data_7XYJ
#
_model_server_result.job_id            Gfk7DGfraY0KKKnW0i-Ffw 
_model_server_result.datetime_utc      '2024-11-23 19:21:35' 
_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          7xyj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":301}' 
#
_entry.id    7XYJ 
#
_exptl.entry_id    7XYJ 
_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         90 
_cell.entry_id            7XYJ 
_cell.length_a            54.91 
_cell.length_b            132.35 
_cell.length_c            234.11 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7XYJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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,I,T,U 1 1 
C,D,J,K,L,M,N,O,P,Q,R,S,V,W 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 H N N 
? 2 J N N 
? 2 Q 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 431 n n 
N1 C6 UMP sing 432 n n 
N1 C1' UMP sing 433 n n 
C2 N3 UMP sing 434 n n 
C2 O2 UMP doub 435 n n 
N3 C4 UMP sing 436 n n 
N3 HN3 UMP sing 437 n n 
C4 C5 UMP sing 438 n n 
C4 O4 UMP doub 439 n n 
C5 C6 UMP doub 440 n n 
C5 H5 UMP sing 441 n n 
C6 H6 UMP sing 442 n n 
C1' C2' UMP sing 443 n n 
C1' O4' UMP sing 444 n n 
C1' H1' UMP sing 445 n n 
C2' C3' UMP sing 446 n n 
C2' H2' UMP sing 447 n n 
C2' "H2''" UMP sing 448 n n 
C3' C4' UMP sing 449 n n 
C3' O3' UMP sing 450 n n 
C3' H3' UMP sing 451 n n 
C4' O4' UMP sing 452 n n 
C4' C5' UMP sing 453 n n 
C4' H4' UMP sing 454 n n 
O3' HO3' UMP sing 455 n n 
C5' O5' UMP sing 456 n n 
C5' H5' UMP sing 457 n n 
C5' "H5''" UMP sing 458 n n 
O5' P UMP sing 459 n n 
P OP1 UMP doub 460 n n 
P OP2 UMP sing 461 n n 
P OP3 UMP sing 462 n n 
OP2 HOP2 UMP sing 463 n n 
OP3 HOP3 UMP sing 464 n n 
#
_atom_sites.entry_id                     7XYJ 
_atom_sites.fract_transf_matrix[1][1]    0.018212 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007556 
_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]    0.004271 
_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 1 301 301 UMP UMP . 
F 3 1PE A 1 302 302 1PE 1PE . 
G 4 SO4 A 1 303 303 SO4 SO4 . 
H 2 UMP B 1 301 301 UMP UMP . 
I 3 1PE B 1 302 302 1PE 1PE . 
J 2 UMP C 1 301 301 UMP UMP . 
K 3 1PE C 1 302 302 1PE 1PE . 
L 5 BTB C 1 303 303 BTB BTB . 
M 4 SO4 C 1 304 304 SO4 SO4 . 
N 4 SO4 C 1 305 305 SO4 SO4 . 
O 4 SO4 C 1 306 306 SO4 SO4 . 
P 4 SO4 C 1 307 304 SO4 SO4 . 
Q 2 UMP D 1 301 301 UMP UMP . 
R 3 1PE D 1 302 302 1PE 1PE . 
S 5 BTB D 1 303 303 BTB BTB . 
T 6 HOH A 1 401 169 HOH HOH . 
T 6 HOH A 2 402 22 HOH HOH . 
T 6 HOH A 3 403 12 HOH HOH . 
T 6 HOH A 4 404 88 HOH HOH . 
T 6 HOH A 5 405 36 HOH HOH . 
T 6 HOH A 6 406 90 HOH HOH . 
T 6 HOH A 7 407 185 HOH HOH . 
T 6 HOH A 8 408 23 HOH HOH . 
T 6 HOH A 9 409 126 HOH HOH . 
T 6 HOH A 10 410 59 HOH HOH . 
T 6 HOH A 11 411 53 HOH HOH . 
T 6 HOH A 12 412 130 HOH HOH . 
T 6 HOH A 13 413 81 HOH HOH . 
T 6 HOH A 14 414 119 HOH HOH . 
T 6 HOH A 15 415 167 HOH HOH . 
T 6 HOH A 16 416 107 HOH HOH . 
T 6 HOH A 17 417 137 HOH HOH . 
T 6 HOH A 18 418 138 HOH HOH . 
T 6 HOH A 19 419 62 HOH HOH . 
