data_6PF3
#
_model_server_result.job_id            5uTiS6_Rdhn9J9AHANI-Ow 
_model_server_result.datetime_utc      '2024-11-27 02:55:35' 
_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          6pf3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":600}' 
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_entry.id    6PF3 
#
_exptl.entry_id    6PF3 
_exptl.method      'X-RAY DIFFRACTION' 
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_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          90.01 
_cell.angle_gamma         90 
_cell.entry_id            6PF3 
_cell.length_a            89.144 
_cell.length_b            89.322 
_cell.length_c            163.48 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PF3 
_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,C,E,F,I,J,M,O 1 1 
B,G,H,N 2 1,2 
D,K,L,P 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_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 89.144 0 0 
3 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 89.115467 0 163.479998 
#
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 408 n n 
N1 C6 UMP sing 409 n n 
N1 C1' UMP sing 410 n n 
C2 N3 UMP sing 411 n n 
C2 O2 UMP doub 412 n n 
N3 C4 UMP sing 413 n n 
N3 HN3 UMP sing 414 n n 
C4 C5 UMP sing 415 n n 
C4 O4 UMP doub 416 n n 
C5 C6 UMP doub 417 n n 
C5 H5 UMP sing 418 n n 
C6 H6 UMP sing 419 n n 
C1' C2' UMP sing 420 n n 
C1' O4' UMP sing 421 n n 
C1' H1' UMP sing 422 n n 
C2' C3' UMP sing 423 n n 
C2' H2' UMP sing 424 n n 
C2' "H2''" UMP sing 425 n n 
C3' C4' UMP sing 426 n n 
C3' O3' UMP sing 427 n n 
C3' H3' UMP sing 428 n n 
C4' O4' UMP sing 429 n n 
C4' C5' UMP sing 430 n n 
C4' H4' UMP sing 431 n n 
O3' HO3' UMP sing 432 n n 
C5' O5' UMP sing 433 n n 
C5' H5' UMP sing 434 n n 
C5' "H5''" UMP sing 435 n n 
O5' P UMP sing 436 n n 
P OP1 UMP doub 437 n n 
P OP2 UMP sing 438 n n 
P OP3 UMP sing 439 n n 
OP2 HOP2 UMP sing 440 n n 
OP3 HOP3 UMP sing 441 n n 
#
_atom_sites.entry_id                     6PF3 
_atom_sites.fract_transf_matrix[1][1]    0.011218 
_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]    0.011195 
_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]    0.006117 
_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 OE7 A 1 601 601 OE7 TS4 . 
G 2 UMP B 1 600 600 UMP UMP . 
H 3 OE7 B 1 601 601 OE7 TS4 . 
I 2 UMP C 1 600 600 UMP UMP . 
J 3 OE7 C 1 601 601 OE7 TS4 . 
K 2 UMP D 1 600 600 UMP UMP . 
L 3 OE7 D 1 601 601 OE7 TS4 . 
M 4 HOH A 1 701 45 HOH HOH . 
M 4 HOH A 2 702 36 HOH HOH . 
M 4 HOH A 3 703 47 HOH HOH . 
M 4 HOH A 4 704 15 HOH HOH . 
M 4 HOH A 5 705 6 HOH HOH . 
M 4 HOH A 6 706 17 HOH HOH . 
M 4 HOH A 7 707 32 HOH HOH . 
M 4 HOH A 8 708 24 HOH HOH . 
M 4 HOH A 9 709 20 HOH HOH . 
M 4 HOH A 10 710 43 HOH HOH . 
M 4 HOH A 11 711 50 HOH HOH . 
N 4 HOH B 1 701 19 HOH HOH . 
N 4 HOH B 2 702 8 HOH HOH . 
N 4 HOH B 3 703 40 HOH HOH . 
N 4 HOH B 4 704 44 HOH HOH . 
N 4 HOH B 5 705 23 HOH HOH . 
N 4 HOH B 6 706 29 HOH HOH . 
N 4 HOH B 7 707 48 HOH HOH . 
N 4 HOH B 8 708 14 HOH HOH . 
N 4 HOH B 9 709 41 HOH HOH . 
