data_6PF5
#
_model_server_result.job_id            9Bz6rpT1pob7nISHBxqnnQ 
_model_server_result.datetime_utc      '2024-10-25 20:38:29' 
_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          6pf5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":600}' 
#
_entry.id    6PF5 
#
_exptl.entry_id    6PF5 
_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          89.93 
_cell.angle_gamma         90 
_cell.entry_id            6PF5 
_cell.length_a            85.155 
_cell.length_b            85.134 
_cell.length_c            175.744 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PF5 
_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 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,M 1 1 
D,K,L,P 1 4 
B,G,H,N 2 1,2 
C,I,J,O 3 1,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -85.155 0 0 
3 'crystal symmetry operation' 2_456 -x-1,y,-z+1 -1 0 0 0 1 0 0 0 -1 -84.940288 0 175.743869 
4 'crystal symmetry operation' 3_445 x-1/2,y-1/2,z 1 0 0 0 1 0 0 0 1 -42.5775 -42.567 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 415 n n 
N1 C6 UMP sing 416 n n 
N1 C1' UMP sing 417 n n 
C2 N3 UMP sing 418 n n 
C2 O2 UMP doub 419 n n 
N3 C4 UMP sing 420 n n 
N3 HN3 UMP sing 421 n n 
C4 C5 UMP sing 422 n n 
C4 O4 UMP doub 423 n n 
C5 C6 UMP doub 424 n n 
C5 H5 UMP sing 425 n n 
C6 H6 UMP sing 426 n n 
C1' C2' UMP sing 427 n n 
C1' O4' UMP sing 428 n n 
C1' H1' UMP sing 429 n n 
C2' C3' UMP sing 430 n n 
C2' H2' UMP sing 431 n n 
C2' "H2''" UMP sing 432 n n 
C3' C4' UMP sing 433 n n 
C3' O3' UMP sing 434 n n 
C3' H3' UMP sing 435 n n 
C4' O4' UMP sing 436 n n 
C4' C5' UMP sing 437 n n 
C4' H4' UMP sing 438 n n 
O3' HO3' UMP sing 439 n n 
C5' O5' UMP sing 440 n n 
C5' H5' UMP sing 441 n n 
C5' "H5''" UMP sing 442 n n 
O5' P UMP sing 443 n n 
P OP1 UMP doub 444 n n 
P OP2 UMP sing 445 n n 
P OP3 UMP sing 446 n n 
OP2 HOP2 UMP sing 447 n n 
OP3 HOP3 UMP sing 448 n n 
#
_atom_sites.entry_id                     6PF5 
_atom_sites.fract_transf_matrix[1][1]    0.011743 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    -0.000015 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011746 
_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]    0.00569 
_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 1 600 600 UMP UMP . 
F 3 OED A 1 601 601 OED T10 . 
G 2 UMP B 1 600 600 UMP UMP . 
H 3 OED B 1 601 601 OED T10 . 
I 2 UMP C 1 600 600 UMP UMP . 
J 3 OED C 1 601 601 OED T10 . 
K 2 UMP D 1 600 600 UMP UMP . 
L 3 OED D 1 601 601 OED T10 . 
M 4 HOH A 1 701 22 HOH HOH . 
M 4 HOH A 2 702 83 HOH HOH . 
M 4 HOH A 3 703 55 HOH HOH . 
M 4 HOH A 4 704 20 HOH HOH . 
M 4 HOH A 5 705 14 HOH HOH . 
M 4 HOH A 6 706 45 HOH HOH . 
M 4 HOH A 7 707 8 HOH HOH . 
M 4 HOH A 8 708 24 HOH HOH . 
M 4 HOH A 9 709 114 HOH HOH . 
M 4 HOH A 10 710 49 HOH HOH . 
M 4 HOH A 11 711 52 HOH HOH . 
M 4 HOH A 12 712 79 HOH HOH . 
M 4 HOH A 13 713 101 HOH HOH . 
M 4 HOH A 14 714 5 HOH HOH . 
M 4 HOH A 15 715 69 HOH HOH . 
M 4 HOH A 16 716 34 HOH HOH . 
M 4 HOH A 17 717 73 HOH HOH . 
M 4 HOH A 18 718 123 HOH HOH . 
M 4 HOH A 19 719 11 HOH HOH . 
M 4 HOH A 20 720 90 HOH HOH . 
M 4 HOH A 21 721 47 HOH HOH . 
M 4 HOH A 22 722 41 HOH HOH . 
