data_5U6N
#
_model_server_result.job_id            uyrSY9IyJa30I8_RRJeydw 
_model_server_result.datetime_utc      '2024-11-24 17:38:55' 
_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          5u6n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":503}' 
#
_entry.id    5U6N 
#
_exptl.entry_id    5U6N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          5 
_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            5U6N 
_cell.length_a            65.18 
_cell.length_b            87.562 
_cell.length_c            163.018 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5U6N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,E,F,G,H,L 1 1 
B,D,I,J,K,M 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
? 5 G N N 
? 5 J N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   BGC 
_pdbx_entity_branch_link.comp_id_2                   BGC 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O3 
_pdbx_entity_branch_link.leaving_atom_id_2           HO3 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n C BGC 1 C 1 BGC A 502 LB2 
2 n C BGC 2 C 2 BGC A 502 LB2 
2 n D BGC 1 D 1 BGC B 502 LB2 
2 n D BGC 2 D 2 BGC B 502 LB2 
#
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
covale ? covale1 A OH TYR 177 A TYR 177 1_555 F C1 BGC . A BGC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? 
covale ? covale2 A OH TYR 180 A TYR 180 1_555 C C1 BGC . C BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? 
covale ? covale3 B OH TYR 177 B TYR 177 1_555 I C1 BGC . B BGC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? 
covale ? covale4 B OH TYR 180 B TYR 180 1_555 D C1 BGC . D BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? 
covale ? covale5 C O3 BGC . C BGC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 sing 
covale ? covale6 D O3 BGC . D BGC 1 1_555 D C1 BGC . D BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 sing 
#
_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 398 n n 
N1 C6 UDP sing 399 n n 
N1 C1' UDP sing 400 n n 
C2 N3 UDP sing 401 n n 
C2 O2 UDP doub 402 n n 
N3 C4 UDP sing 403 n n 
N3 HN3 UDP sing 404 n n 
C4 C5 UDP sing 405 n n 
C4 O4 UDP doub 406 n n 
C5 C6 UDP doub 407 n n 
C5 H5 UDP sing 408 n n 
C6 H6 UDP sing 409 n n 
C1' C2' UDP sing 410 n n 
C1' O4' UDP sing 411 n n 
C1' H1' UDP sing 412 n n 
C2' O2' UDP sing 413 n n 
C2' C3' UDP sing 414 n n 
C2' H2' UDP sing 415 n n 
O2' HO2' UDP sing 416 n n 
C3' C4' UDP sing 417 n n 
C3' O3' UDP sing 418 n n 
C3' H3' UDP sing 419 n n 
C4' O4' UDP sing 420 n n 
C4' C5' UDP sing 421 n n 
C4' H4' UDP sing 422 n n 
O3' HO3' UDP sing 423 n n 
C5' O5' UDP sing 424 n n 
C5' "H5'1" UDP sing 425 n n 
C5' "H5'2" UDP sing 426 n n 
O5' PA UDP sing 427 n n 
PA O1A UDP doub 428 n n 
PA O2A UDP sing 429 n n 
PA O3A UDP sing 430 n n 
O2A HOA2 UDP sing 431 n n 
O3A PB UDP sing 432 n n 
PB O1B UDP doub 433 n n 
PB O2B UDP sing 434 n n 
PB O3B UDP sing 435 n n 
O2B HOB2 UDP sing 436 n n 
O3B HOB3 UDP sing 437 n n 
#
_atom_sites.entry_id                     5U6N 
_atom_sites.fract_transf_matrix[1][1]    0.015342 
_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]    0.01142 
_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]    0.006134 
_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 3 GLN A 1 501 447 GLN GLN . 
F 4 BGC A 1 502 501 BGC BGC . 
G 5 UDP A 1 504 2 UDP UDP . 
H 6 SAL A 1 505 3 SAL SAL . 
I 4 BGC B 1 501 501 BGC BGC . 
J 5 UDP B 1 503 1 UDP UDP . 
K 6 SAL B 1 504 4 SAL SAL . 
L 7 HOH A 1 601 20 HOH HOH . 
L 7 HOH A 2 602 36 HOH HOH . 
L 7 HOH A 3 603 34 HOH HOH . 
L 7 HOH A 4 604 19 HOH HOH . 
L 7 HOH A 5 605 2 HOH HOH . 
L 7 HOH A 6 606 43 HOH HOH . 
L 7 HOH A 7 607 45 HOH HOH . 
L 7 HOH A 8 608 53 HOH HOH . 
L 7 HOH A 9 609 23 HOH HOH . 
L 7 HOH A 10 610 12 HOH HOH . 
L 7 HOH A 11 611 54 HOH HOH . 
L 7 HOH A 12 612 24 HOH HOH . 
L 7 HOH A 13 613 10 HOH HOH . 
L 7 HOH A 14 614 35 HOH HOH . 
L 7 HOH A 15 615 31 HOH HOH . 
L 7 HOH A 16 616 56 HOH HOH . 
L 7 HOH A 17 617 27 HOH HOH . 
L 7 HOH A 18 618 13 HOH HOH . 
L 7 HOH A 19 619 63 HOH HOH . 
L 7 HOH A 20 620 22 HOH HOH . 
L 7 HOH A 21 621 66 HOH HOH . 
L 7 HOH A 22 622 62 HOH HOH . 
L 7 HOH A 23 623 29 HOH HOH . 
L 7 HOH A 24 624 59 HOH HOH . 
L 7 HOH A 25 625 65 HOH HOH . 
M 7 HOH B 1 601 30 HOH HOH . 
M 7 HOH B 2 602 51 HOH HOH . 
M 7 HOH B 3 603 32 HOH HOH . 
M 7 HOH B 4 604 7 HOH HOH . 
