data_7MIF
#
_model_server_result.job_id            ooDNsWzuYM7atIhl64TQgQ 
_model_server_result.datetime_utc      '2025-09-07 14:22:29' 
_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          7mif 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":601}' 
#
_entry.id    7MIF 
#
_exptl.entry_id    7MIF 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              484.141 
_entity.id                          5 
_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                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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,Q,R,S,T 
_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    ? 
_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
? 5 H N N 
? 5 J N N 
? 5 Q N N 
? 5 R 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 C CYS 218 1_555 A SG CYS 243 C CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf2 B SG CYS 218 G CYS 218 1_555 B SG CYS 243 G CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf3 C SG CYS 218 H CYS 218 1_555 C SG CYS 243 H CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf4 D SG CYS 218 I CYS 218 1_555 D SG CYS 243 I CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc1 G MG MG . C MG 603 1_555 H O1B UTP . C UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc2 G MG MG . C MG 603 1_555 H O1A UTP . C UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc3 G MG MG . C MG 603 1_555 H O3G UTP . C UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc4 I MG MG . G MG 601 1_555 J O2A UTP . G UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc5 I MG MG . G MG 601 1_555 J O3G UTP . G UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc6 I MG MG . G MG 601 1_555 J O2B UTP . G UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc7 N MG MG . H MG 602 1_555 R O1B UTP . I UTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc8 N MG MG . H MG 602 1_555 R O1A UTP . I UTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc9 N MG MG . H MG 602 1_555 R O3G UTP . I UTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc10 P MG MG . H MG 604 1_555 Q O2A UTP . H UTP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc11 P MG MG . H MG 604 1_555 Q O2B UTP . H UTP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc12 P MG MG . H MG 604 1_555 Q O3G UTP . H UTP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
#
_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 356 n n 
PA O2A UTP sing 357 n n 
PA O3A UTP sing 358 n n 
PA O5' UTP sing 359 n n 
O2A H2A UTP sing 360 n n 
O3A PB UTP sing 361 n n 
O5' C5' UTP sing 362 n n 
PB O1B UTP sing 363 n n 
PB O2B UTP doub 364 n n 
PB O3B UTP sing 365 n n 
O1B H1B UTP sing 366 n n 
O3B PG UTP sing 367 n n 
PG O1G UTP sing 368 n n 
PG O2G UTP doub 369 n n 
PG O3G UTP sing 370 n n 
O1G H1G UTP sing 371 n n 
O3G H3G UTP sing 372 n n 
C5' C4' UTP sing 373 n n 
C5' "H5'1" UTP sing 374 n n 
C5' "H5'2" UTP sing 375 n n 
C4' O4' UTP sing 376 n n 
C4' C3' UTP sing 377 n n 
C4' H4' UTP sing 378 n n 
O4' C1' UTP sing 379 n n 
C1' C2' UTP sing 380 n n 
C1' N1 UTP sing 381 n n 
C1' H1' UTP sing 382 n n 
C2' O2' UTP sing 383 n n 
C2' C3' UTP sing 384 n n 
C2' H2' UTP sing 385 n n 
O2' HA UTP sing 386 n n 
C3' O3' UTP sing 387 n n 
C3' H3' UTP sing 388 n n 
O3' HB UTP sing 389 n n 
N1 C6 UTP sing 390 n y 
N1 C2 UTP sing 391 n y 
C6 C5 UTP doub 392 n y 
C6 H6 UTP sing 393 n n 
C2 O2 UTP doub 394 n n 
C2 N3 UTP sing 395 n y 
N3 C4 UTP sing 396 n y 
N3 H3 UTP sing 397 n n 
C4 O4 UTP doub 398 n n 
C4 C5 UTP sing 399 n y 
C5 H5 UTP sing 400 n n 
#
_atom_sites.entry_id                     7MIF 
_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 GLN C 1 601 611 GLN GLN . 
F 3 ZG4 C 1 602 999 ZG4 LIG . 
G 4 MG C 1 603 1 MG MG . 
H 5 UTP C 1 604 602 UTP UTP . 
I 4 MG G 1 601 1 MG MG . 
J 5 UTP G 1 602 602 UTP UTP . 
K 2 GLN G 1 603 611 GLN GLN . 
L 3 ZG4 G 1 604 999 ZG4 LIG . 
M 2 GLN H 1 601 611 GLN GLN . 
N 4 MG H 1 602 1 MG MG . 
O 3 ZG4 H 1 603 999 ZG4 LIG . 
P 4 MG H 1 604 1 MG MG . 
Q 5 UTP H 1 605 602 UTP UTP . 
R 5 UTP I 1 601 602 UTP UTP . 
S 2 GLN I 1 602 611 GLN GLN . 
T 3 ZG4 I 1 603 999 ZG4 LIG . 