M 4 HOH A 23 723 9 HOH HOH . 
M 4 HOH A 24 724 112 HOH HOH . 
M 4 HOH A 25 725 128 HOH HOH . 
M 4 HOH A 26 726 109 HOH HOH . 
M 4 HOH A 27 727 42 HOH HOH . 
M 4 HOH A 28 728 40 HOH HOH . 
N 4 HOH B 1 701 127 HOH HOH . 
N 4 HOH B 2 702 75 HOH HOH . 
N 4 HOH B 3 703 29 HOH HOH . 
N 4 HOH B 4 704 33 HOH HOH . 
N 4 HOH B 5 705 12 HOH HOH . 
N 4 HOH B 6 706 98 HOH HOH . 
N 4 HOH B 7 707 10 HOH HOH . 
N 4 HOH B 8 708 96 HOH HOH . 
N 4 HOH B 9 709 56 HOH HOH . 
N 4 HOH B 10 710 119 HOH HOH . 
N 4 HOH B 11 711 36 HOH HOH . 
N 4 HOH B 12 712 43 HOH HOH . 
N 4 HOH B 13 713 64 HOH HOH . 
N 4 HOH B 14 714 113 HOH HOH . 
N 4 HOH B 15 715 60 HOH HOH . 
N 4 HOH B 16 716 28 HOH HOH . 
N 4 HOH B 17 717 7 HOH HOH . 
N 4 HOH B 18 718 103 HOH HOH . 
N 4 HOH B 19 719 26 HOH HOH . 
N 4 HOH B 20 720 63 HOH HOH . 
N 4 HOH B 21 721 97 HOH HOH . 
N 4 HOH B 22 722 80 HOH HOH . 
N 4 HOH B 23 723 19 HOH HOH . 
N 4 HOH B 24 724 81 HOH HOH . 
N 4 HOH B 25 725 95 HOH HOH . 
N 4 HOH B 26 726 68 HOH HOH . 
N 4 HOH B 27 727 116 HOH HOH . 
N 4 HOH B 28 728 21 HOH HOH . 
N 4 HOH B 29 729 72 HOH HOH . 
N 4 HOH B 30 730 89 HOH HOH . 
N 4 HOH B 31 731 108 HOH HOH . 
N 4 HOH B 32 732 126 HOH HOH . 
N 4 HOH B 33 733 99 HOH HOH . 
N 4 HOH B 34 734 88 HOH HOH . 
O 4 HOH C 1 701 35 HOH HOH . 
O 4 HOH C 2 702 91 HOH HOH . 
O 4 HOH C 3 703 107 HOH HOH . 
O 4 HOH C 4 704 17 HOH HOH . 
O 4 HOH C 5 705 15 HOH HOH . 
O 4 HOH C 6 706 44 HOH HOH . 
O 4 HOH C 7 707 48 HOH HOH . 
O 4 HOH C 8 708 66 HOH HOH . 
O 4 HOH C 9 709 86 HOH HOH . 
O 4 HOH C 10 710 4 HOH HOH . 
O 4 HOH C 11 711 105 HOH HOH . 
O 4 HOH C 12 712 61 HOH HOH . 
O 4 HOH C 13 713 54 HOH HOH . 
O 4 HOH C 14 714 62 HOH HOH . 
O 4 HOH C 15 715 87 HOH HOH . 
O 4 HOH C 16 716 3 HOH HOH . 
O 4 HOH C 17 717 78 HOH HOH . 
O 4 HOH C 18 718 106 HOH HOH . 
O 4 HOH C 19 719 94 HOH HOH . 
O 4 HOH C 20 720 39 HOH HOH . 
O 4 HOH C 21 721 118 HOH HOH . 
O 4 HOH C 22 722 84 HOH HOH . 
O 4 HOH C 23 723 37 HOH HOH . 
O 4 HOH C 24 724 57 HOH HOH . 
O 4 HOH C 25 725 18 HOH HOH . 
O 4 HOH C 26 726 82 HOH HOH . 
O 4 HOH C 27 727 65 HOH HOH . 
O 4 HOH C 28 728 50 HOH HOH . 
O 4 HOH C 29 729 32 HOH HOH . 
O 4 HOH C 30 730 53 HOH HOH . 
O 4 HOH C 31 731 85 HOH HOH . 
O 4 HOH C 32 732 102 HOH HOH . 
O 4 HOH C 33 733 117 HOH HOH . 
