data_4Q19
#
_model_server_result.job_id            XoCvKl5I4uNBpXF63nJnWQ 
_model_server_result.datetime_utc      '2024-11-17 11:00:32' 
_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          4q19 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    4Q19 
#
_exptl.entry_id    4Q19 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_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            4Q19 
_cell.length_a            68.535 
_cell.length_b            68.535 
_cell.length_c            119.793 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Q19 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_pdbx_struct_assembly.method_details        PISA 
_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 
_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
? 3 D N N 
? 3 F N N 
#
_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 408 n n 
N1 C6 UDP sing 409 n n 
N1 C1' UDP sing 410 n n 
C2 N3 UDP sing 411 n n 
C2 O2 UDP doub 412 n n 
N3 C4 UDP sing 413 n n 
N3 HN3 UDP sing 414 n n 
C4 C5 UDP sing 415 n n 
C4 O4 UDP doub 416 n n 
C5 C6 UDP doub 417 n n 
C5 H5 UDP sing 418 n n 
C6 H6 UDP sing 419 n n 
C1' C2' UDP sing 420 n n 
C1' O4' UDP sing 421 n n 
C1' H1' UDP sing 422 n n 
C2' O2' UDP sing 423 n n 
C2' C3' UDP sing 424 n n 
C2' H2' UDP sing 425 n n 
O2' HO2' UDP sing 426 n n 
C3' C4' UDP sing 427 n n 
C3' O3' UDP sing 428 n n 
C3' H3' UDP sing 429 n n 
C4' O4' UDP sing 430 n n 
C4' C5' UDP sing 431 n n 
C4' H4' UDP sing 432 n n 
O3' HO3' UDP sing 433 n n 
C5' O5' UDP sing 434 n n 
C5' "H5'1" UDP sing 435 n n 
C5' "H5'2" UDP sing 436 n n 
O5' PA UDP sing 437 n n 
PA O1A UDP doub 438 n n 
PA O2A UDP sing 439 n n 
PA O3A UDP sing 440 n n 
O2A HOA2 UDP sing 441 n n 
O3A PB UDP sing 442 n n 
PB O1B UDP doub 443 n n 
PB O2B UDP sing 444 n n 
PB O3B UDP sing 445 n n 
O2B HOB2 UDP sing 446 n n 
O3B HOB3 UDP sing 447 n n 
#
_atom_sites.entry_id                     4Q19 
_atom_sites.fract_transf_matrix[1][1]    0.014591 
_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]    0.014591 
_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]    0.008348 
_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 2XL A 1 301 301 2XL DRG . 
D 3 UDP A 1 302 401 UDP UDP . 
E 2 2XL B 1 301 301 2XL DRG . 
F 3 UDP B 1 302 401 UDP UDP . 
G 4 HOH A 1 401 2 HOH HOH . 
G 4 HOH A 2 402 3 HOH HOH . 
G 4 HOH A 3 403 5 HOH HOH . 
G 4 HOH A 4 404 6 HOH HOH . 
G 4 HOH A 5 405 7 HOH HOH . 
G 4 HOH A 6 406 9 HOH HOH . 
G 4 HOH A 7 407 13 HOH HOH . 
G 4 HOH A 8 408 14 HOH HOH . 
G 4 HOH A 9 409 21 HOH HOH . 
G 4 HOH A 10 410 22 HOH HOH . 
G 4 HOH A 11 411 26 HOH HOH . 
G 4 HOH A 12 412 27 HOH HOH . 
G 4 HOH A 13 413 28 HOH HOH . 
G 4 HOH A 14 414 29 HOH HOH . 
G 4 HOH A 15 415 33 HOH HOH . 
G 4 HOH A 16 416 34 HOH HOH . 
G 4 HOH A 17 417 35 HOH HOH . 
G 4 HOH A 18 418 36 HOH HOH . 
G 4 HOH A 19 419 39 HOH HOH . 
G 4 HOH A 20 420 42 HOH HOH . 
G 4 HOH A 21 421 43 HOH HOH . 
G 4 HOH A 22 422 46 HOH HOH . 
G 4 HOH A 23 423 48 HOH HOH . 
G 4 HOH A 24 424 50 HOH HOH . 