T 6 HOH A 20 420 5 HOH HOH . 
T 6 HOH A 21 421 60 HOH HOH . 
T 6 HOH A 22 422 162 HOH HOH . 
T 6 HOH A 23 423 129 HOH HOH . 
T 6 HOH A 24 424 184 HOH HOH . 
T 6 HOH A 25 425 47 HOH HOH . 
T 6 HOH A 26 426 21 HOH HOH . 
T 6 HOH A 27 427 154 HOH HOH . 
T 6 HOH A 28 428 149 HOH HOH . 
T 6 HOH A 29 429 170 HOH HOH . 
T 6 HOH A 30 430 69 HOH HOH . 
T 6 HOH A 31 431 133 HOH HOH . 
T 6 HOH A 32 432 93 HOH HOH . 
T 6 HOH A 33 433 152 HOH HOH . 
T 6 HOH A 34 434 168 HOH HOH . 
T 6 HOH A 35 435 102 HOH HOH . 
U 6 HOH B 1 401 34 HOH HOH . 
U 6 HOH B 2 402 141 HOH HOH . 
U 6 HOH B 3 403 37 HOH HOH . 
U 6 HOH B 4 404 10 HOH HOH . 
U 6 HOH B 5 405 72 HOH HOH . 
U 6 HOH B 6 406 2 HOH HOH . 
U 6 HOH B 7 407 114 HOH HOH . 
U 6 HOH B 8 408 193 HOH HOH . 
U 6 HOH B 9 409 71 HOH HOH . 
U 6 HOH B 10 410 38 HOH HOH . 
U 6 HOH B 11 411 139 HOH HOH . 
U 6 HOH B 12 412 131 HOH HOH . 
U 6 HOH B 13 413 123 HOH HOH . 
U 6 HOH B 14 414 29 HOH HOH . 
U 6 HOH B 15 415 32 HOH HOH . 
U 6 HOH B 16 416 26 HOH HOH . 
U 6 HOH B 17 417 164 HOH HOH . 
U 6 HOH B 18 418 174 HOH HOH . 
U 6 HOH B 19 419 118 HOH HOH . 
U 6 HOH B 20 420 159 HOH HOH . 
U 6 HOH B 21 421 35 HOH HOH . 
U 6 HOH B 22 422 43 HOH HOH . 
U 6 HOH B 23 423 1 HOH HOH . 
U 6 HOH B 24 424 177 HOH HOH . 
U 6 HOH B 25 425 142 HOH HOH . 
U 6 HOH B 26 426 161 HOH HOH . 
U 6 HOH B 27 427 150 HOH HOH . 
U 6 HOH B 28 428 111 HOH HOH . 
U 6 HOH B 29 429 191 HOH HOH . 
U 6 HOH B 30 430 27 HOH HOH . 
U 6 HOH B 31 431 9 HOH HOH . 
U 6 HOH B 32 432 86 HOH HOH . 
U 6 HOH B 33 433 144 HOH HOH . 
U 6 HOH B 34 434 79 HOH HOH . 
U 6 HOH B 35 435 112 HOH HOH . 
U 6 HOH B 36 436 187 HOH HOH . 
U 6 HOH B 37 437 146 HOH HOH . 
U 6 HOH B 38 438 63 HOH HOH . 
U 6 HOH B 39 439 163 HOH HOH . 
U 6 HOH B 40 440 160 HOH HOH . 
U 6 HOH B 41 441 153 HOH HOH . 
U 6 HOH B 42 442 97 HOH HOH . 
U 6 HOH B 43 443 44 HOH HOH . 
U 6 HOH B 44 444 135 HOH HOH . 
U 6 HOH B 45 445 140 HOH HOH . 
U 6 HOH B 46 446 28 HOH HOH . 
U 6 HOH B 47 447 165 HOH HOH . 
U 6 HOH B 48 448 156 HOH HOH . 
U 6 HOH B 49 449 124 HOH HOH . 
U 6 HOH B 50 450 74 HOH HOH . 
U 6 HOH B 51 451 76 HOH HOH . 
U 6 HOH B 52 452 103 HOH HOH . 
U 6 HOH B 53 453 173 HOH HOH . 
U 6 HOH B 54 454 73 HOH HOH . 
U 6 HOH B 55 455 178 HOH HOH . 
U 6 HOH B 56 456 109 HOH HOH . 
U 6 HOH B 57 457 58 HOH HOH . 
