data_5U03
#
_model_server_result.job_id            dXFbQYbjOiNpz9TWqCcj0w 
_model_server_result.datetime_utc      '2024-11-24 03:14:24' 
_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          5u03 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":602}' 
#
_entry.id    5U03 
#
_exptl.entry_id    5U03 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              484.141 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE 5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? hexadecameric 16 'representative helical assembly' 1 
? tetrameric 4 'helical asymmetric unit' 2 
? tetrameric 4 'helical asymmetric unit, std helical frame' 3 
#
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 1 (1-4) 
A,B,C,D,E,F,G,H,I,J,K,L 2 3 
A,B,C,D,E,F,G,H,I,J,K,L 3 H 
#
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]
H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
1 'helical symmetry operation' ? ? -0.518027 0.855364 0 -0.855364 -0.518027 0 0 0 1 0 0 -208.2 
2 'helical symmetry operation' ? ? 0.490904 0.871214 0 -0.871214 0.490904 0 0 0 1 0 0 -104.1 
3 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
4 'helical symmetry operation' ? ? 0.490904 -0.871214 0 0.871214 0.490904 0 0 0 1 0 0 104.1 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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
disulf ? disulf1 A SG CYS 218 A CYS 218 1_555 A SG CYS 243 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
disulf ? disulf2 B SG CYS 218 B CYS 218 1_555 B SG CYS 243 B CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
disulf ? disulf3 C SG CYS 218 C CYS 218 1_555 C SG CYS 243 C CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
disulf ? disulf4 D SG CYS 218 D CYS 218 1_555 D SG CYS 243 D CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
#
_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 405 n n 
PA O2A UTP sing 406 n n 
PA O3A UTP sing 407 n n 
PA O5' UTP sing 408 n n 
O2A H2A UTP sing 409 n n 
O3A PB UTP sing 410 n n 
O5' C5' UTP sing 411 n n 
PB O1B UTP sing 412 n n 
PB O2B UTP doub 413 n n 
PB O3B UTP sing 414 n n 
O1B H1B UTP sing 415 n n 
O3B PG UTP sing 416 n n 
PG O1G UTP sing 417 n n 
PG O2G UTP doub 418 n n 
PG O3G UTP sing 419 n n 
O1G H1G UTP sing 420 n n 
O3G H3G UTP sing 421 n n 
C5' C4' UTP sing 422 n n 
C5' "H5'1" UTP sing 423 n n 
C5' "H5'2" UTP sing 424 n n 
C4' O4' UTP sing 425 n n 
C4' C3' UTP sing 426 n n 
C4' H4' UTP sing 427 n n 
O4' C1' UTP sing 428 n n 
C1' C2' UTP sing 429 n n 
C1' N1 UTP sing 430 n n 
C1' H1' UTP sing 431 n n 
C2' O2' UTP sing 432 n n 
C2' C3' UTP sing 433 n n 
C2' H2' UTP sing 434 n n 
O2' HA UTP sing 435 n n 
C3' O3' UTP sing 436 n n 
C3' H3' UTP sing 437 n n 
O3' HB UTP sing 438 n n 
N1 C6 UTP sing 439 n y 
N1 C2 UTP sing 440 n y 
C6 C5 UTP doub 441 n y 
C6 H6 UTP sing 442 n n 
C2 O2 UTP doub 443 n n 
C2 N3 UTP sing 444 n y 
N3 C4 UTP sing 445 n y 
N3 H3 UTP sing 446 n n 
C4 O4 UTP doub 447 n n 
C4 C5 UTP sing 448 n y 
C5 H5 UTP sing 449 n n 
#
_atom_sites.entry_id                     5U03 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 ATP A 1 601 602 ATP ATP . 
F 3 UTP A 1 602 603 UTP UTP . 
G 2 ATP B 1 601 602 ATP ATP . 
H 3 UTP B 1 602 603 UTP UTP . 
I 2 ATP C 1 601 602 ATP ATP . 
J 3 UTP C 1 602 603 UTP UTP . 
K 2 ATP D 1 601 602 ATP ATP . 
L 3 UTP D 1 602 603 UTP UTP . 
