 C 1 
HETATM 12 C C4' UMP . . . G 2 -2.978 13.661 3.208 1 35.59 ? C4' UMP 1001 C 1 
HETATM 13 O O3' UMP . . . G 2 -2.908 11.349 2.899 1 39.75 ? O3' UMP 1001 C 1 
HETATM 14 O O4' UMP . . . G 2 -1.754 14.341 2.419 1 81.8 ? O4' UMP 1001 C 1 
HETATM 15 C C5' UMP . . . G 2 -3.5 14.608 4.281 1 34.17 ? C5' UMP 1001 C 1 
HETATM 16 O O5' UMP . . . G 2 -4.892 14.415 4.434 1 28.72 ? O5' UMP 1001 C 1 
HETATM 17 P P UMP . . . G 2 -5.608 15.077 5.668 1 38.48 ? P UMP 1001 C 1 
HETATM 18 O OP1 UMP . . . G 2 -6.298 16.374 5.214 1 35.11 -1 OP1 UMP 1001 C 1 
HETATM 19 O OP2 UMP . . . G 2 -4.593 15.437 6.727 1 36.65 ? OP2 UMP 1001 C 1 
HETATM 20 O OP3 UMP . . . G 2 -6.63 14.103 6.245 1 29.35 -1 OP3 UMP 1001 C 1 
#
_model_server_stats.io_time_ms              51 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           221 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           20 
#