data_1SLH
#
_model_server_result.job_id            iUHBevgon1GhBOpD9SOtmg 
_model_server_result.datetime_utc      '2024-10-25 20:19:15' 
_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          1slh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":3170}' 
#
_entry.id    1SLH 
#
_exptl.entry_id    1SLH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              388.162 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "DEOXYURIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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         120 
_cell.entry_id            1SLH 
_cell.length_a            108.273 
_cell.length_b            108.273 
_cell.length_c            100.792 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1SLH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 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 trimeric 3 author_and_software_defined_assembly 1 
PISA hexameric 6 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,C,D,E,F,G,H,I,J,K,L,M,N 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N 2 1,2 
#
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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 67.194667 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 I N N 
? 3 K N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 E O2B DUD . A DUD 2170 1_555 J MG MG . C MG 2171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? 
metalc ? metalc2 E O1A DUD . A DUD 2170 1_555 J MG MG . C MG 2171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc3 D MG MG . A MG 3171 1_555 M O HOH . B HOH 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.731 ? 
metalc ? metalc4 D MG MG . A MG 3171 1_555 M O HOH . B HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? 
metalc ? metalc5 D MG MG . A MG 3171 1_555 I O1A DUD . B DUD 3170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc6 D MG MG . A MG 3171 1_555 I O2B DUD . B DUD 3170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc7 H MG MG . B MG 1171 1_555 K O3A DUD . C DUD 1170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.067 ? 
metalc ? metalc8 H MG MG . B MG 1171 1_555 K O1B DUD . C DUD 1170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? 
metalc ? metalc9 H MG MG . B MG 1171 1_555 K O1A DUD . C DUD 1170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? 
#
_chem_comp.formula           'C9 H14 N2 O11 P2' 
_chem_comp.formula_weight    388.162 
_chem_comp.id                DUD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "DEOXYURIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
N1 C2 DUD sing 70 n n 
N1 C6 DUD sing 71 n n 
N1 C1' DUD sing 72 n n 
C2 N3 DUD sing 73 n n 
C2 O2 DUD doub 74 n n 
N3 C4 DUD sing 75 n n 
N3 HN3 DUD sing 76 n n 
C4 C5 DUD sing 77 n n 
C4 O4 DUD doub 78 n n 
C5 C6 DUD doub 79 n n 
C5 H5 DUD sing 80 n n 
C6 H6 DUD sing 81 n n 
C1' C2' DUD sing 82 n n 
C1' O4' DUD sing 83 n n 
C1' H1' DUD sing 84 n n 
C2' C3' DUD sing 85 n n 
C2' "H2'1" DUD sing 86 n n 
C2' "H2'2" DUD sing 87 n n 
C3' C4' DUD sing 88 n n 
C3' O3' DUD sing 89 n n 
C3' H3' DUD sing 90 n n 
C4' O4' DUD sing 91 n n 
C4' C5' DUD sing 92 n n 
C4' H4' DUD sing 93 n n 
O3' HO3' DUD sing 94 n n 
C5' O5' DUD sing 95 n n 
C5' "H5'1" DUD sing 96 n n 
C5' "H5'2" DUD sing 97 n n 
O5' PA DUD sing 98 n n 
PA O1A DUD doub 99 n n 
PA O2A DUD sing 100 n n 
PA O3A DUD sing 101 n n 
O2A HOA2 DUD sing 102 n n 
O3A PB DUD sing 103 n n 
PB O1B DUD doub 104 n n 
PB O2B DUD sing 105 n n 
PB O3B DUD sing 106 n n 
O2B HOB2 DUD sing 107 n n 
O3B HOB3 DUD sing 108 n n 
#
_atom_sites.entry_id                     1SLH 
_atom_sites.fract_transf_matrix[1][1]    0.009236 
_atom_sites.fract_transf_matrix[1][2]    0.005332 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010665 
_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]    0.009921 
_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
D 2 MG A 1 3171 503 MG MG2 . 
E 3 DUD A 1 2170 170 DUD DUD . 
F 4 TRS A 1 504 504 TRS TRS . 
G 4 TRS A 1 505 505 TRS TRS . 
H 2 MG B 1 1171 501 MG MG2 . 
I 3 DUD B 1 3170 170 DUD DUD . 
J 2 MG C 1 2171 502 MG MG2 . 
K 3 DUD C 1 1170 170 DUD DUD . 
L 5 HOH A 1 506 506 HOH HOH . 
L 5 HOH A 2 507 507 HOH HOH . 
L 5 HOH A 3 509 509 HOH HOH . 
L 5 HOH A 4 514 514 HOH HOH . 
L 5 HOH A 5 515 515 HOH HOH . 
L 5 HOH A 6 516 516 HOH HOH . 
L 5 HOH A 7 517 517 HOH HOH . 
L 5 HOH A 8 524 524 HOH HOH . 
L 5 HOH A 9 526 526 HOH HOH . 
L 5 HOH A 10 528 528 HOH HOH . 
L 5 HOH A 11 531 531 HOH HOH . 
