data_2J4L
#
_model_server_result.job_id            uigjuww_LQntbQ1h5gcE3g 
_model_server_result.datetime_utc      '2025-09-13 09:57:08' 
_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          2j4l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":1227}' 
#
_entry.id    2J4L 
#
_exptl.entry_id    2J4L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              484.141 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE 5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          96.56 
_cell.angle_gamma         90 
_cell.entry_id            2J4L 
_cell.length_a            224.75 
_cell.length_b            79.03 
_cell.length_c            223.47 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2J4L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 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
PQS hexameric 6 author_and_software_defined_assembly 1 
PQS hexameric 6 author_and_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,M,N,O,P,Q,R,S,T,U,V 1 1 
G,H,I,J,K,L,W,X,Y,Z,AA,BA,CA,DA,EA 2 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 M N N 
? 2 N N N 
? 2 P N N 
? 2 R N N 
? 2 T N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 AA N N 
? 2 CA N N 
? 2 DA 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 N O1A UTP . B UTP 1227 1_555 O MG MG . B MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.917 ? 
metalc ? metalc2 N O3A UTP . B UTP 1227 1_555 O MG MG . B MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc3 C NH2 ARG 48 C ARG 48 1_555 Q MG MG . C MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? 
metalc ? metalc4 P O3B UTP . C UTP 1227 1_555 Q MG MG . C MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? 
metalc ? metalc5 P O1A UTP . C UTP 1227 1_555 Q MG MG . C MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.059 ? 
metalc ? metalc6 R O3A UTP . D UTP 1227 1_555 S MG MG . D MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? 
metalc ? metalc7 R O1B UTP . D UTP 1227 1_555 S MG MG . D MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? 
metalc ? metalc8 T O3A UTP . E UTP 1227 1_555 U MG MG . E MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.104 ? 
metalc ? metalc9 T O3B UTP . E UTP 1227 1_555 U MG MG . E MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
metalc ? metalc10 T O1A UTP . E UTP 1227 1_555 U MG MG . E MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? 
metalc ? metalc11 AA O3A UTP . J UTP 1227 1_555 BA MG MG . J MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? 
metalc ? metalc12 AA O2B UTP . J UTP 1227 1_555 BA MG MG . J MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? 
metalc ? metalc13 DA O1A UTP . L UTP 1227 1_555 EA MG MG . L MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.134 ? 
metalc ? metalc14 DA O5' UTP . L UTP 1227 1_555 EA MG MG . L MG 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
#
_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 343 n n 
PA O2A UTP sing 344 n n 
PA O3A UTP sing 345 n n 
PA O5' UTP sing 346 n n 
O2A H2A UTP sing 347 n n 
O3A PB UTP sing 348 n n 
O5' C5' UTP sing 349 n n 
PB O1B UTP sing 350 n n 
PB O2B UTP doub 351 n n 
PB O3B UTP sing 352 n n 
O1B H1B UTP sing 353 n n 
O3B PG UTP sing 354 n n 
PG O1G UTP sing 355 n n 
PG O2G UTP doub 356 n n 
PG O3G UTP sing 357 n n 
O1G H1G UTP sing 358 n n 
O3G H3G UTP sing 359 n n 
C5' C4' UTP sing 360 n n 
C5' "H5'1" UTP sing 361 n n 
C5' "H5'2" UTP sing 362 n n 
C4' O4' UTP sing 363 n n 
C4' C3' UTP sing 364 n n 
C4' H4' UTP sing 365 n n 
O4' C1' UTP sing 366 n n 
C1' C2' UTP sing 367 n n 
C1' N1 UTP sing 368 n n 
C1' H1' UTP sing 369 n n 
C2' O2' UTP sing 370 n n 
C2' C3' UTP sing 371 n n 
C2' H2' UTP sing 372 n n 
O2' HA UTP sing 373 n n 
C3' O3' UTP sing 374 n n 
C3' H3' UTP sing 375 n n 
O3' HB UTP sing 376 n n 
N1 C6 UTP sing 377 n y 
N1 C2 UTP sing 378 n y 
C6 C5 UTP doub 379 n y 
C6 H6 UTP sing 380 n n 
C2 O2 UTP doub 381 n n 
C2 N3 UTP sing 382 n y 
N3 C4 UTP sing 383 n y 
N3 H3 UTP sing 384 n n 
C4 O4 UTP doub 385 n n 
C4 C5 UTP sing 386 n y 
C5 H5 UTP sing 387 n n 
#
_atom_sites.entry_id                     2J4L 
_atom_sites.fract_transf_matrix[1][1]    0.004449 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000512 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012653 
_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]    0.004504 
_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
M 2 UTP A 1 1227 1227 UTP UTP . 
N 2 UTP B 1 1227 1227 UTP UTP . 
O 3 MG B 1 1228 1228 MG MG . 
P 2 UTP C 1 1227 1227 UTP UTP . 
Q 3 MG C 1 1228 1228 MG MG . 
R 2 UTP D 1 1227 1227 UTP UTP . 