M 7 HOH B 5 605 41 HOH HOH . 
M 7 HOH B 6 606 55 HOH HOH . 
M 7 HOH B 7 607 18 HOH HOH . 
M 7 HOH B 8 608 4 HOH HOH . 
M 7 HOH B 9 609 37 HOH HOH . 
M 7 HOH B 10 610 57 HOH HOH . 
M 7 HOH B 11 611 1 HOH HOH . 
M 7 HOH B 12 612 33 HOH HOH . 
M 7 HOH B 13 613 64 HOH HOH . 
M 7 HOH B 14 614 5 HOH HOH . 
M 7 HOH B 15 615 38 HOH HOH . 
M 7 HOH B 16 616 26 HOH HOH . 
M 7 HOH B 17 617 6 HOH HOH . 
M 7 HOH B 18 618 11 HOH HOH . 
M 7 HOH B 19 619 58 HOH HOH . 
M 7 HOH B 20 620 9 HOH HOH . 
M 7 HOH B 21 621 40 HOH HOH . 
M 7 HOH B 22 622 42 HOH HOH . 
M 7 HOH B 23 623 21 HOH HOH . 
M 7 HOH B 24 624 49 HOH HOH . 
M 7 HOH B 25 625 39 HOH HOH . 
M 7 HOH B 26 626 25 HOH HOH . 
M 7 HOH B 27 627 14 HOH HOH . 
M 7 HOH B 28 628 15 HOH HOH . 
M 7 HOH B 29 629 67 HOH HOH . 
M 7 HOH B 30 630 46 HOH HOH . 
M 7 HOH B 31 631 3 HOH HOH . 
M 7 HOH B 32 632 28 HOH HOH . 
M 7 HOH B 33 633 52 HOH HOH . 
M 7 HOH B 34 634 44 HOH HOH . 
M 7 HOH B 35 635 60 HOH HOH . 
M 7 HOH B 36 636 8 HOH HOH . 
M 7 HOH B 37 637 17 HOH HOH . 
M 7 HOH B 38 638 16 HOH HOH . 
M 7 HOH B 39 639 47 HOH HOH . 
M 7 HOH B 40 640 61 HOH HOH . 
M 7 HOH B 41 641 48 HOH HOH . 
M 7 HOH B 42 642 50 HOH HOH . 
#
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 . . . J 5 43.823 86.928 74.157 1 62.7 ? N1 UDP 503 B 1 
HETATM 2 C C2 UDP . . . J 5 43.417 87.396 72.848 1 61.15 ? C2 UDP 503 B 1 
HETATM 3 N N3 UDP . . . J 5 42.002 87.411 72.553 1 63.01 ? N3 UDP 503 B 1 
HETATM 4 C C4 UDP . . . J 5 41.012 86.991 73.515 1 61.52 ? C4 UDP 503 B 1 
HETATM 5 C C5 UDP . . . J 5 41.432 86.501 74.857 1 56.23 ? C5 UDP 503 B 1 
HETATM 6 C C6 UDP . . . J 5 42.885 86.474 75.181 1 52.16 ? C6 UDP 503 B 1 
HETATM 7 O O2 UDP . . . J 5 44.213 87.742 72.057 1 58.92 ? O2 UDP 503 B 1 
HETATM 8 O O4 UDP . . . J 5 39.874 87.05 73.186 1 63.94 ? O4 UDP 503 B 1 
HETATM 9 C C1' UDP . . . J 5 45.248 86.906 74.376 1 59.25 ? C1' UDP 503 B 1 
HETATM 10 C C2' UDP . . . J 5 45.706 87.779 75.581 1 62.2 ? C2' UDP 503 B 1 
HETATM 11 O O2' UDP . . . J 5 46.106 89.01 75.098 1 61.96 ? O2' UDP 503 B 1 
HETATM 12 C C3' UDP . . . J 5 46.771 86.872 76.176 1 53.28 ? C3' UDP 503 B 1 
HETATM 13 C C4' UDP . . . J 5 46.456 85.566 75.881 1 50.48 ? C4' UDP 503 B 1 
HETATM 14 O O4' UDP . . . J 5 45.452 85.63 74.666 1 51.17 ? O4' UDP 503 B 1 
HETATM 15 O O3' UDP . . . J 5 48.097 87.165 75.581 1 48.86 ? O3' UDP 503 B 1 
HETATM 16 C C5' UDP . . . J 5 45.784 84.841 77.01 1 54.62 ? C5' UDP 503 B 1 
HETATM 17 O O5' UDP . . . J 5 46.858 84.391 77.825 1 54.62 ? O5' UDP 503 B 1 
HETATM 18 P PA UDP . . . J 5 46.793 84.48 79.458 1 60.66 ? PA UDP 503 B 1 
HETATM 19 O O1A UDP . . . J 5 46.122 85.757 79.888 1 60.15 ? O1A UDP 503 B 1 
HETATM 20 O O2A UDP . . . J 5 48.153 84.198 80.06 1 59.31 ? O2A UDP 503 B 1 
HETATM 21 O O3A UDP . . . J 5 45.72 83.326 79.921 1 52.78 ? O3A UDP 503 B 1 
HETATM 22 P PB UDP . . . J 5 45.449 81.746 79.489 1 55.06 ? PB UDP 503 B 1 
HETATM 23 O O1B UDP . . . J 5 44.745 81.908 78.168 1 46.45 ? O1B UDP 503 B 1 
HETATM 24 O O2B UDP . . . J 5 44.543 81.101 80.53 1 50.75 ? O2B UDP 503 B 1 
HETATM 25 O O3B UDP . . . J 5 46.819 81.149 79.391 1 52.49 ? O3B UDP 503 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          16 
_model_server_stats.element_count           25 
#