data_4KAT
#
_model_server_result.job_id            1jx1MCO3u1o7s-s6cAV01A 
_model_server_result.datetime_utc      '2024-11-23 05:31:42' 
_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          4kat 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":302}' 
#
_entry.id    4KAT 
#
_exptl.entry_id    4KAT 
_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            4KAT 
_cell.length_a            53.68 
_cell.length_b            115.74 
_cell.length_c            140.46 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KAT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,K,L,M,N,O,P 
_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 E N N 
? 2 G N N 
? 2 J N N 
? 2 L N N 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                DU 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'dna linking' 
_chem_comp.pdbx_synonyms     ? 
#
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
OP3 P DU sing 83 n n 
OP3 HOP3 DU sing 84 n n 
P OP1 DU doub 85 n n 
P OP2 DU sing 86 n n 
P O5' DU sing 87 n n 
OP2 HOP2 DU sing 88 n n 
O5' C5' DU sing 89 n n 
C5' C4' DU sing 90 n n 
C5' H5' DU sing 91 n n 
C5' "H5''" DU sing 92 n n 
C4' O4' DU sing 93 n n 
C4' C3' DU sing 94 n n 
C4' H4' DU sing 95 n n 
O4' C1' DU sing 96 n n 
C3' O3' DU sing 97 n n 
C3' C2' DU sing 98 n n 
C3' H3' DU sing 99 n n 
O3' HO3' DU sing 100 n n 
C2' C1' DU sing 101 n n 
C2' H2' DU sing 102 n n 
C2' "H2''" DU sing 103 n n 
C1' N1 DU sing 104 n n 
C1' H1' DU sing 105 n n 
N1 C2 DU sing 106 n n 
N1 C6 DU sing 107 n n 
C2 O2 DU doub 108 n n 
C2 N3 DU sing 109 n n 
N3 C4 DU sing 110 n n 
N3 H3 DU sing 111 n n 
C4 O4 DU doub 112 n n 
C4 C5 DU sing 113 n n 
C5 C6 DU doub 114 n n 
C5 H5 DU sing 115 n n 
C6 H6 DU sing 116 n n 
#
_atom_sites.entry_id                     4KAT 
_atom_sites.fract_transf_matrix[1][1]    0.018629 
_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]    0.00864 
_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]    0.007119 
_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 DU A 1 301 303 DU DDP . 
F 3 FDA A 1 302 315 FDA FDD . 
G 2 DU B 1 301 308 DU DDP . 
H 3 FDA B 1 302 310 FDA FDD . 
I 3 FDA C 1 301 305 FDA FDD . 
J 2 DU C 1 302 313 DU DDP . 
K 3 FDA D 1 301 300 FDA FDD . 
L 2 DU D 1 302 318 DU DDP . 
M 4 HOH A 1 401 5 HOH HOH . 
M 4 HOH A 2 402 12 HOH HOH . 
M 4 HOH A 3 403 18 HOH HOH . 
M 4 HOH A 4 404 19 HOH HOH . 
M 4 HOH A 5 405 20 HOH HOH . 
M 4 HOH A 6 406 24 HOH HOH . 
M 4 HOH A 7 407 26 HOH HOH . 
M 4 HOH A 8 408 29 HOH HOH . 
M 4 HOH A 9 409 30 HOH HOH . 
M 4 HOH A 10 410 37 HOH HOH . 
M 4 HOH A 11 411 39 HOH HOH . 
M 4 HOH A 12 412 49 HOH HOH . 
M 4 HOH A 13 413 53 HOH HOH . 
M 4 HOH A 14 414 59 HOH HOH . 
M 4 HOH A 15 415 63 HOH HOH . 
M 4 HOH A 16 416 67 HOH HOH . 
M 4 HOH A 17 417 68 HOH HOH . 
M 4 HOH A 18 418 71 HOH HOH . 
M 4 HOH A 19 419 76 HOH HOH . 
