data_4ECK
#
_model_server_result.job_id            Q3oP3R430sxGmoiylXpnjQ 
_model_server_result.datetime_utc      '2024-11-27 00:10:11' 
_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          4eck 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":701}' 
#
_entry.id    4ECK 
#
_exptl.entry_id    4ECK 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.02 
_cell.angle_gamma         90 
_cell.entry_id            4ECK 
_cell.length_a            185.944 
_cell.length_b            143.015 
_cell.length_c            59.84 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4ECK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 2 C N N 
? 2 G 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 551 n n 
N1 C6 UMP sing 552 n n 
N1 C1' UMP sing 553 n n 
C2 N3 UMP sing 554 n n 
C2 O2 UMP doub 555 n n 
N3 C4 UMP sing 556 n n 
N3 HN3 UMP sing 557 n n 
C4 C5 UMP sing 558 n n 
C4 O4 UMP doub 559 n n 
C5 C6 UMP doub 560 n n 
C5 H5 UMP sing 561 n n 
C6 H6 UMP sing 562 n n 
C1' C2' UMP sing 563 n n 
C1' O4' UMP sing 564 n n 
C1' H1' UMP sing 565 n n 
C2' C3' UMP sing 566 n n 
C2' H2' UMP sing 567 n n 
C2' "H2''" UMP sing 568 n n 
C3' C4' UMP sing 569 n n 
C3' O3' UMP sing 570 n n 
C3' H3' UMP sing 571 n n 
C4' O4' UMP sing 572 n n 
C4' C5' UMP sing 573 n n 
C4' H4' UMP sing 574 n n 
O3' HO3' UMP sing 575 n n 
C5' O5' UMP sing 576 n n 
C5' H5' UMP sing 577 n n 
C5' "H5''" UMP sing 578 n n 
O5' P UMP sing 579 n n 
P OP1 UMP doub 580 n n 
P OP2 UMP sing 581 n n 
P OP3 UMP sing 582 n n 
OP2 HOP2 UMP sing 583 n n 
OP3 HOP3 UMP sing 584 n n 
#
_atom_sites.entry_id                     4ECK 
_atom_sites.fract_transf_matrix[1][1]    0.005378 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000002 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006992 
_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]    0.016711 
_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
C 2 UMP A 1 701 703 UMP UMP . 
D 3 CB3 A 1 702 704 CB3 CB3 . 
E 4 FOL A 1 703 705 FOL FOL . 
F 5 NDP A 1 704 706 NDP NDP . 
G 2 UMP B 1 701 703 UMP UMP . 
H 3 CB3 B 1 702 704 CB3 CB3 . 
I 4 FOL B 1 703 705 FOL FOL . 
J 5 NDP B 1 704 706 NDP NDP . 
#
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 . . . C 2 -39.527 8.674 -20.694 1 77.96 ? N1 UMP 701 A 1 
HETATM 2 C C2 UMP . . . C 2 -40.531 8.58 -21.695 1 73.56 ? C2 UMP 701 A 1 
HETATM 3 N N3 UMP . . . C 2 -40.188 8.772 -22.969 1 72.77 ? N3 UMP 701 A 1 
HETATM 4 C C4 UMP . . . C 2 -38.923 9.049 -23.318 1 74 ? C4 UMP 701 A 1 
HETATM 5 C C5 UMP . . . C 2 -37.925 9.155 -22.36 1 75.59 ? C5 UMP 701 A 1 
HETATM 6 C C6 UMP . . . C 2 -38.257 8.958 -21.027 1 77.5 ? C6 UMP 701 A 1 
HETATM 7 O O2 UMP . . . C 2 -41.723 8.321 -21.415 1 71.48 ? O2 UMP 701 A 1 
HETATM 8 O O4 UMP . . . C 2 -38.627 9.218 -24.518 1 73.02 ? O4 UMP 701 A 1 
HETATM 9 C C1' UMP . . . C 2 -39.863 8.483 -19.279 1 80.01 ? C1' UMP 701 A 1 
HETATM 10 C C2' UMP . . . C 2 -40.561 7.149 -19.023 1 77.25 ? C2' UMP 701 A 1 
HETATM 11 C C3' UMP . . . C 2 -40.151 6.809 -17.611 1 78.31 ? C3' UMP 701 A 1 
HETATM 12 C C4' UMP . . . C 2 -39.058 7.802 -17.267 1 82.29 ? C4' UMP 701 A 1 
HETATM 13 O O3' UMP . . . C 2 -41.229 7.146 -16.752 1 78.92 ? O3' UMP 701 A 1 
HETATM 14 O O4' UMP . . . C 2 -38.679 8.455 -18.478 1 80.85 ? O4' UMP 701 A 1 
HETATM 15 C C5' UMP . . . C 2 -37.922 7.236 -16.421 1 87.26 ? C5' UMP 701 A 1 
HETATM 16 O O5' UMP . . . C 2 -36.98 6.389 -17.091 1 92.32 ? O5' UMP 701 A 1 
HETATM 17 P P UMP . . . C 2 -36.551 4.969 -16.454 1 97.94 ? P UMP 701 A 1 
HETATM 18 O OP1 UMP . . . C 2 -37.621 4.018 -16.943 1 94.23 ? OP1 UMP 701 A 1 
HETATM 19 O OP2 UMP . . . C 2 -35.172 4.748 -17.051 1 95.98 ? OP2 UMP 701 A 1 
HETATM 20 O OP3 UMP . . . C 2 -36.548 5.139 -14.951 1 93.66 ? OP3 UMP 701 A 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           743 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           20 
#