L 5 HOH A 12 533 533 HOH HOH . 
L 5 HOH A 13 534 534 HOH HOH . 
L 5 HOH A 14 541 541 HOH HOH . 
L 5 HOH A 15 544 544 HOH HOH . 
L 5 HOH A 16 545 545 HOH HOH . 
L 5 HOH A 17 548 548 HOH HOH . 
L 5 HOH A 18 549 549 HOH HOH . 
M 5 HOH B 1 512 512 HOH HOH . 
M 5 HOH B 2 520 520 HOH HOH . 
M 5 HOH B 3 522 522 HOH HOH . 
M 5 HOH B 4 523 523 HOH HOH . 
M 5 HOH B 5 530 530 HOH HOH . 
M 5 HOH B 6 535 535 HOH HOH . 
M 5 HOH B 7 536 536 HOH HOH . 
M 5 HOH B 8 540 540 HOH HOH . 
M 5 HOH B 9 542 542 HOH HOH . 
M 5 HOH B 10 543 543 HOH HOH . 
M 5 HOH B 11 547 547 HOH HOH . 
N 5 HOH C 1 508 508 HOH HOH . 
N 5 HOH C 2 510 510 HOH HOH . 
N 5 HOH C 3 513 513 HOH HOH . 
N 5 HOH C 4 519 519 HOH HOH . 
N 5 HOH C 5 521 521 HOH HOH . 
N 5 HOH C 6 525 525 HOH HOH . 
N 5 HOH C 7 527 527 HOH HOH . 
N 5 HOH C 8 529 529 HOH HOH . 
N 5 HOH C 9 537 537 HOH HOH . 
N 5 HOH C 10 539 539 HOH HOH . 
N 5 HOH C 11 550 550 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 DUD . . . I 3 53.807 22.33 21.769 1 33.92 ? N1 DUD 3170 B 1 
HETATM 2 C C2 DUD . . . I 3 53.016 22.544 20.613 1 35.99 ? C2 DUD 3170 B 1 
HETATM 3 N N3 DUD . . . I 3 53.644 22.171 19.392 1 35.95 ? N3 DUD 3170 B 1 
HETATM 4 C C4 DUD . . . I 3 54.983 21.688 19.227 1 35.11 ? C4 DUD 3170 B 1 
HETATM 5 C C5 DUD . . . I 3 55.718 21.512 20.46 1 34.06 ? C5 DUD 3170 B 1 
HETATM 6 C C6 DUD . . . I 3 55.131 21.859 21.628 1 33.78 ? C6 DUD 3170 B 1 
HETATM 7 O O2 DUD . . . I 3 51.835 22.955 20.653 1 37.13 ? O2 DUD 3170 B 1 
HETATM 8 O O4 DUD . . . I 3 55.443 21.405 18.129 1 34.83 ? O4 DUD 3170 B 1 
HETATM 9 C C1' DUD . . . I 3 53.236 22.687 23.116 1 32.14 ? C1' DUD 3170 B 1 
HETATM 10 C C2' DUD . . . I 3 52.746 21.432 23.792 1 31.65 ? C2' DUD 3170 B 1 
HETATM 11 C C3' DUD . . . I 3 53.68 21.124 24.942 1 31.43 ? C3' DUD 3170 B 1 
HETATM 12 C C4' DUD . . . I 3 54.369 22.435 25.13 1 31.17 ? C4' DUD 3170 B 1 
HETATM 13 O O4' DUD . . . I 3 54.198 23.276 23.983 1 31.47 ? O4' DUD 3170 B 1 
HETATM 14 O O3' DUD . . . I 3 52.953 20.719 26.124 1 31.81 ? O3' DUD 3170 B 1 
HETATM 15 C C5' DUD . . . I 3 55.827 22.066 25.218 1 31 ? C5' DUD 3170 B 1 
HETATM 16 O O5' DUD . . . I 3 56.669 23.12 25.357 1 28.2 ? O5' DUD 3170 B 1 
HETATM 17 P PA DUD . . . I 3 58.23 22.811 25.061 1 30.4 ? PA DUD 3170 B 1 
HETATM 18 O O1A DUD . . . I 3 58.948 22.236 26.226 1 31.71 ? O1A DUD 3170 B 1 
HETATM 19 O O2A DUD . . . I 3 58.452 22.201 23.692 1 31.63 ? O2A DUD 3170 B 1 
HETATM 20 O O3A DUD . . . I 3 58.592 24.369 25.064 1 31.88 ? O3A DUD 3170 B 1 
HETATM 21 P PB DUD . . . I 3 58.986 25.435 26.168 1 31.98 ? PB DUD 3170 B 1 
HETATM 22 O O1B DUD . . . I 3 60.273 26.002 25.745 1 30.32 ? O1B DUD 3170 B 1 
HETATM 23 O O2B DUD . . . I 3 59.038 24.755 27.445 1 31.13 ? O2B DUD 3170 B 1 
HETATM 24 O O3B DUD . . . I 3 57.862 26.412 26.083 1 30.67 ? O3B DUD 3170 B 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           24 
#