V 6 HOH C 1 401 17 HOH HOH . 
V 6 HOH C 2 402 75 HOH HOH . 
V 6 HOH C 3 403 40 HOH HOH . 
V 6 HOH C 4 404 84 HOH HOH . 
V 6 HOH C 5 405 20 HOH HOH . 
V 6 HOH C 6 406 66 HOH HOH . 
V 6 HOH C 7 407 95 HOH HOH . 
V 6 HOH C 8 408 18 HOH HOH . 
V 6 HOH C 9 409 145 HOH HOH . 
V 6 HOH C 10 410 91 HOH HOH . 
V 6 HOH C 11 411 68 HOH HOH . 
V 6 HOH C 12 412 19 HOH HOH . 
V 6 HOH C 13 413 190 HOH HOH . 
V 6 HOH C 14 414 188 HOH HOH . 
V 6 HOH C 15 415 186 HOH HOH . 
V 6 HOH C 16 416 33 HOH HOH . 
V 6 HOH C 17 417 77 HOH HOH . 
V 6 HOH C 18 418 8 HOH HOH . 
V 6 HOH C 19 419 104 HOH HOH . 
V 6 HOH C 20 420 166 HOH HOH . 
V 6 HOH C 21 421 101 HOH HOH . 
V 6 HOH C 22 422 182 HOH HOH . 
V 6 HOH C 23 423 113 HOH HOH . 
V 6 HOH C 24 424 7 HOH HOH . 
V 6 HOH C 25 425 155 HOH HOH . 
V 6 HOH C 26 426 31 HOH HOH . 
V 6 HOH C 27 427 78 HOH HOH . 
V 6 HOH C 28 428 143 HOH HOH . 
V 6 HOH C 29 429 67 HOH HOH . 
V 6 HOH C 30 430 157 HOH HOH . 
V 6 HOH C 31 431 51 HOH HOH . 
V 6 HOH C 32 432 183 HOH HOH . 
V 6 HOH C 33 433 106 HOH HOH . 
V 6 HOH C 34 434 127 HOH HOH . 
V 6 HOH C 35 435 110 HOH HOH . 
V 6 HOH C 36 436 181 HOH HOH . 
V 6 HOH C 37 437 147 HOH HOH . 
V 6 HOH C 38 438 158 HOH HOH . 
V 6 HOH C 39 439 49 HOH HOH . 
V 6 HOH C 40 440 176 HOH HOH . 
W 6 HOH D 1 401 172 HOH HOH . 
W 6 HOH D 2 402 115 HOH HOH . 
W 6 HOH D 3 403 25 HOH HOH . 
W 6 HOH D 4 404 3 HOH HOH . 
W 6 HOH D 5 405 13 HOH HOH . 
W 6 HOH D 6 406 4 HOH HOH . 
W 6 HOH D 7 407 39 HOH HOH . 
W 6 HOH D 8 408 56 HOH HOH . 
W 6 HOH D 9 409 189 HOH HOH . 
W 6 HOH D 10 410 48 HOH HOH . 
W 6 HOH D 11 411 57 HOH HOH . 
W 6 HOH D 12 412 50 HOH HOH . 
W 6 HOH D 13 413 42 HOH HOH . 
W 6 HOH D 14 414 6 HOH HOH . 
W 6 HOH D 15 415 96 HOH HOH . 
W 6 HOH D 16 416 30 HOH HOH . 
W 6 HOH D 17 417 15 HOH HOH . 
W 6 HOH D 18 418 61 HOH HOH . 
W 6 HOH D 19 419 87 HOH HOH . 
W 6 HOH D 20 420 194 HOH HOH . 
W 6 HOH D 21 421 148 HOH HOH . 
W 6 HOH D 22 422 100 HOH HOH . 
W 6 HOH D 23 423 151 HOH HOH . 
W 6 HOH D 24 424 54 HOH HOH . 
W 6 HOH D 25 425 92 HOH HOH . 
W 6 HOH D 26 426 70 HOH HOH . 
W 6 HOH D 27 427 98 HOH HOH . 
W 6 HOH D 28 428 11 HOH HOH . 
W 6 HOH D 29 429 120 HOH HOH . 
W 6 HOH D 30 430 80 HOH HOH . 
W 6 HOH D 31 431 89 HOH HOH . 
W 6 HOH D 32 432 16 HOH HOH . 
W 6 HOH D 33 433 65 HOH HOH . 
W 6 HOH D 34 434 99 HOH HOH . 