M 4 HOH A 20 420 77 HOH HOH . 
M 4 HOH A 21 421 79 HOH HOH . 
M 4 HOH A 22 422 81 HOH HOH . 
M 4 HOH A 23 423 82 HOH HOH . 
M 4 HOH A 24 424 85 HOH HOH . 
M 4 HOH A 25 425 89 HOH HOH . 
M 4 HOH A 26 426 93 HOH HOH . 
M 4 HOH A 27 427 95 HOH HOH . 
N 4 HOH B 1 401 8 HOH HOH . 
N 4 HOH B 2 402 17 HOH HOH . 
N 4 HOH B 3 403 21 HOH HOH . 
N 4 HOH B 4 404 23 HOH HOH . 
N 4 HOH B 5 405 31 HOH HOH . 
N 4 HOH B 6 406 33 HOH HOH . 
N 4 HOH B 7 407 34 HOH HOH . 
N 4 HOH B 8 408 36 HOH HOH . 
N 4 HOH B 9 409 41 HOH HOH . 
N 4 HOH B 10 410 45 HOH HOH . 
N 4 HOH B 11 411 46 HOH HOH . 
N 4 HOH B 12 412 51 HOH HOH . 
N 4 HOH B 13 413 52 HOH HOH . 
N 4 HOH B 14 414 55 HOH HOH . 
N 4 HOH B 15 415 62 HOH HOH . 
N 4 HOH B 16 416 83 HOH HOH . 
N 4 HOH B 17 417 88 HOH HOH . 
N 4 HOH B 18 418 96 HOH HOH . 
N 4 HOH B 19 419 98 HOH HOH . 
N 4 HOH B 20 420 100 HOH HOH . 
N 4 HOH B 21 421 102 HOH HOH . 
N 4 HOH B 22 422 103 HOH HOH . 
O 4 HOH C 1 401 7 HOH HOH . 
O 4 HOH C 2 402 2 HOH HOH . 
O 4 HOH C 3 403 4 HOH HOH . 
O 4 HOH C 4 404 9 HOH HOH . 
O 4 HOH C 5 405 10 HOH HOH . 
O 4 HOH C 6 406 11 HOH HOH . 
O 4 HOH C 7 407 13 HOH HOH . 
O 4 HOH C 8 408 14 HOH HOH . 
O 4 HOH C 9 409 15 HOH HOH . 
O 4 HOH C 10 410 16 HOH HOH . 
O 4 HOH C 11 411 22 HOH HOH . 
O 4 HOH C 12 412 25 HOH HOH . 
O 4 HOH C 13 413 27 HOH HOH . 
O 4 HOH C 14 414 35 HOH HOH . 
O 4 HOH C 15 415 42 HOH HOH . 
O 4 HOH C 16 416 43 HOH HOH . 
O 4 HOH C 17 417 56 HOH HOH . 
O 4 HOH C 18 418 57 HOH HOH . 
O 4 HOH C 19 419 60 HOH HOH . 
O 4 HOH C 20 420 61 HOH HOH . 
O 4 HOH C 21 421 64 HOH HOH . 
O 4 HOH C 22 422 65 HOH HOH . 
O 4 HOH C 23 423 69 HOH HOH . 
O 4 HOH C 24 424 70 HOH HOH . 
O 4 HOH C 25 425 78 HOH HOH . 
O 4 HOH C 26 426 80 HOH HOH . 
O 4 HOH C 27 427 87 HOH HOH . 
O 4 HOH C 28 428 90 HOH HOH . 
O 4 HOH C 29 429 91 HOH HOH . 
O 4 HOH C 30 430 92 HOH HOH . 
O 4 HOH C 31 431 94 HOH HOH . 
O 4 HOH C 32 432 97 HOH HOH . 
P 4 HOH D 1 401 1 HOH HOH . 
P 4 HOH D 2 402 3 HOH HOH . 
