data_5MQJ
#
_model_server_result.job_id            6vpfwtnncJa9c1sMPCVLdA 
_model_server_result.datetime_utc      '2024-11-22 13:53:20' 
_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          5mqj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":301}' 
#
_entry.id    5MQJ 
#
_exptl.entry_id    5MQJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_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            5MQJ 
_cell.length_a            92.695 
_cell.length_b            92.695 
_cell.length_c            338.083 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5MQJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,E,F,G,H,I,J 1 1 
C,D,K,L,M,N,O,P 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 E N N 
? 2 H N N 
? 2 K N N 
? 2 N 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 F OP1 UMP . A UMP 302 1_555 G MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc2 B OE1 GLU 74 B GLU 53 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
metalc ? metalc3 B OE2 GLU 148 B GLU 127 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc4 I OP2 UMP . B UMP 302 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc5 C OE2 GLU 148 C GLU 127 1_555 M MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? 
metalc ? metalc6 L OP2 UMP . C UMP 302 1_555 M MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc7 N O1B UDP . D UDP 301 1_555 P MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? 
metalc ? metalc8 O OP2 UMP . D UMP 302 1_555 P MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
N1 C2 UDP sing 356 n n 
N1 C6 UDP sing 357 n n 
N1 C1' UDP sing 358 n n 
C2 N3 UDP sing 359 n n 
C2 O2 UDP doub 360 n n 
N3 C4 UDP sing 361 n n 
N3 HN3 UDP sing 362 n n 
C4 C5 UDP sing 363 n n 
C4 O4 UDP doub 364 n n 
C5 C6 UDP doub 365 n n 
C5 H5 UDP sing 366 n n 
C6 H6 UDP sing 367 n n 
C1' C2' UDP sing 368 n n 
C1' O4' UDP sing 369 n n 
C1' H1' UDP sing 370 n n 
C2' O2' UDP sing 371 n n 
C2' C3' UDP sing 372 n n 
C2' H2' UDP sing 373 n n 
O2' HO2' UDP sing 374 n n 
C3' C4' UDP sing 375 n n 
C3' O3' UDP sing 376 n n 
C3' H3' UDP sing 377 n n 
C4' O4' UDP sing 378 n n 
C4' C5' UDP sing 379 n n 
C4' H4' UDP sing 380 n n 
O3' HO3' UDP sing 381 n n 
C5' O5' UDP sing 382 n n 
C5' "H5'1" UDP sing 383 n n 
C5' "H5'2" UDP sing 384 n n 
O5' PA UDP sing 385 n n 
PA O1A UDP doub 386 n n 
PA O2A UDP sing 387 n n 
PA O3A UDP sing 388 n n 
O2A HOA2 UDP sing 389 n n 
O3A PB UDP sing 390 n n 
PB O1B UDP doub 391 n n 
PB O2B UDP sing 392 n n 
PB O3B UDP sing 393 n n 
O2B HOB2 UDP sing 394 n n 
O3B HOB3 UDP sing 395 n n 
#
_atom_sites.entry_id                     5MQJ 
_atom_sites.fract_transf_matrix[1][1]    0.010788 
_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]    0.010788 
_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]    0.002958 
_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 UDP A 1 301 500 UDP UDP . 
F 3 UMP A 1 302 510 UMP DU . 
G 4 MG A 1 303 520 MG MG . 
H 2 UDP B 1 301 500 UDP UDP . 
I 3 UMP B 1 302 510 UMP DU . 
J 4 MG B 1 303 520 MG MG . 
K 2 UDP C 1 301 500 UDP UDP . 
L 3 UMP C 1 302 510 UMP DU . 
M 4 MG C 1 303 520 MG MG . 
N 2 UDP D 1 301 500 UDP UDP . 
O 3 UMP D 1 302 510 UMP DU . 
P 4 MG D 1 303 520 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 N N1 UDP . . . N 2 -110.566 17.419 327.183 1 154.31 ? N1 UDP 301 D 1 
HETATM 2 C C2 UDP . . . N 2 -110.767 16.058 327.314 1 161.53 ? C2 UDP 301 D 1 
HETATM 3 N N3 UDP . . . N 2 -111.751 15.701 328.208 1 160.46 ? N3 UDP 301 D 1 
HETATM 4 C C4 UDP . . . N 2 -112.535 16.547 328.968 1 154.3 ? C4 UDP 301 D 1 
HETATM 5 C C5 UDP . . . N 2 -112.267 17.943 328.782 1 148.65 ? C5 UDP 301 D 1 
HETATM 6 C C6 UDP . . . N 2 -111.312 18.33 327.918 1 148.81 ? C6 UDP 301 D 1 
HETATM 7 O O2 UDP . . . N 2 -110.15 15.222 326.665 1 167.96 ? O2 UDP 301 D 1 
HETATM 8 O O4 UDP . . . N 2 -113.389 16.072 329.725 1 155.2 ? O4 UDP 301 D 1 
HETATM 9 C C1' UDP . . . N 2 -109.581 17.869 326.174 1 152.73 ? C1' UDP 301 D 1 
HETATM 10 C C2' UDP . . . N 2 -110.218 18.54 324.948 1 151.84 ? C2' UDP 301 D 1 
HETATM 11 O O2' UDP . . . N 2 -110.396 17.626 323.869 1 156.55 ? O2' UDP 301 D 1 
HETATM 12 C C3' UDP . . . N 2 -109.229 19.668 324.64 1 148.72 ? C3' UDP 301 D 1 
HETATM 13 C C4' UDP . . . N 2 -108.698 20.039 326.024 1 144.86 ? C4' UDP 301 D 1 
HETATM 14 O O4' UDP . . . N 2 -108.706 18.808 326.776 1 147.38 ? O4' UDP 301 D 1 
HETATM 15 O O3' UDP . . . N 2 -108.184 19.265 323.76 1 152.69 ? O3' UDP 301 D 1 
HETATM 16 C C5' UDP . . . N 2 -109.435 21.112 326.796 1 140.8 ? C5' UDP 301 D 1 
HETATM 17 O O5' UDP . . . N 2 -110.061 22.062 325.904 1 140.29 ? O5' UDP 301 D 1 
HETATM 18 P PA UDP . . . N 2 -111.479 22.81 326.096 1 137.8 ? PA UDP 301 D 1 
HETATM 19 O O1A UDP . . . N 2 -112.243 22.961 324.836 1 138.43 ? O1A UDP 301 D 1 
HETATM 20 O O2A UDP . . . N 2 -112.309 21.983 327.079 1 139.1 ? O2A UDP 301 D 1 
HETATM 21 O O3A UDP . . . N 2 -111.155 24.241 326.726 1 132.56 ? O3A UDP 301 D 1 
HETATM 22 P PB UDP . . . N 2 -112.044 25.384 327.393 1 126.97 ? PB UDP 301 D 1 
HETATM 23 O O1B UDP . . . N 2 -112.225 26.552 326.463 1 124.07 ? O1B UDP 301 D 1 
HETATM 24 O O2B UDP . . . N 2 -113.263 24.668 327.626 1 129.19 ? O2B UDP 301 D 1 
HETATM 25 O O3B UDP . . . N 2 -111.498 25.729 328.783 1 123.44 ? O3B UDP 301 D 1 
#
_model_server_stats.io_time_ms              190 
_model_server_stats.parse_time_ms           65 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#