data_5NOO
#
_model_server_result.job_id            CDbu38ZaflzqLBSB-7F3DQ 
_model_server_result.datetime_utc      '2024-11-18 05:58:43' 
_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          5noo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":401}' 
#
_entry.id    5NOO 
#
_exptl.entry_id    5NOO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_entity.src_method                  man 
_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                     2.1.1.45 
#
_cell.angle_alpha         90 
_cell.angle_beta          105.36 
_cell.angle_gamma         90 
_cell.entry_id            5NOO 
_cell.length_a            70.085 
_cell.length_b            94.314 
_cell.length_c            122.048 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NOO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 software_defined_assembly 1 
PISA dimeric 2 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                     5NOO 
_atom_sites.fract_transf_matrix[1][1]    0.014268 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003919 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010603 
_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]    0.008497 
_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 1 401 401 UMP UMP . 
F 3 D16 A 1 402 402 D16 D16 . 
G 2 UMP B 1 401 401 UMP UMP . 
H 3 D16 B 1 402 402 D16 D16 . 
I 2 UMP C 1 401 401 UMP UMP . 
J 3 D16 C 1 402 402 D16 D16 . 
K 2 UMP D 1 401 401 UMP UMP . 
L 3 D16 D 1 402 402 D16 D16 . 
M 4 HOH A 1 501 575 HOH HOH . 
M 4 HOH A 2 502 557 HOH HOH . 
M 4 HOH A 3 503 537 HOH HOH . 
M 4 HOH A 4 504 501 HOH HOH . 
M 4 HOH A 5 505 516 HOH HOH . 
M 4 HOH A 6 506 564 HOH HOH . 
M 4 HOH A 7 507 515 HOH HOH . 
M 4 HOH A 8 508 506 HOH HOH . 
M 4 HOH A 9 509 545 HOH HOH . 
M 4 HOH A 10 510 509 HOH HOH . 
M 4 HOH A 11 511 566 HOH HOH . 
M 4 HOH A 12 512 574 HOH HOH . 
M 4 HOH A 13 513 573 HOH HOH . 
M 4 HOH A 14 514 560 HOH HOH . 
M 4 HOH A 15 515 529 HOH HOH . 
M 4 HOH A 16 516 532 HOH HOH . 
M 4 HOH A 17 517 572 HOH HOH . 
N 4 HOH B 1 501 512 HOH HOH . 
N 4 HOH B 2 502 502 HOH HOH . 
N 4 HOH B 3 503 565 HOH HOH . 
N 4 HOH B 4 504 569 HOH HOH . 
N 4 HOH B 5 505 530 HOH HOH . 
N 4 HOH B 6 506 561 HOH HOH . 
N 4 HOH B 7 507 584 HOH HOH . 
N 4 HOH B 8 508 558 HOH HOH . 
N 4 HOH B 9 509 544 HOH HOH . 
N 4 HOH B 10 510 508 HOH HOH . 
N 4 HOH B 11 511 517 HOH HOH . 
N 4 HOH B 12 512 560 HOH HOH . 
N 4 HOH B 13 513 570 HOH HOH . 
N 4 HOH B 14 514 562 HOH HOH . 
N 4 HOH B 15 515 521 HOH HOH . 
N 4 HOH B 16 516 575 HOH HOH . 
N 4 HOH B 17 517 503 HOH HOH . 
N 4 HOH B 18 518 576 HOH HOH . 
N 4 HOH B 19 519 533 HOH HOH . 
N 4 HOH B 20 520 523 HOH HOH . 
N 4 HOH B 21 521 583 HOH HOH . 
N 4 HOH B 22 522 571 HOH HOH . 
N 4 HOH B 23 523 585 HOH HOH . 
N 4 HOH B 24 524 546 HOH HOH . 
O 4 HOH C 1 501 529 HOH HOH . 
O 4 HOH C 2 502 578 HOH HOH . 
O 4 HOH C 3 503 588 HOH HOH . 
O 4 HOH C 4 504 511 HOH HOH . 
O 4 HOH C 5 505 584 HOH HOH . 
O 4 HOH C 6 506 602 HOH HOH . 
O 4 HOH C 7 507 547 HOH HOH . 
O 4 HOH C 8 508 574 HOH HOH . 
O 4 HOH C 9 509 507 HOH HOH . 
O 4 HOH C 10 510 545 HOH HOH . 
O 4 HOH C 11 511 544 HOH HOH . 
O 4 HOH C 12 512 506 HOH HOH . 
O 4 HOH C 13 513 518 HOH HOH . 
O 4 HOH C 14 514 552 HOH HOH . 