P 4 HOH D 3 403 6 HOH HOH . 
P 4 HOH D 4 404 28 HOH HOH . 
P 4 HOH D 5 405 32 HOH HOH . 
P 4 HOH D 6 406 38 HOH HOH . 
P 4 HOH D 7 407 40 HOH HOH . 
P 4 HOH D 8 408 44 HOH HOH . 
P 4 HOH D 9 409 47 HOH HOH . 
P 4 HOH D 10 410 48 HOH HOH . 
P 4 HOH D 11 411 50 HOH HOH . 
P 4 HOH D 12 412 54 HOH HOH . 
P 4 HOH D 13 413 58 HOH HOH . 
P 4 HOH D 14 414 66 HOH HOH . 
P 4 HOH D 15 415 72 HOH HOH . 
P 4 HOH D 16 416 73 HOH HOH . 
P 4 HOH D 17 417 74 HOH HOH . 
P 4 HOH D 18 418 75 HOH HOH . 
P 4 HOH D 19 419 84 HOH HOH . 
P 4 HOH D 20 420 86 HOH HOH . 
P 4 HOH D 21 421 99 HOH HOH . 
P 4 HOH D 22 422 101 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 O OP3 DU . . . L 2 25.074 50.759 134.857 1 50.6 ? OP3 DU 302 D 1 
HETATM 2 P P DU . . . L 2 24.457 51.022 133.518 1 51.7 ? P DU 302 D 1 
HETATM 3 O OP1 DU . . . L 2 24.661 52.452 133.066 1 47.37 ? OP1 DU 302 D 1 
HETATM 4 O OP2 DU . . . L 2 23.001 50.527 133.39 1 54.29 ? OP2 DU 302 D 1 
HETATM 5 O O5' DU . . . L 2 25.239 50.135 132.414 1 46.77 ? O5' DU 302 D 1 
HETATM 6 C C5' DU . . . L 2 25.456 48.717 132.545 1 45.98 ? C5' DU 302 D 1 
HETATM 7 C C4' DU . . . L 2 26.102 48.097 131.291 1 46.81 ? C4' DU 302 D 1 
HETATM 8 O O4' DU . . . L 2 25.164 48.206 130.211 1 46.76 ? O4' DU 302 D 1 
HETATM 9 C C3' DU . . . L 2 27.383 48.815 130.861 1 44.58 ? C3' DU 302 D 1 
HETATM 10 O O3' DU . . . L 2 28.286 47.891 130.232 1 51.96 ? O3' DU 302 D 1 
HETATM 11 C C2' DU . . . L 2 26.899 49.78 129.799 1 47.51 ? C2' DU 302 D 1 
HETATM 12 C C1' DU . . . L 2 25.644 49.105 129.218 1 52.42 ? C1' DU 302 D 1 
HETATM 13 N N1 DU . . . L 2 24.604 50.067 128.788 1 57.14 ? N1 DU 302 D 1 
HETATM 14 C C2 DU . . . L 2 24.65 50.512 127.434 1 58.5 ? C2 DU 302 D 1 
HETATM 15 O O2 DU . . . L 2 25.518 50.086 126.64 1 59.05 ? O2 DU 302 D 1 
HETATM 16 N N3 DU . . . L 2 23.744 51.387 126.953 1 67.32 ? N3 DU 302 D 1 
HETATM 17 C C4 DU . . . L 2 22.782 51.873 127.745 1 71.83 ? C4 DU 302 D 1 
HETATM 18 O O4 DU . . . L 2 21.986 52.68 127.202 1 77.92 ? O4 DU 302 D 1 
HETATM 19 C C5 DU . . . L 2 22.69 51.465 129.106 1 61.16 ? C5 DU 302 D 1 
HETATM 20 C C6 DU . . . L 2 23.634 50.546 129.618 1 62.35 ? C6 DU 302 D 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           247 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           20 
#