#
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 . . . R 5 173.838 145.314 156.119 1 46.2 ? PA UTP 601 I 1 
HETATM 2 O O1A UTP . . . R 5 175.064 144.459 155.869 1 46.2 ? O1A UTP 601 I 1 
HETATM 3 O O2A UTP . . . R 5 173.795 146.393 157.174 1 46.2 ? O2A UTP 601 I 1 
HETATM 4 O O3A UTP . . . R 5 173.379 145.992 154.638 1 46.2 ? O3A UTP 601 I 1 
HETATM 5 O O5' UTP . . . R 5 172.479 144.293 156.343 1 46.2 ? O5' UTP 601 I 1 
HETATM 6 P PB UTP . . . R 5 173.735 145.864 152.991 1 46.2 ? PB UTP 601 I 1 
HETATM 7 O O1B UTP . . . R 5 174.555 144.602 152.814 1 46.2 ? O1B UTP 601 I 1 
HETATM 8 O O2B UTP . . . R 5 172.484 146.148 152.195 1 46.2 ? O2B UTP 601 I 1 
HETATM 9 O O3B UTP . . . R 5 174.773 147.185 152.871 1 46.2 ? O3B UTP 601 I 1 
HETATM 10 P PG UTP . . . R 5 176.406 147.45 153.344 1 46.2 ? PG UTP 601 I 1 
HETATM 11 O O1G UTP . . . R 5 176.389 148.658 154.286 1 46.2 ? O1G UTP 601 I 1 
HETATM 12 O O2G UTP . . . R 5 177.186 147.715 152.056 1 46.2 ? O2G UTP 601 I 1 
HETATM 13 O O3G UTP . . . R 5 176.854 146.152 154.04 1 46.2 ? O3G UTP 601 I 1 
HETATM 14 C C5' UTP . . . R 5 172.251 143.254 155.404 1 46.2 ? C5' UTP 601 I 1 
HETATM 15 C C4' UTP . . . R 5 171.47 142.105 156.066 1 46.2 ? C4' UTP 601 I 1 
HETATM 16 O O4' UTP . . . R 5 172.305 141.467 157.022 1 46.2 ? O4' UTP 601 I 1 
HETATM 17 C C1' UTP . . . R 5 171.527 140.895 158.037 1 46.2 ? C1' UTP 601 I 1 
HETATM 18 C C2' UTP . . . R 5 170.063 141.381 157.876 1 46.2 ? C2' UTP 601 I 1 
HETATM 19 O O2' UTP . . . R 5 169.27 140.289 157.407 1 46.2 ? O2' UTP 601 I 1 
HETATM 20 C C3' UTP . . . R 5 170.227 142.523 156.865 1 46.2 ? C3' UTP 601 I 1 
HETATM 21 O O3' UTP . . . R 5 169.099 142.785 156.03 1 46.2 ? O3' UTP 601 I 1 
HETATM 22 N N1 UTP . . . R 5 172.191 141.047 159.321 1 46.2 ? N1 UTP 601 I 1 
HETATM 23 C C6 UTP . . . R 5 172.508 139.958 160.109 1 46.2 ? C6 UTP 601 I 1 
HETATM 24 C C2 UTP . . . R 5 172.497 142.319 159.729 1 46.2 ? C2 UTP 601 I 1 
HETATM 25 O O2 UTP . . . R 5 172.198 143.37 159.182 1 46.2 ? O2 UTP 601 I 1 
HETATM 26 N N3 UTP . . . R 5 173.192 142.381 160.881 1 46.2 ? N3 UTP 601 I 1 
HETATM 27 C C4 UTP . . . R 5 173.524 141.408 161.745 1 46.2 ? C4 UTP 601 I 1 
HETATM 28 O O4 UTP . . . R 5 174.02 141.704 162.826 1 46.2 ? O4 UTP 601 I 1 
HETATM 29 C C5 UTP . . . R 5 173.162 140.087 161.281 1 46.2 ? C5 UTP 601 I 1 
HETATM 30 H "H5'1" UTP . . . R 5 171.685 143.659 154.564 1 0 ? "H5'1" UTP 601 I 1 
HETATM 31 H "H5'2" UTP . . . R 5 173.184 142.865 154.996 1 0 ? "H5'2" UTP 601 I 1 
HETATM 32 H H4' UTP . . . R 5 171.207 141.357 155.314 1 0 ? H4' UTP 601 I 1 
HETATM 33 H H1' UTP . . . R 5 171.589 139.822 157.84 1 0 ? H1' UTP 601 I 1 
HETATM 34 H H2' UTP . . . R 5 169.676 141.746 158.83 1 0 ? H2' UTP 601 I 1 
HETATM 35 H HA UTP . . . R 5 168.339 140.533 157.465 1 0 ? HA UTP 601 I 1 
HETATM 36 H H3' UTP . . . R 5 170.438 143.438 157.418 1 0 ? H3' UTP 601 I 1 
HETATM 37 H HB UTP . . . R 5 168.378 143.124 156.571 1 0 ? HB UTP 601 I 1 
HETATM 38 H H6 UTP . . . R 5 172.221 139.003 159.707 1 0 ? H6 UTP 601 I 1 
HETATM 39 H H3 UTP . . . R 5 173.427 143.314 161.177 1 0 ? H3 UTP 601 I 1 
HETATM 40 H H5 UTP . . . R 5 173.426 139.222 161.868 1 0 ? H5 UTP 601 I 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    40 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           40 
#