P 4 HOH D 1 701 31 HOH HOH . 
P 4 HOH D 2 702 93 HOH HOH . 
P 4 HOH D 3 703 115 HOH HOH . 
P 4 HOH D 4 704 13 HOH HOH . 
P 4 HOH D 5 705 121 HOH HOH . 
P 4 HOH D 6 706 27 HOH HOH . 
P 4 HOH D 7 707 23 HOH HOH . 
P 4 HOH D 8 708 67 HOH HOH . 
P 4 HOH D 9 709 70 HOH HOH . 
P 4 HOH D 10 710 111 HOH HOH . 
P 4 HOH D 11 711 104 HOH HOH . 
P 4 HOH D 12 712 92 HOH HOH . 
P 4 HOH D 13 713 100 HOH HOH . 
P 4 HOH D 14 714 58 HOH HOH . 
P 4 HOH D 15 715 77 HOH HOH . 
P 4 HOH D 16 716 110 HOH HOH . 
P 4 HOH D 17 717 1 HOH HOH . 
P 4 HOH D 18 718 46 HOH HOH . 
P 4 HOH D 19 719 2 HOH HOH . 
P 4 HOH D 20 720 38 HOH HOH . 
P 4 HOH D 21 721 16 HOH HOH . 
P 4 HOH D 22 722 30 HOH HOH . 
P 4 HOH D 23 723 51 HOH HOH . 
P 4 HOH D 24 724 71 HOH HOH . 
P 4 HOH D 25 725 76 HOH HOH . 
P 4 HOH D 26 726 6 HOH HOH . 
P 4 HOH D 27 727 74 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 . . . E 2 -37.758 -8.255 29.612 1 45.12 ? N1 UMP 600 A 1 
HETATM 2 C C2 UMP . . . E 2 -36.858 -7.755 30.586 1 44.12 ? C2 UMP 600 A 1 
HETATM 3 N N3 UMP . . . E 2 -37.378 -6.875 31.536 1 46.45 ? N3 UMP 600 A 1 
HETATM 4 C C4 UMP . . . E 2 -38.703 -6.441 31.611 1 48.25 ? C4 UMP 600 A 1 
HETATM 5 C C5 UMP . . . E 2 -39.574 -6.988 30.578 1 48.6 ? C5 UMP 600 A 1 
HETATM 6 C C6 UMP . . . E 2 -39.082 -7.84 29.649 1 46.87 ? C6 UMP 600 A 1 
HETATM 7 O O2 UMP . . . E 2 -35.665 -8.056 30.635 1 42.08 ? O2 UMP 600 A 1 
HETATM 8 O O4 UMP . . . E 2 -39.053 -5.66 32.494 1 46.92 ? O4 UMP 600 A 1 
HETATM 9 C C1' UMP . . . E 2 -37.312 -9.215 28.526 1 43.51 ? C1' UMP 600 A 1 
HETATM 10 C C2' UMP . . . E 2 -36.827 -10.586 29.015 1 41.42 ? C2' UMP 600 A 1 
HETATM 11 C C3' UMP . . . E 2 -37.144 -11.431 27.79 1 43.57 ? C3' UMP 600 A 1 
HETATM 12 C C4' UMP . . . E 2 -38.444 -10.812 27.264 1 40.05 ? C4' UMP 600 A 1 
HETATM 13 O O3' UMP . . . E 2 -36.102 -11.361 26.837 1 41.77 ? O3' UMP 600 A 1 
HETATM 14 O O4' UMP . . . E 2 -38.407 -9.452 27.697 1 42.74 ? O4' UMP 600 A 1 
HETATM 15 C C5' UMP . . . E 2 -39.712 -11.502 27.798 1 42.8 ? C5' UMP 600 A 1 
HETATM 16 O O5' UMP . . . E 2 -39.974 -12.753 27.181 1 46.16 ? O5' UMP 600 A 1 
HETATM 17 P P UMP . . . E 2 -40.545 -14.038 28 1 46.12 ? P UMP 600 A 1 
HETATM 18 O OP1 UMP . . . E 2 -40.404 -15.225 26.905 1 51.96 -1 OP1 UMP 600 A 1 
HETATM 19 O OP2 UMP . . . E 2 -41.895 -13.881 28.612 1 45.85 ? OP2 UMP 600 A 1 
HETATM 20 O OP3 UMP . . . E 2 -39.33 -14.386 29.014 1 45.57 -1 OP3 UMP 600 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#