data_2J4L
#
_model_server_result.job_id            r2ZudK1rvshKx3DWI3Btqw 
_model_server_result.datetime_utc      '2025-09-13 07:36:50' 
_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":"M","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 . . . M 2 -33.935 2.528 -104.593 1 79.98 ? PA UTP 1227 A 1 
HETATM 2 O O1A UTP . . . M 2 -32.827 2.324 -103.642 1 80.2 ? O1A UTP 1227 A 1 
HETATM 3 O O2A UTP . . . M 2 -34.613 1.355 -105.225 1 82.2 ? O2A UTP 1227 A 1 
HETATM 4 O O3A UTP . . . M 2 -33.429 3.505 -105.798 1 90.54 ? O3A UTP 1227 A 1 
HETATM 5 O O5' UTP . . . M 2 -35.022 3.443 -103.937 1 77.54 ? O5' UTP 1227 A 1 
HETATM 6 P PB UTP . . . M 2 -32.396 3.174 -106.97 1 100.53 ? PB UTP 1227 A 1 
HETATM 7 O O1B UTP . . . M 2 -31.051 3.72 -106.811 1 97.85 ? O1B UTP 1227 A 1 
HETATM 8 O O2B UTP . . . M 2 -33.116 3.543 -108.192 1 98.77 ? O2B UTP 1227 A 1 
HETATM 9 O O3B UTP . . . M 2 -32.366 1.555 -106.741 1 105.24 ? O3B UTP 1227 A 1 
HETATM 10 P PG UTP . . . M 2 -31.619 0.305 -107.415 1 110.35 ? PG UTP 1227 A 1 
HETATM 11 O O1G UTP . . . M 2 -31.956 0.294 -108.93 1 110.43 ? O1G UTP 1227 A 1 
HETATM 12 O O2G UTP . . . M 2 -30.161 0.551 -107.119 1 109.28 ? O2G UTP 1227 A 1 
HETATM 13 O O3G UTP . . . M 2 -32.127 -0.961 -106.726 1 109.18 ? O3G UTP 1227 A 1 
HETATM 14 C C5' UTP . . . M 2 -36.191 3.764 -104.638 1 74.58 ? C5' UTP 1227 A 1 
HETATM 15 C C4' UTP . . . M 2 -36.518 5.221 -104.548 1 73.38 ? C4' UTP 1227 A 1 
HETATM 16 O O4' UTP . . . M 2 -37.237 5.566 -103.329 1 72.4 ? O4' UTP 1227 A 1 
HETATM 17 C C1' UTP . . . M 2 -36.561 6.553 -102.575 1 69.57 ? C1' UTP 1227 A 1 
HETATM 18 C C2' UTP . . . M 2 -35.514 7.162 -103.503 1 71.72 ? C2' UTP 1227 A 1 
HETATM 19 O O2' UTP . . . M 2 -35.963 8.431 -103.937 1 72.6 ? O2' UTP 1227 A 1 
HETATM 20 C C3' UTP . . . M 2 -35.341 6.181 -104.666 1 72.26 ? C3' UTP 1227 A 1 
HETATM 21 O O3' UTP . . . M 2 -35.383 6.835 -105.934 1 74.33 ? O3' UTP 1227 A 1 
HETATM 22 N N1 UTP . . . M 2 -35.981 5.976 -101.305 1 67.75 ? N1 UTP 1227 A 1 
HETATM 23 C C6 UTP . . . M 2 -35.528 4.648 -101.204 1 66.75 ? C6 UTP 1227 A 1 
HETATM 24 C C2 UTP . . . M 2 -35.897 6.828 -100.179 1 66.2 ? C2 UTP 1227 A 1 
HETATM 25 O O2 UTP . . . M 2 -36.259 7.972 -100.182 1 67.3 ? O2 UTP 1227 A 1 
HETATM 26 N N3 UTP . . . M 2 -35.362 6.253 -99.047 1 65.08 ? N3 UTP 1227 A 1 
HETATM 27 C C4 UTP . . . M 2 -34.898 4.943 -98.895 1 64.62 ? C4 UTP 1227 A 1 
HETATM 28 O O4 UTP . . . M 2 -34.444 4.584 -97.798 1 65.12 ? O4 UTP 1227 A 1 
HETATM 29 C C5 UTP . . . M 2 -35.005 4.119 -100.074 1 65.12 ? C5 UTP 1227 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           371 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           29 
#