data_8K3U
#
_model_server_result.job_id            44YVuo3awI97hu7Xg_Zeig 
_model_server_result.datetime_utc      '2024-10-19 01:37:49' 
_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          8k3u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1504}' 
#
_entry.id    8K3U 
#
_exptl.entry_id    8K3U 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            8K3U 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8K3U 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_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 
_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    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
? 4 F N N 
? 4 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
metalc ? metalc1 A OD1 ASP 745 A ASP 745 1_555 C MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? 
metalc ? metalc2 C MG MG . A MG 1501 1_555 F O1A UDP . A UDP 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc3 D MG MG . A MG 1502 1_555 F O2A UDP . A UDP 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? 
metalc ? metalc4 D MG MG . A MG 1502 1_555 F O3' UDP . A UDP 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc5 B OD1 ASP 745 B ASP 745 1_555 I MG MG . B MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? 
metalc ? metalc6 I MG MG . B MG 1202 1_555 L O1A UDP . B UDP 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc7 J MG MG . B MG 1203 1_555 L O2A UDP . B UDP 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? 
metalc ? metalc8 J MG MG . B MG 1203 1_555 L O3' UDP . B UDP 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
#
_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 519 n n 
N1 C6 UDP sing 520 n n 
N1 C1' UDP sing 521 n n 
C2 N3 UDP sing 522 n n 
C2 O2 UDP doub 523 n n 
N3 C4 UDP sing 524 n n 
N3 HN3 UDP sing 525 n n 
C4 C5 UDP sing 526 n n 
C4 O4 UDP doub 527 n n 
C5 C6 UDP doub 528 n n 
C5 H5 UDP sing 529 n n 
C6 H6 UDP sing 530 n n 
C1' C2' UDP sing 531 n n 
C1' O4' UDP sing 532 n n 
C1' H1' UDP sing 533 n n 
C2' O2' UDP sing 534 n n 
C2' C3' UDP sing 535 n n 
C2' H2' UDP sing 536 n n 
O2' HO2' UDP sing 537 n n 
C3' C4' UDP sing 538 n n 
C3' O3' UDP sing 539 n n 
C3' H3' UDP sing 540 n n 
C4' O4' UDP sing 541 n n 
C4' C5' UDP sing 542 n n 
C4' H4' UDP sing 543 n n 
O3' HO3' UDP sing 544 n n 
C5' O5' UDP sing 545 n n 
C5' "H5'1" UDP sing 546 n n 
C5' "H5'2" UDP sing 547 n n 
O5' PA UDP sing 548 n n 
PA O1A UDP doub 549 n n 
PA O2A UDP sing 550 n n 
PA O3A UDP sing 551 n n 
O2A HOA2 UDP sing 552 n n 
O3A PB UDP sing 553 n n 
PB O1B UDP doub 554 n n 
PB O2B UDP sing 555 n n 
PB O3B UDP sing 556 n n 
O2B HOB2 UDP sing 557 n n 
O3B HOB3 UDP sing 558 n n 
#
_atom_sites.entry_id                     8K3U 
_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
C 2 MG A 1 1501 1501 MG MG . 
D 2 MG A 1 1502 1502 MG MG . 
E 3 NAG A 1 1503 1503 NAG NAG . 
F 4 UDP A 1 1504 1504 UDP UDP . 
G 5 POV A 1 1505 1505 POV POV . 
H 5 POV B 1 1201 1505 POV POV . 
I 2 MG B 1 1202 1501 MG MG . 
J 2 MG B 1 1203 1502 MG MG . 
K 3 NAG B 1 1204 1503 NAG NAG . 
L 4 UDP B 1 1205 1504 UDP UDP . 
#
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 . . . F 4 137.853 110.692 136.667 1 69.92 ? N1 UDP 1504 A 1 
HETATM 2 C C2 UDP . . . F 4 137.034 111.013 137.73 1 69.92 ? C2 UDP 1504 A 1 
HETATM 3 N N3 UDP . . . F 4 135.807 111.521 137.383 1 69.92 ? N3 UDP 1504 A 1 
HETATM 4 C C4 UDP . . . F 4 135.33 111.735 136.104 1 69.92 ? C4 UDP 1504 A 1 
HETATM 5 C C5 UDP . . . F 4 136.237 111.378 135.061 1 69.92 ? C5 UDP 1504 A 1 
HETATM 6 C C6 UDP . . . F 4 137.444 110.878 135.366 1 69.92 ? C6 UDP 1504 A 1 
HETATM 7 O O2 UDP . . . F 4 137.369 110.862 138.894 1 69.92 ? O2 UDP 1504 A 1 
HETATM 8 O O4 UDP . . . F 4 134.192 112.202 135.945 1 69.92 ? O4 UDP 1504 A 1 
HETATM 9 C C1' UDP . . . F 4 139.181 110.144 136.97 1 69.92 ? C1' UDP 1504 A 1 
HETATM 10 C C2' UDP . . . F 4 139.127 108.762 137.608 1 69.92 ? C2' UDP 1504 A 1 
HETATM 11 O O2' UDP . . . F 4 140.294 108.527 138.386 1 69.92 ? O2' UDP 1504 A 1 
HETATM 12 C C3' UDP . . . F 4 139.083 107.866 136.373 1 69.92 ? C3' UDP 1504 A 1 
HETATM 13 C C4' UDP . . . F 4 140 108.605 135.406 1 69.92 ? C4' UDP 1504 A 1 
HETATM 14 O O4' UDP . . . F 4 139.889 110.001 135.753 1 69.92 ? O4' UDP 1504 A 1 
HETATM 15 O O3' UDP . . . F 4 139.565 106.556 136.64 1 69.92 ? O3' UDP 1504 A 1 
HETATM 16 C C5' UDP . . . F 4 139.658 108.422 133.95 1 69.92 ? C5' UDP 1504 A 1 
HETATM 17 O O5' UDP . . . F 4 138.382 107.753 133.871 1 69.92 ? O5' UDP 1504 A 1 
HETATM 18 P PA UDP . . . F 4 138.157 106.527 132.897 1 69.92 ? PA UDP 1504 A 1 
HETATM 19 O O1A UDP . . . F 4 139.494 106.084 132.44 1 69.92 ? O1A UDP 1504 A 1 
HETATM 20 O O2A UDP . . . F 4 137.257 105.476 133.539 1 69.92 ? O2A UDP 1504 A 1 
HETATM 21 O O3A UDP . . . F 4 137.339 107.13 131.688 1 69.92 ? O3A UDP 1504 A 1 
HETATM 22 P PB UDP . . . F 4 137.679 108.536 131.047 1 69.92 ? PB UDP 1504 A 1 
HETATM 23 O O1B UDP . . . F 4 136.772 108.586 129.818 1 69.92 ? O1B UDP 1504 A 1 
HETATM 24 O O2B UDP . . . F 4 137.178 109.523 132.094 1 69.92 ? O2B UDP 1504 A 1 
HETATM 25 O O3B UDP . . . F 4 139.128 108.671 130.731 1 69.92 ? O3B UDP 1504 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           351 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#