G 4 HOH A 25 425 52 HOH HOH . 
G 4 HOH A 26 426 54 HOH HOH . 
G 4 HOH A 27 427 57 HOH HOH . 
G 4 HOH A 28 428 58 HOH HOH . 
G 4 HOH A 29 429 59 HOH HOH . 
G 4 HOH A 30 430 60 HOH HOH . 
G 4 HOH A 31 431 61 HOH HOH . 
G 4 HOH A 32 432 62 HOH HOH . 
G 4 HOH A 33 433 63 HOH HOH . 
G 4 HOH A 34 434 64 HOH HOH . 
G 4 HOH A 35 435 65 HOH HOH . 
G 4 HOH A 36 436 82 HOH HOH . 
G 4 HOH A 37 437 83 HOH HOH . 
G 4 HOH A 38 438 84 HOH HOH . 
G 4 HOH A 39 439 85 HOH HOH . 
G 4 HOH A 40 440 86 HOH HOH . 
G 4 HOH A 41 441 87 HOH HOH . 
G 4 HOH A 42 442 88 HOH HOH . 
G 4 HOH A 43 443 89 HOH HOH . 
G 4 HOH A 44 444 90 HOH HOH . 
G 4 HOH A 45 445 91 HOH HOH . 
G 4 HOH A 46 446 98 HOH HOH . 
G 4 HOH A 47 447 99 HOH HOH . 
G 4 HOH A 48 448 100 HOH HOH . 
G 4 HOH A 49 449 101 HOH HOH . 
H 4 HOH B 1 401 1 HOH HOH . 
H 4 HOH B 2 402 4 HOH HOH . 
H 4 HOH B 3 403 8 HOH HOH . 
H 4 HOH B 4 404 10 HOH HOH . 
H 4 HOH B 5 405 11 HOH HOH . 
H 4 HOH B 6 406 12 HOH HOH . 
H 4 HOH B 7 407 15 HOH HOH . 
H 4 HOH B 8 408 16 HOH HOH . 
H 4 HOH B 9 409 17 HOH HOH . 
H 4 HOH B 10 410 18 HOH HOH . 
H 4 HOH B 11 411 19 HOH HOH . 
H 4 HOH B 12 412 20 HOH HOH . 
H 4 HOH B 13 413 23 HOH HOH . 
H 4 HOH B 14 414 24 HOH HOH . 
H 4 HOH B 15 415 25 HOH HOH . 
H 4 HOH B 16 416 30 HOH HOH . 
H 4 HOH B 17 417 31 HOH HOH . 
H 4 HOH B 18 418 32 HOH HOH . 
H 4 HOH B 19 419 37 HOH HOH . 
H 4 HOH B 20 420 38 HOH HOH . 
H 4 HOH B 21 421 40 HOH HOH . 
H 4 HOH B 22 422 41 HOH HOH . 
H 4 HOH B 23 423 44 HOH HOH . 
H 4 HOH B 24 424 45 HOH HOH . 
H 4 HOH B 25 425 47 HOH HOH . 
H 4 HOH B 26 426 49 HOH HOH . 
H 4 HOH B 27 427 51 HOH HOH . 
H 4 HOH B 28 428 53 HOH HOH . 
H 4 HOH B 29 429 55 HOH HOH . 
H 4 HOH B 30 430 56 HOH HOH . 
H 4 HOH B 31 431 66 HOH HOH . 
H 4 HOH B 32 432 67 HOH HOH . 
H 4 HOH B 33 433 68 HOH HOH . 
H 4 HOH B 34 434 69 HOH HOH . 
H 4 HOH B 35 435 70 HOH HOH . 
H 4 HOH B 36 436 71 HOH HOH . 
H 4 HOH B 37 437 72 HOH HOH . 
H 4 HOH B 38 438 73 HOH HOH . 
H 4 HOH B 39 439 74 HOH HOH . 
H 4 HOH B 40 440 75 HOH HOH . 
H 4 HOH B 41 441 76 HOH HOH . 
H 4 HOH B 42 442 77 HOH HOH . 
H 4 HOH B 43 443 78 HOH HOH . 
H 4 HOH B 44 444 79 HOH HOH . 