W 6 HOH D 35 435 82 HOH HOH . 
W 6 HOH D 36 436 116 HOH HOH . 
W 6 HOH D 37 437 132 HOH HOH . 
W 6 HOH D 38 438 24 HOH HOH . 
W 6 HOH D 39 439 179 HOH HOH . 
W 6 HOH D 40 440 121 HOH HOH . 
W 6 HOH D 41 441 128 HOH HOH . 
W 6 HOH D 42 442 41 HOH HOH . 
W 6 HOH D 43 443 64 HOH HOH . 
W 6 HOH D 44 444 14 HOH HOH . 
W 6 HOH D 45 445 94 HOH HOH . 
W 6 HOH D 46 446 85 HOH HOH . 
W 6 HOH D 47 447 105 HOH HOH . 
W 6 HOH D 48 448 122 HOH HOH . 
W 6 HOH D 49 449 55 HOH HOH . 
W 6 HOH D 50 450 125 HOH HOH . 
W 6 HOH D 51 451 108 HOH HOH . 
W 6 HOH D 52 452 52 HOH HOH . 
W 6 HOH D 53 453 46 HOH HOH . 
W 6 HOH D 54 454 171 HOH HOH . 
W 6 HOH D 55 455 134 HOH HOH . 
W 6 HOH D 56 456 192 HOH HOH . 
W 6 HOH D 57 457 136 HOH HOH . 
W 6 HOH D 58 458 180 HOH HOH . 
W 6 HOH D 59 459 83 HOH HOH . 
W 6 HOH D 60 460 117 HOH HOH . 
W 6 HOH D 61 461 45 HOH HOH . 
W 6 HOH D 62 462 175 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 . . . H 2 3.051 46.255 19.702 1 47.59 ? N1 UMP 301 B 1 
HETATM 2 C C2 UMP . . . H 2 4.021 45.278 19.534 1 43.29 ? C2 UMP 301 B 1 
HETATM 3 N N3 UMP . . . H 2 5.276 45.748 19.219 1 44.24 ? N3 UMP 301 B 1 
HETATM 4 C C4 UMP . . . H 2 5.647 47.072 19.03 1 47.45 ? C4 UMP 301 B 1 
HETATM 5 C C5 UMP . . . H 2 4.587 48.031 19.201 1 49.74 ? C5 UMP 301 B 1 
HETATM 6 C C6 UMP . . . H 2 3.352 47.608 19.535 1 49.44 ? C6 UMP 301 B 1 
HETATM 7 O O2 UMP . . . H 2 3.791 44.083 19.639 1 43.19 ? O2 UMP 301 B 1 
HETATM 8 O O4 UMP . . . H 2 6.81 47.339 18.705 1 47.26 ? O4 UMP 301 B 1 
HETATM 9 C C1' UMP . . . H 2 1.666 45.822 20.013 1 46.06 ? C1' UMP 301 B 1 
HETATM 10 C C2' UMP . . . H 2 1.44 45.411 21.466 1 44.65 ? C2' UMP 301 B 1 
HETATM 11 C C3' UMP . . . H 2 -0.025 45.771 21.669 1 45.79 ? C3' UMP 301 B 1 
HETATM 12 C C4' UMP . . . H 2 -0.162 47.052 20.851 1 49.78 ? C4' UMP 301 B 1 
HETATM 13 O O3' UMP . . . H 2 -0.863 44.777 21.084 1 45.36 ? O3' UMP 301 B 1 
HETATM 14 O O4' UMP . . . H 2 0.797 46.926 19.773 1 49.66 ? O4' UMP 301 B 1 
HETATM 15 C C5' UMP . . . H 2 0.083 48.33 21.62 1 48.8 ? C5' UMP 301 B 1 
HETATM 16 O O5' UMP . . . H 2 -0.987 48.478 22.572 1 50.47 ? O5' UMP 301 B 1 
HETATM 17 P P UMP . . . H 2 -0.801 48.95 24.097 1 50.82 ? P UMP 301 B 1 
HETATM 18 O OP1 UMP . . . H 2 -2.165 49.026 24.704 1 51.1 ? OP1 UMP 301 B 1 
HETATM 19 O OP2 UMP . . . H 2 0.124 47.93 24.759 1 45.98 ? OP2 UMP 301 B 1 
HETATM 20 O OP3 UMP . . . H 2 -0.085 50.309 24.081 1 49.18 ? OP3 UMP 301 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#