data_4LIL
#
_model_server_result.job_id            vzOn9GTNcmW2KkJFoeQ0Xg 
_model_server_result.datetime_utc      '2024-10-28 02:24:49' 
_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          4lil 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":504}' 
#
_entry.id    4LIL 
#
_exptl.entry_id    4LIL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              484.141 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE 5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            4LIL 
_cell.length_a            79.346 
_cell.length_b            79.346 
_cell.length_c            148.2 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4LIL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 A OD1 ASP 113 A ASP 109 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? 
metalc ? metalc2 A OD2 ASP 113 A ASP 109 1_555 D MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? 
metalc ? metalc3 A SG CYS 125 A CYS 121 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc4 A SG CYS 126 A CYS 122 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
metalc ? metalc5 A SG CYS 132 A CYS 128 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc6 A SG CYS 135 A CYS 131 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc7 C MN MN . A MN 502 1_555 E O1B UTP . A UTP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc8 C MN MN . A MN 502 1_555 E O2G UTP . A UTP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? 
metalc ? metalc9 C MN MN . A MN 502 1_555 E O1A UTP . A UTP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? 
#
_chem_comp.formula           'C9 H15 N2 O15 P3' 
_chem_comp.formula_weight    484.141 
_chem_comp.id                UTP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE 5'-TRIPHOSPHATE" 
_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
PA O1A UTP doub 358 n n 
PA O2A UTP sing 359 n n 
PA O3A UTP sing 360 n n 
PA O5' UTP sing 361 n n 
O2A H2A UTP sing 362 n n 
O3A PB UTP sing 363 n n 
O5' C5' UTP sing 364 n n 
PB O1B UTP sing 365 n n 
PB O2B UTP doub 366 n n 
PB O3B UTP sing 367 n n 
O1B H1B UTP sing 368 n n 
O3B PG UTP sing 369 n n 
PG O1G UTP sing 370 n n 
PG O2G UTP doub 371 n n 
PG O3G UTP sing 372 n n 
O1G H1G UTP sing 373 n n 
O3G H3G UTP sing 374 n n 
C5' C4' UTP sing 375 n n 
C5' "H5'1" UTP sing 376 n n 
C5' "H5'2" UTP sing 377 n n 
C4' O4' UTP sing 378 n n 
C4' C3' UTP sing 379 n n 
C4' H4' UTP sing 380 n n 
O4' C1' UTP sing 381 n n 
C1' C2' UTP sing 382 n n 
C1' N1 UTP sing 383 n n 
C1' H1' UTP sing 384 n n 
C2' O2' UTP sing 385 n n 
C2' C3' UTP sing 386 n n 
C2' H2' UTP sing 387 n n 
O2' HA UTP sing 388 n n 
C3' O3' UTP sing 389 n n 
C3' H3' UTP sing 390 n n 
O3' HB UTP sing 391 n n 
N1 C6 UTP sing 392 n y 
N1 C2 UTP sing 393 n y 
C6 C5 UTP doub 394 n y 
C6 H6 UTP sing 395 n n 
C2 O2 UTP doub 396 n n 
C2 N3 UTP sing 397 n y 
N3 C4 UTP sing 398 n y 
N3 H3 UTP sing 399 n n 
C4 O4 UTP doub 400 n n 
C4 C5 UTP sing 401 n y 
C5 H5 UTP sing 402 n n 
#
_atom_sites.entry_id                     4LIL 
_atom_sites.fract_transf_matrix[1][1]    0.012603 
_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]    0.012603 
_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]    0.006748 
_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
B 2 ZN A 1 501 501 ZN ZN . 
C 3 MN A 1 502 502 MN MN . 
D 3 MN A 1 503 503 MN MN . 
E 4 UTP A 1 504 504 UTP UTP . 
F 5 HOH A 1 601 601 HOH HOH . 
F 5 HOH A 2 602 602 HOH HOH . 
F 5 HOH A 3 603 603 HOH HOH . 
F 5 HOH A 4 604 604 HOH HOH . 
F 5 HOH A 5 605 605 HOH HOH . 
F 5 HOH A 6 606 606 HOH HOH . 
F 5 HOH A 7 607 607 HOH HOH . 
F 5 HOH A 8 608 608 HOH HOH . 
F 5 HOH A 9 609 609 HOH HOH . 
F 5 HOH A 10 610 610 HOH HOH . 
F 5 HOH A 11 611 611 HOH HOH . 
F 5 HOH A 12 612 612 HOH HOH . 
F 5 HOH A 13 613 613 HOH HOH . 
F 5 HOH A 14 614 614 HOH HOH . 
F 5 HOH A 15 615 615 HOH HOH . 
F 5 HOH A 16 616 616 HOH HOH . 
F 5 HOH A 17 617 617 HOH HOH . 
F 5 HOH A 18 618 618 HOH HOH . 
F 5 HOH A 19 619 619 HOH HOH . 
F 5 HOH A 20 620 620 HOH HOH . 
F 5 HOH A 21 621 622 HOH HOH . 
F 5 HOH A 22 622 623 HOH HOH . 
F 5 HOH A 23 623 624 HOH HOH . 
F 5 HOH A 24 624 625 HOH HOH . 
F 5 HOH A 25 625 626 HOH HOH . 
F 5 HOH A 26 626 627 HOH HOH . 
F 5 HOH A 27 627 628 HOH HOH . 
F 5 HOH A 28 628 629 HOH HOH . 
F 5 HOH A 29 629 630 HOH HOH . 
F 5 HOH A 30 630 631 HOH HOH . 
F 5 HOH A 31 631 632 HOH HOH . 
F 5 HOH A 32 632 633 HOH HOH . 
F 5 HOH A 33 633 634 HOH HOH . 
F 5 HOH A 34 634 635 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 P PA UTP . . . E 4 13.392 57.898 5.887 0.38 57.68 ? PA UTP 504 A 1 
HETATM 2 O O1A UTP . . . E 4 13.769 57.084 7.077 0.87 56.83 1 O1A UTP 504 A 1 
HETATM 3 O O2A UTP . . . E 4 12.47 57.081 4.949 0.87 55.64 ? O2A UTP 504 A 1 
HETATM 4 O O3A UTP . . . E 4 12.624 59.177 6.342 0.48 55.65 ? O3A UTP 504 A 1 
HETATM 5 O O5' UTP . . . E 4 14.704 58.275 5.112 1 56.64 ? O5' UTP 504 A 1 
HETATM 6 P PB UTP . . . E 4 12.45 59.615 7.854 0.99 56.91 ? PB UTP 504 A 1 
HETATM 7 O O1B UTP . . . E 4 13.338 58.74 8.739 0.43 58.91 1 O1B UTP 504 A 1 
HETATM 8 O O2B UTP . . . E 4 12.906 60.996 7.982 0.08 61.38 ? O2B UTP 504 A 1 
HETATM 9 O O3B UTP . . . E 4 10.925 59.538 8.312 0.54 56.96 ? O3B UTP 504 A 1 
HETATM 10 P PG UTP . . . E 4 10.082 58.254 8.663 0.65 54.02 ? PG UTP 504 A 1 
HETATM 11 O O1G UTP . . . E 4 9.428 58.395 10.064 1 49.18 1 O1G UTP 504 A 1 
HETATM 12 O O2G UTP . . . E 4 10.993 57.025 8.65 0.7 54.93 1 O2G UTP 504 A 1 
HETATM 13 O O3G UTP . . . E 4 8.961 58.063 7.669 0.98 56.98 ? O3G UTP 504 A 1 
#
_model_server_stats.io_time_ms              70 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           13 
#