H 4 HOH B 45 445 80 HOH HOH . 
H 4 HOH B 46 446 81 HOH HOH . 
H 4 HOH B 47 447 92 HOH HOH . 
H 4 HOH B 48 448 93 HOH HOH . 
H 4 HOH B 49 449 94 HOH HOH . 
H 4 HOH B 50 450 95 HOH HOH . 
H 4 HOH B 51 451 96 HOH HOH . 
H 4 HOH B 52 452 97 HOH HOH . 
H 4 HOH B 53 453 102 HOH HOH . 
H 4 HOH B 54 454 103 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 . . . F 3 -24.624 -29.288 -28.67 1 30.23 ? N1 UDP 302 B 1 
HETATM 2 C C2 UDP . . . F 3 -24.737 -30.459 -29.456 1 30.51 ? C2 UDP 302 B 1 
HETATM 3 N N3 UDP . . . F 3 -23.857 -30.693 -30.439 1 30.09 ? N3 UDP 302 B 1 
HETATM 4 C C4 UDP . . . F 3 -22.877 -29.823 -30.712 1 30.18 ? C4 UDP 302 B 1 
HETATM 5 C C5 UDP . . . F 3 -22.76 -28.654 -29.974 1 30.38 ? C5 UDP 302 B 1 
HETATM 6 C C6 UDP . . . F 3 -23.655 -28.399 -28.938 1 30.42 ? C6 UDP 302 B 1 
HETATM 7 O O2 UDP . . . F 3 -25.646 -31.296 -29.204 1 30.57 ? O2 UDP 302 B 1 
HETATM 8 O O4 UDP . . . F 3 -22.091 -30.053 -31.657 1 30.64 ? O4 UDP 302 B 1 
HETATM 9 C C1' UDP . . . F 3 -25.598 -29.059 -27.596 1 29.92 ? C1' UDP 302 B 1 
HETATM 10 C C2' UDP . . . F 3 -25.051 -29.151 -26.178 1 30.36 ? C2' UDP 302 B 1 
HETATM 11 O O2' UDP . . . F 3 -25.084 -30.484 -25.611 1 30.12 ? O2' UDP 302 B 1 
HETATM 12 C C3' UDP . . . F 3 -25.935 -28.157 -25.427 1 30.11 ? C3' UDP 302 B 1 
HETATM 13 C C4' UDP . . . F 3 -26.456 -27.181 -26.472 1 30.12 ? C4' UDP 302 B 1 
HETATM 14 O O4' UDP . . . F 3 -26.106 -27.733 -27.74 1 29.72 ? O4' UDP 302 B 1 
HETATM 15 O O3' UDP . . . F 3 -27.054 -28.831 -24.847 1 30.49 ? O3' UDP 302 B 1 
HETATM 16 C C5' UDP . . . F 3 -25.83 -25.796 -26.372 1 30.53 ? C5' UDP 302 B 1 
HETATM 17 O O5' UDP . . . F 3 -24.391 -25.912 -26.386 1 30.72 ? O5' UDP 302 B 1 
HETATM 18 P PA UDP . . . F 3 -23.505 -25.034 -25.385 1 30.04 ? PA UDP 302 B 1 
HETATM 19 O O1A UDP . . . F 3 -22.082 -24.957 -25.842 1 30.27 ? O1A UDP 302 B 1 
HETATM 20 O O2A UDP . . . F 3 -23.865 -25.319 -23.952 1 30.22 ? O2A UDP 302 B 1 
HETATM 21 O O3A UDP . . . F 3 -24.136 -23.586 -25.783 1 30.07 ? O3A UDP 302 B 1 
HETATM 22 P PB UDP . . . F 3 -23.592 -22.105 -25.428 1 30.14 ? PB UDP 302 B 1 
HETATM 23 O O1B UDP . . . F 3 -23.221 -21.472 -26.742 1 29.79 ? O1B UDP 302 B 1 
HETATM 24 O O2B UDP . . . F 3 -24.85 -21.622 -24.771 1 30.53 ? O2B UDP 302 B 1 
HETATM 25 O O3B UDP . . . F 3 -22.429 -22.187 -24.49 1 30.3 ? O3B UDP 302 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#