#
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 . . . F 3 -13.311 -0.343 3.261 1 214.64 ? PA UTP 602 A 1 
HETATM 2 O O1A UTP . . . F 3 -14.29 0.093 2.166 1 214.94 ? O1A UTP 602 A 1 
HETATM 3 O O2A UTP . . . F 3 -12.162 -1.06 2.654 1 214.14 ? O2A UTP 602 A 1 
HETATM 4 O O3A UTP . . . F 3 -12.792 0.955 4.029 1 215.59 ? O3A UTP 602 A 1 
HETATM 5 O O5' UTP . . . F 3 -14.11 -1.219 4.329 1 213.58 ? O5' UTP 602 A 1 
HETATM 6 P PB UTP . . . F 3 -12.968 2.515 3.761 1 216.6 ? PB UTP 602 A 1 
HETATM 7 O O1B UTP . . . F 3 -12.746 3.265 5.02 1 217.18 ? O1B UTP 602 A 1 
HETATM 8 O O2B UTP . . . F 3 -14.378 2.773 3.23 1 217.03 ? O2B UTP 602 A 1 
HETATM 9 O O3B UTP . . . F 3 -11.913 2.942 2.644 1 216.53 ? O3B UTP 602 A 1 
HETATM 10 P PG UTP . . . F 3 -11.416 2.251 1.295 1 215.54 ? PG UTP 602 A 1 
HETATM 11 O O1G UTP . . . F 3 -11.508 0.741 1.522 1 215.11 ? O1G UTP 602 A 1 
HETATM 12 O O2G UTP . . . F 3 -12.27 2.702 0.167 1 216.54 ? O2G UTP 602 A 1 
HETATM 13 O O3G UTP . . . F 3 -9.928 2.624 1.116 1 214.33 ? O3G UTP 602 A 1 
HETATM 14 C C5' UTP . . . F 3 -13.516 -2.068 5.336 1 213.07 ? C5' UTP 602 A 1 
HETATM 15 C C4' UTP . . . F 3 -14.627 -2.859 5.977 1 211.56 ? C4' UTP 602 A 1 
HETATM 16 O O4' UTP . . . F 3 -14.746 -4.144 5.337 1 211.32 ? O4' UTP 602 A 1 
HETATM 17 C C1' UTP . . . F 3 -15.316 -5.022 6.277 1 211.31 ? C1' UTP 602 A 1 
HETATM 18 C C2' UTP . . . F 3 -14.69 -4.647 7.617 1 212.12 ? C2' UTP 602 A 1 
HETATM 19 O O2' UTP . . . F 3 -15.581 -4.976 8.68 1 212.25 ? O2' UTP 602 A 1 
HETATM 20 C C3' UTP . . . F 3 -14.487 -3.129 7.479 1 211.75 ? C3' UTP 602 A 1 
HETATM 21 O O3' UTP . . . F 3 -15.483 -2.403 8.184 1 211.29 ? O3' UTP 602 A 1 
HETATM 22 N N1 UTP . . . F 3 -15.063 -6.411 5.847 1 211.47 ? N1 UTP 602 A 1 
HETATM 23 C C6 UTP . . . F 3 -13.999 -6.732 5.019 1 212.08 ? C6 UTP 602 A 1 
HETATM 24 C C2 UTP . . . F 3 -15.985 -7.369 6.23 1 211.56 ? C2 UTP 602 A 1 
HETATM 25 O O2 UTP . . . F 3 -16.932 -7.126 6.967 1 210.93 ? O2 UTP 602 A 1 
HETATM 26 N N3 UTP . . . F 3 -15.777 -8.624 5.7 1 212.66 ? N3 UTP 602 A 1 
HETATM 27 C C4 UTP . . . F 3 -14.761 -9.006 4.842 1 213.44 ? C4 UTP 602 A 1 
HETATM 28 O O4 UTP . . . F 3 -14.739 -10.165 4.398 1 214.47 ? O4 UTP 602 A 1 
HETATM 29 C C5 UTP . . . F 3 -13.827 -7.968 4.514 1 213.15 ? C5 UTP 602 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           223 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           29 
#