S 3 MG D 1 1228 1228 MG MG . 
T 2 UTP E 1 1227 1227 UTP UTP . 
U 3 MG E 1 1228 1228 MG MG . 
V 2 UTP F 1 1227 1227 UTP UTP . 
W 2 UTP G 1 1227 1227 UTP UTP . 
X 2 UTP H 1 1227 1227 UTP UTP . 
Y 2 UTP I 1 1227 1227 UTP UTP . 
Z 3 MG I 1 1228 1228 MG MG . 
AA 2 UTP J 1 1227 1227 UTP UTP . 
BA 3 MG J 1 1228 1228 MG MG . 
CA 2 UTP K 1 1227 1227 UTP UTP . 
DA 2 UTP L 1 1227 1227 UTP UTP . 
EA 3 MG L 1 1228 1228 MG MG . 
#
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 . . . W 2 -7.336 22.675 -14.408 1 98.2 ? PA UTP 1227 G 1 
HETATM 2 O O1A UTP . . . W 2 -7.976 21.505 -15.048 1 98.1 ? O1A UTP 1227 G 1 
HETATM 3 O O2A UTP . . . W 2 -6.03 23.177 -14.918 1 97.58 ? O2A UTP 1227 G 1 
HETATM 4 O O3A UTP . . . W 2 -7.177 22.421 -12.793 1 105.05 ? O3A UTP 1227 G 1 
HETATM 5 O O5' UTP . . . W 2 -8.351 23.893 -14.371 1 94.57 ? O5' UTP 1227 G 1 
HETATM 6 P PB UTP . . . W 2 -6.942 21.109 -11.913 1 110.05 ? PB UTP 1227 G 1 
HETATM 7 O O1B UTP . . . W 2 -6.346 21.317 -10.606 1 109.61 ? O1B UTP 1227 G 1 
HETATM 8 O O2B UTP . . . W 2 -6.237 20.217 -12.801 1 109.69 ? O2B UTP 1227 G 1 
HETATM 9 O O3B UTP . . . W 2 -8.458 20.646 -11.72 1 114.91 ? O3B UTP 1227 G 1 
HETATM 10 P PG UTP . . . W 2 -9.097 19.399 -10.961 1 119.74 ? PG UTP 1227 G 1 
HETATM 11 O O1G UTP . . . W 2 -7.94 18.453 -10.587 1 118.85 ? O1G UTP 1227 G 1 
HETATM 12 O O2G UTP . . . W 2 -9.793 20.026 -9.773 1 119.39 ? O2G UTP 1227 G 1 
HETATM 13 O O3G UTP . . . W 2 -10.089 18.71 -11.907 1 119.43 ? O3G UTP 1227 G 1 
HETATM 14 C C5' UTP . . . W 2 -7.961 25.118 -13.785 1 88.91 ? C5' UTP 1227 G 1 
HETATM 15 C C4' UTP . . . W 2 -7.68 26.188 -14.8 1 85.44 ? C4' UTP 1227 G 1 
HETATM 16 O O4' UTP . . . W 2 -7.037 25.684 -16.005 1 82.57 ? O4' UTP 1227 G 1 
HETATM 17 C C1' UTP . . . W 2 -7.512 26.378 -17.148 1 79.8 ? C1' UTP 1227 G 1 
HETATM 18 C C2' UTP . . . W 2 -8.892 26.938 -16.746 1 81.23 ? C2' UTP 1227 G 1 
HETATM 19 O O2' UTP . . . W 2 -9.074 28.209 -17.31 1 79.68 ? O2' UTP 1227 G 1 
HETATM 20 C C3' UTP . . . W 2 -8.91 26.968 -15.229 1 83.16 ? C3' UTP 1227 G 1 
HETATM 21 O O3' UTP . . . W 2 -8.856 28.308 -14.715 1 85.52 ? O3' UTP 1227 G 1 
HETATM 22 N N1 UTP . . . W 2 -7.572 25.43 -18.329 1 76.27 ? N1 UTP 1227 G 1 
HETATM 23 C C6 UTP . . . W 2 -7.217 24.078 -18.19 1 75.39 ? C6 UTP 1227 G 1 
HETATM 24 C C2 UTP . . . W 2 -8.007 25.925 -19.598 1 74.29 ? C2 UTP 1227 G 1 
HETATM 25 O O2 UTP . . . W 2 -8.335 27.078 -19.81 1 71.14 ? O2 UTP 1227 G 1 
HETATM 26 N N3 UTP . . . W 2 -8.025 24.981 -20.609 1 74.47 ? N3 UTP 1227 G 1 
HETATM 27 C C4 UTP . . . W 2 -7.677 23.624 -20.517 1 74.95 ? C4 UTP 1227 G 1 
HETATM 28 O O4 UTP . . . W 2 -7.751 22.911 -21.527 1 74.81 ? O4 UTP 1227 G 1 
HETATM 29 C C5 UTP . . . W 2 -7.249 23.187 -19.205 1 74.23 ? C5 UTP 1227 G 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           29 
#