O 4 HOH C 15 515 595 HOH HOH . 
O 4 HOH C 16 516 537 HOH HOH . 
O 4 HOH C 17 517 596 HOH HOH . 
O 4 HOH C 18 518 567 HOH HOH . 
O 4 HOH C 19 519 601 HOH HOH . 
O 4 HOH C 20 520 531 HOH HOH . 
O 4 HOH C 21 521 508 HOH HOH . 
O 4 HOH C 22 522 568 HOH HOH . 
O 4 HOH C 23 523 538 HOH HOH . 
O 4 HOH C 24 524 516 HOH HOH . 
O 4 HOH C 25 525 524 HOH HOH . 
O 4 HOH C 26 526 603 HOH HOH . 
O 4 HOH C 27 527 576 HOH HOH . 
O 4 HOH C 28 528 569 HOH HOH . 
O 4 HOH C 29 529 586 HOH HOH . 
O 4 HOH C 30 530 522 HOH HOH . 
O 4 HOH C 31 531 579 HOH HOH . 
O 4 HOH C 32 532 583 HOH HOH . 
O 4 HOH C 33 533 587 HOH HOH . 
O 4 HOH C 34 534 540 HOH HOH . 
O 4 HOH C 35 535 575 HOH HOH . 
P 4 HOH D 1 501 532 HOH HOH . 
P 4 HOH D 2 502 512 HOH HOH . 
P 4 HOH D 3 503 574 HOH HOH . 
P 4 HOH D 4 504 516 HOH HOH . 
P 4 HOH D 5 505 525 HOH HOH . 
P 4 HOH D 6 506 519 HOH HOH . 
P 4 HOH D 7 507 534 HOH HOH . 
P 4 HOH D 8 508 521 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 -45.423 -0.429 -34.681 1 41.3 ? N1 UMP 401 D 1 
HETATM 2 C C2 UMP . . . K 2 -45.266 -1.492 -35.543 1 41.76 ? C2 UMP 401 D 1 
HETATM 3 N N3 UMP . . . K 2 -45.525 -1.328 -36.885 1 43.07 ? N3 UMP 401 D 1 
HETATM 4 C C4 UMP . . . K 2 -45.942 -0.113 -37.381 1 42.54 ? C4 UMP 401 D 1 
HETATM 5 C C5 UMP . . . K 2 -46.101 0.956 -36.514 1 42.85 ? C5 UMP 401 D 1 
HETATM 6 C C6 UMP . . . K 2 -45.837 0.785 -35.161 1 43.12 ? C6 UMP 401 D 1 
HETATM 7 O O2 UMP . . . K 2 -44.895 -2.588 -35.122 1 41.62 ? O2 UMP 401 D 1 
HETATM 8 O O4 UMP . . . K 2 -46.171 0.022 -38.582 1 42.92 ? O4 UMP 401 D 1 
HETATM 9 C C1' UMP . . . K 2 -45.151 -0.614 -33.242 1 40.61 ? C1' UMP 401 D 1 
HETATM 10 C C2' UMP . . . K 2 -43.686 -0.961 -32.975 1 39.91 ? C2' UMP 401 D 1 
HETATM 11 C C3' UMP . . . K 2 -43.411 -0.079 -31.776 1 39.86 ? C3' UMP 401 D 1 
HETATM 12 C C4' UMP . . . K 2 -44.399 1.071 -31.77 1 39.94 ? C4' UMP 401 D 1 
HETATM 13 O O3' UMP . . . K 2 -42.669 -0.498 -30.64 1 39.76 ? O3' UMP 401 D 1 
HETATM 14 O O4' UMP . . . K 2 -45.483 0.583 -32.538 1 40.18 ? O4' UMP 401 D 1 
HETATM 15 C C5' UMP . . . K 2 -43.825 2.331 -32.403 1 39.06 ? C5' UMP 401 D 1 
HETATM 16 O O5' UMP . . . K 2 -43.091 3.035 -31.429 1 36.31 ? O5' UMP 401 D 1 
HETATM 17 P P UMP . . . K 2 -41.728 3.785 -31.829 1 35.07 ? P UMP 401 D 1 
HETATM 18 O OP1 UMP . . . K 2 -41.965 4.704 -33.003 1 34.24 -1 OP1 UMP 401 D 1 
HETATM 19 O OP2 UMP . . . K 2 -40.701 2.736 -32.174 1 34.8 -1 OP2 UMP 401 D 1 
HETATM 20 O OP3 UMP . . . K 2 -41.249 4.569 -30.668 1 34.54 ? OP3 UMP 401 D 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           38 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           1315 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           20 
#