N 4 HOH B 10 710 52 HOH HOH . 
O 4 HOH C 1 701 13 HOH HOH . 
O 4 HOH C 2 702 27 HOH HOH . 
O 4 HOH C 3 703 46 HOH HOH . 
O 4 HOH C 4 704 9 HOH HOH . 
O 4 HOH C 5 705 5 HOH HOH . 
O 4 HOH C 6 706 2 HOH HOH . 
O 4 HOH C 7 707 38 HOH HOH . 
O 4 HOH C 8 708 18 HOH HOH . 
O 4 HOH C 9 709 21 HOH HOH . 
O 4 HOH C 10 710 37 HOH HOH . 
O 4 HOH C 11 711 22 HOH HOH . 
O 4 HOH C 12 712 42 HOH HOH . 
P 4 HOH D 1 701 12 HOH HOH . 
P 4 HOH D 2 702 7 HOH HOH . 
P 4 HOH D 3 703 51 HOH HOH . 
P 4 HOH D 4 704 11 HOH HOH . 
P 4 HOH D 5 705 39 HOH HOH . 
P 4 HOH D 6 706 1 HOH HOH . 
P 4 HOH D 7 707 10 HOH HOH . 
P 4 HOH D 8 708 28 HOH HOH . 
P 4 HOH D 9 709 25 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 . . . I 2 -4.643 25.323 54.688 1 60.29 ? N1 UMP 600 C 1 
HETATM 2 C C2 UMP . . . I 2 -5.65 25.764 53.8 1 57.96 ? C2 UMP 600 C 1 
HETATM 3 N N3 UMP . . . I 2 -5.26 26.654 52.797 1 59.03 ? N3 UMP 600 C 1 
HETATM 4 C C4 UMP . . . I 2 -3.966 27.147 52.602 1 59.14 ? C4 UMP 600 C 1 
HETATM 5 C C5 UMP . . . I 2 -2.981 26.654 53.552 1 58.91 ? C5 UMP 600 C 1 
HETATM 6 C C6 UMP . . . I 2 -3.35 25.8 54.531 1 61.54 ? C6 UMP 600 C 1 
HETATM 7 O O2 UMP . . . I 2 -6.823 25.398 53.874 1 56.26 ? O2 UMP 600 C 1 
HETATM 8 O O4 UMP . . . I 2 -3.726 27.931 51.687 1 58.8 ? O4 UMP 600 C 1 
HETATM 9 C C1' UMP . . . I 2 -4.959 24.365 55.817 1 60.02 ? C1' UMP 600 C 1 
HETATM 10 C C2' UMP . . . I 2 -5.377 22.957 55.381 1 56.06 ? C2' UMP 600 C 1 
HETATM 11 C C3' UMP . . . I 2 -5.035 22.192 56.653 1 58.45 ? C3' UMP 600 C 1 
HETATM 12 C C4' UMP . . . I 2 -3.782 22.909 57.183 1 59.56 ? C4' UMP 600 C 1 
HETATM 13 O O3' UMP . . . I 2 -6.099 22.226 57.587 1 56.87 ? O3' UMP 600 C 1 
HETATM 14 O O4' UMP . . . I 2 -3.82 24.213 56.604 1 64.29 ? O4' UMP 600 C 1 
HETATM 15 C C5' UMP . . . I 2 -2.465 22.204 56.807 1 58.07 ? C5' UMP 600 C 1 
HETATM 16 O O5' UMP . . . I 2 -2.373 20.903 57.362 1 58.51 ? O5' UMP 600 C 1 
HETATM 17 P P UMP . . . I 2 -1.746 19.619 56.586 1 57.7 ? P UMP 600 C 1 
HETATM 18 O OP1 UMP . . . I 2 -0.542 19.869 55.745 1 60.13 ? OP1 UMP 600 C 1 
HETATM 19 O OP2 UMP . . . I 2 -1.53 18.563 57.796 1 63.15 -1 OP2 UMP 600 C 1 
HETATM 20 O OP3 UMP . . . I 2 -3.057 19.007 55.855 1 54.49 -1 OP3 UMP 600 C 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           20 
#